1.2
14:05:2015 13:11
OBO-Edit 2.3.1
autogenerated-by: DAG-Edit version 1.417
saved-by: eilbeck
date: Tue May 11 15:18:44 PDT 2004
version: $Revision: 1.45 $
kareneilbeck
sequence
dbsnp variant terms
in_subset
has_obo_format_version
has_scope
SO feature annotation
amino acid modification
term replaced by
definition
has_synonym_type
biosapiens protein feature ontology
database_cross_reference
has_alternative_id
has_obo_namespace
DBVAR
subset_property
database of genomic structural variation
ensembl variant terms
synonym_type_property
biosapiens
has_exact_synonym
RNA modification
has_related_synonym
amino acid 1 letter code
variant annotation term
amino acid 3 letter code
has_narrow_synonym
consider
has_broad_synonym
adjacent_to
A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
adjacent_to
sequence
A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
PMID:20226267
SO:ke
associated_with
This relationship is vague and up for discussion.
associated_with
sequence
complete_evidence_for_feature
B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
complete_evidence_for_feature
sequence
B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
SO:ke
connects_on
2010-10-14T01:38:51Z
Example: A splice_junction connects_on exon, exon, mature_transcript.
X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.
connects_on
kareneilbeck
sequence
PMID:20226267
X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.
contained_by
2010-10-14T01:26:16Z
The inverse is contains. Example: intein contained_by immature_peptide_region.
X contained_by Y iff X starts after start of Y and X ends before end of Y.
contained_by
kareneilbeck
sequence
PMID:20226267
X contained_by Y iff X starts after start of Y and X ends before end of Y.
contains
2010-10-14T01:32:15Z
Example: pre_miRNA contains miRNA_loop.
The inverse of contained_by.
contains
kareneilbeck
sequence
PMID:20226267
The inverse of contained_by.
derives_from
derives_from
sequence
disconnected_from
2010-10-14T01:42:10Z
X is disconnected_from Y iff it is not the case that X overlaps Y.
disconnected_from
kareneilbeck
sequence
PMID:20226267
X is disconnected_from Y iff it is not the case that X overlaps Y.
edited_from
2009-08-19T02:19:45Z
edited_from
kareneilbeck
sequence
edited_to
2009-08-19T02:19:11Z
edited_to
kareneilbeck
sequence
evidence_for_feature
B is evidence_for_feature A, if an instance of B supports the existence of A.
This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
evidence_for_feature
sequence
B is evidence_for_feature A, if an instance of B supports the existence of A.
SO:ke
exemplar_of
Tracker id: 2594157.
X is exemplar of Y if X is the best evidence for Y.
exemplar_of
sequence
SO:ke
X is exemplar of Y if X is the best evidence for Y.
finished_by
2010-10-14T01:45:45Z
Example CDS finished_by stop_codon.
Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.
finished_by
kareneilbeck
sequence
PMID:20226267
Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.
finishes
2010-10-14T02:17:53Z
Example: stop_codon finishes CDS.
X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.
finishes
kareneilbeck
sequence
PMID:20226267
X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.
gained
2011-06-28T12:51:10Z
A relation with which to annotate the changes in a variant sequence with respect to a reference.
For example a variant transcript may gain a stop codon not present in the reference sequence.
X gained Y if X is a variant_of X' and Y part of X but not X'.
gained
kareneilbeck
sequence
SO:ke
X gained Y if X is a variant_of X' and Y part of X but not X'.
genome_of
genome_of
sequence
guided_by
2009-08-19T02:27:04Z
guided_by
kareneilbeck
sequence
guides
2009-08-19T02:27:24Z
guides
kareneilbeck
sequence
has_integral_part
2009-08-19T12:01:46Z
Example: mRNA has_integral_part CDS.
X has_integral_part Y if and only if: X has_part Y and Y part_of X.
has_integral_part
kareneilbeck
sequence
X has_integral_part Y if and only if: X has_part Y and Y part_of X.
http://precedings.nature.com/documents/3495/version/1
has_origin
has_origin
sequence
has_part
Example: operon has_part gene.
Inverse of part_of.
has_part
sequence
Inverse of part_of.
http://precedings.nature.com/documents/3495/version/1
has_quality
The relationship between a feature and an attribute.
has_quality
sequence
homologous_to
homologous_to
sequence
integral_part_of
2009-08-19T12:03:28Z
Example: exon integral_part_of transcript.
X integral_part_of Y if and only if: X part_of Y and Y has_part X.
integral_part_of
kareneilbeck
sequence
X integral_part_of Y if and only if: X part_of Y and Y has_part X.
http://precedings.nature.com/documents/3495/version/1
is_consecutive_sequence_of
2010-10-14T02:19:48Z
Example: region is consecutive_sequence of base.
R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).
is_consecutive_sequence_of
kareneilbeck
sequence
PMID:20226267
R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).
lost
2011-06-28T12:53:16Z
A relation with which to annotate the changes in a variant sequence with respect to a reference.
For example a variant transcript may have lost a stop codon present in the reference sequence.
X lost Y if X is a variant_of X' and Y part of X' but not X.
kareneilbeck
lost
sequence
SO:ke
X lost Y if X is a variant_of X' and Y part of X' but not X.
maximally_overlaps
2010-10-14T01:34:48Z
A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.
Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.
kareneilbeck
maximally_overlaps
sequence
A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.
PMID:20226267
member_of
A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
member_of
sequence
non_functional_homolog_of
A relationship between a pseudogenic feature and its functional ancestor.
non_functional_homolog_of
sequence
A relationship between a pseudogenic feature and its functional ancestor.
SO:ke
orthologous_to
orthologous_to
sequence
overlaps
2010-10-14T01:33:15Z
Example: coding_exon overlaps CDS.
X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
kareneilbeck
overlaps
sequence
PMID:20226267
X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
paralogous_to
paralogous_to
sequence
part_of
Example: amino_acid part_of polypeptide.
X part_of Y if X is a subregion of Y.
part_of
sequence
X part_of Y if X is a subregion of Y.
http://precedings.nature.com/documents/3495/version/1
partial_evidence_for_feature
B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
partial_evidence_for_feature
sequence
B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
SO:ke
position_of
position_of
sequence
processed_from
2009-08-19T12:14:00Z
Example: miRNA processed_from miRNA_primary_transcript.
Inverse of processed_into.
kareneilbeck
processed_from
sequence
Inverse of processed_into.
http://precedings.nature.com/documents/3495/version/1
processed_into
2009-08-19T12:15:02Z
Example: miRNA_primary_transcript processed into miRNA.
X is processed_into Y if a region X is modified to create Y.
kareneilbeck
processed_into
sequence
X is processed_into Y if a region X is modified to create Y.
http://precedings.nature.com/documents/3495/version/1
recombined_from
2009-08-19T02:21:03Z
kareneilbeck
recombined_from
sequence
recombined_to
2009-08-19T02:20:07Z
kareneilbeck
recombined_to
sequence
sequence_of
sequence
sequence_of
similar_to
sequence
similar_to
started_by
2010-10-14T01:43:55Z
Example: CDS started_by start_codon.
X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.
kareneilbeck
sequence
started_by
PMID:20226267
X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.
starts
2010-10-14T01:47:53Z
Example: start_codon starts CDS.
X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.
kareneilbeck
sequence
starts
PMID:20226267
X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.
trans_spliced_from
2009-08-19T02:22:14Z
kareneilbeck
sequence
trans_spliced_from
trans_spliced_to
2009-08-19T02:22:00Z
kareneilbeck
sequence
trans_spliced_to
transcribed_from
2009-08-19T12:05:39Z
Example: primary_transcript transcribed_from gene.
X is transcribed_from Y if X is synthesized from template Y.
kareneilbeck
sequence
transcribed_from
X is transcribed_from Y if X is synthesized from template Y.
http://precedings.nature.com/documents/3495/version/1
transcribed_to
2009-08-19T12:08:24Z
Example: gene transcribed_to primary_transcript.
Inverse of transcribed_from.
kareneilbeck
sequence
transcribed_to
Inverse of transcribed_from.
http://precedings.nature.com/documents/3495/version/1
translates_to
2009-08-19T12:11:53Z
Example: codon translates_to amino_acid.
Inverse of translation _of.
kareneilbeck
sequence
translates_to
Inverse of translation _of.
http://precedings.nature.com/documents/3495/version/1
translation_of
2009-08-19T12:09:59Z
Example: Polypeptide translation_of CDS.
X is translation of Y if Y is translated by ribosome to create X.
kareneilbeck
sequence
translation_of
X is translation of Y if Y is translated by ribosome to create X.
http://precedings.nature.com/documents/3495/version/1
variant_of
A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.
sequence
variant_of
A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
SO:immuno_workshop
Sequence_Ontology
SO:0000000
sequence
true
region
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
SO:0000001
sequence
sequence
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
SO:ke
sequence_secondary_structure
A folded sequence.
SO:0000002
sequence
sequence secondary structure
A folded sequence.
SO:ke
G_quartet
G quartet
G tetrad
G-quadruplex
G-quartet
G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.
G-tetrad
G_quadruplex
SO:0000003
guanine tetrad
http://en.wikipedia.org/wiki/G-quadruplex
sequence
wiki
http://en.wikipedia.org/wiki/G-quadruplex
G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.
http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract
interior_coding_exon
SO:0000004
interior coding exon
sequence
satellite_DNA
SO:0000005
The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
http://en.wikipedia.org/wiki/Satellite_DNA
satellite DNA
sequence
The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
wiki
http://en.wikipedia.org/wiki/Satellite_DNA
PCR_product
A region amplified by a PCR reaction.
PCR product
SO:0000006
This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.
amplicon
http://en.wikipedia.org/wiki/RAPD
sequence
wiki
http://en.wikipedia.org/wiki/RAPD
A region amplified by a PCR reaction.
SO:ke
read_pair
One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
SO:0000007
mate pair
read-pair
sequence
One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.
SO:ls
gene_sensu_your_favorite_organism
SO:0000008
sequence
true
gene_class
SO:0000009
sequence
true
protein_coding
SO:0000010
protein-coding
sequence
non_protein_coding
SO:0000011
non protein-coding
sequence
scRNA_primary_transcript
SO:0000012
The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.
scRNA primary transcript
scRNA transcript
sequence
small cytoplasmic RNA
small cytoplasmic RNA transcript
small_cytoplasmic_RNA
The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.
http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html
scRNA
A small non coding RNA sequence, present in the cytoplasm.
SO:0000013
sequence
small cytoplasmic RNA
A small non coding RNA sequence, present in the cytoplasm.
SO:ke
INR_motif
A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element.
Binds TAF1, TAF2.
DMp2
INR motif
SO:0000014
initiator
initiator motif
sequence
A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element.
PMID:12651739
PMID:16858867
DPE_motif
A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C).
Binds TAF6, TAF9.
CRWMGCGWKCGCTTS
DPE motif
SO:0000015
downstream core promoter element
sequence
A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C).
PMID:12651739:12537576
PMID:16858867
BREu_motif
A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB.
B-recognition element
BRE motif
BREu
BREu motif
Binds TFIIB.
SO:0000016
TFIIB recognition element
sequence
transcription factor B-recognition element
A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB.
PMID:12651739
PMID:16858867
PSE_motif
A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G).
PSE motif
SO:0000017
proximal sequence element
sequence
A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G).
PMID:12651739
linkage_group
A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.
SO:0000018
http://en.wikipedia.org/wiki/Linkage_group
linkage group
sequence
A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.
ISBN:038752046
wiki
http://en.wikipedia.org/wiki/Linkage_group
RNA_internal_loop
A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge.
RNA internal loop
SO:0000020
sequence
A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge.
SO:ke
asymmetric_RNA_internal_loop
An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.
SO:0000021
asymmetric RNA internal loop
sequence
An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.
SO:ke
A_minor_RNA_motif
A minor RNA motif
A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.
SO:0000022
sequence
A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.
SO:ke
K_turn_RNA_motif
K turn RNA motif
K-turn
SO:0000023
The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.
http://en.wikipedia.org/wiki/K-turn
kink turn
kink-turn motif
sequence
wiki
http://en.wikipedia.org/wiki/K-turn
SO:ke
The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.
sarcin_like_RNA_motif
A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.
SO:0000024
sarcin like RNA motif
sarcin/ricin RNA domain
sarcin/ricin domain
sarcin/ricin loop
sequence
A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.
http://www.ncbi.nlm.nih.gov/pubmed/7897662
symmetric_RNA_internal_loop
A-minor RNA motif
An internal RNA loop where the extent of the loop on both stands is the same size.
SO:0000025
sequence
An internal RNA loop where the extent of the loop on both stands is the same size.
SO:ke
RNA_junction_loop
RNA junction loop
SO:0000026
sequence
RNA_hook_turn
RNA hook turn
SO:0000027
hook turn
hook-turn motif
sequence
base_pair
SO:0000028
base pair
http://en.wikipedia.org/wiki/Base_pair
sequence
wiki
http://en.wikipedia.org/wiki/Base_pair
WC_base_pair
SO:0000029
The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation.
WC base pair
Watson Crick base pair
Watson-Crick base pair
Watson-Crick pair
canonical base pair
sequence
PMID:12177293
The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation.
sugar_edge_base_pair
A type of non-canonical base-pairing.
SO:0000030
sequence
sugar edge base pair
A type of non-canonical base-pairing.
PMID:12177293
aptamer
DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.
SO:0000031
http://en.wikipedia.org/wiki/Aptamer
sequence
DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.
http://aptamer.icmb.utexas.edu
wiki
http://en.wikipedia.org/wiki/Aptamer
DNA_aptamer
DNA aptamer
DNA molecules that have been selected from random pools based on their ability to bind other molecules.
SO:0000032
sequence
DNA molecules that have been selected from random pools based on their ability to bind other molecules.
http:aptamer.icmb.utexas.edu
RNA_aptamer
RNA aptamer
RNA molecules that have been selected from random pools based on their ability to bind other molecules.
SO:0000033
sequence
RNA molecules that have been selected from random pools based on their ability to bind other molecules.
http://aptamer.icmb.utexas.edu
morpholino_oligo
Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.
SO:0000034
morphant
morpholino
morpholino oligo
sequence
Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.
http://www.gene-tools.com/
riboswitch
A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites.
SO:0000035
http://en.wikipedia.org/wiki/Riboswitch
riboswitch RNA
sequence
A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites.
PMID:2820954
wiki
http://en.wikipedia.org/wiki/Riboswitch
matrix_attachment_site
A DNA region that is required for the binding of chromatin to the nuclear matrix.
MAR
S/MAR
S/MAR element
SMAR
SO:0000036
http://en.wikipedia.org/wiki/Matrix_attachment_site
matrix association region
matrix attachment region
matrix attachment site
nuclear matrix association region
nuclear matrix attachment site
scaffold attachment site
scaffold matrix attachment region
sequence
A DNA region that is required for the binding of chromatin to the nuclear matrix.
SO:ma
wiki
http://en.wikipedia.org/wiki/Matrix_attachment_site
locus_control_region
A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.
LCR
SO:0000037
http://en.wikipedia.org/wiki/Locus_control_region
locus control element
locus control region
sequence
A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.
SO:ma
wiki
http://en.wikipedia.org/wiki/Locus_control_region
match_set
A collection of match parts.
SO:0000038
sequence
true
A collection of match parts.
SO:ke
match_part
A part of a match, for example an hsp from blast is a match_part.
SO:0000039
match part
sequence
A part of a match, for example an hsp from blast is a match_part.
SO:ke
genomic_clone
A clone of a DNA region of a genome.
SO:0000040
genomic clone
sequence
A clone of a DNA region of a genome.
SO:ma
sequence_operation
An operation that can be applied to a sequence, that results in a change.
SO:0000041
sequence
sequence operation
true
An operation that can be applied to a sequence, that results in a change.
SO:ke
pseudogene_attribute
An attribute of a pseudogene (SO:0000336).
SO:0000042
pseudogene attribute
sequence
true
An attribute of a pseudogene (SO:0000336).
SO:ma
processed_pseudogene
A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail.
Please not the synonym R psi M uses the spelled out form of the greek letter.
R psi G
SO:0000043
processed pseudogene
pseudogene by reverse transcription
retropseudogene
sequence
A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail.
SO:xp
pseudogene_by_unequal_crossing_over
A pseudogene caused by unequal crossing over at recombination.
SO:0000044
pseudogene by unequal crossing over
sequence
A pseudogene caused by unequal crossing over at recombination.
SO:ke
delete
SO:0000045
To remove a subsection of sequence.
sequence
true
SO:ke
To remove a subsection of sequence.
insert
SO:0000046
To insert a subsection of sequence.
sequence
true
SO:ke
To insert a subsection of sequence.
invert
SO:0000047
To invert a subsection of sequence.
sequence
true
SO:ke
To invert a subsection of sequence.
substitute
SO:0000048
To substitute a subsection of sequence for another.
sequence
true
SO:ke
To substitute a subsection of sequence for another.
translocate
SO:0000049
To translocate a subsection of sequence.
sequence
true
SO:ke
To translocate a subsection of sequence.
gene_part
A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.
SO:0000050
sequence
true
A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene.
SO:ke
probe
A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.
SO:0000051
http://en.wikipedia.org/wiki/Hybridization_probe
sequence
A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.
SO:ma
wiki
http://en.wikipedia.org/wiki/Hybridization_probe
assortment_derived_deficiency
SO:0000052
assortment-derived_deficiency
sequence
true
sequence_variant_affecting_regulatory_region
A sequence_variant_effect which changes the regulatory region of a gene.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0000053
SO:0001556
mutation affecting regulatory region
sequence
sequence variant affecting regulatory region
true
A sequence_variant_effect which changes the regulatory region of a gene.
SO:ke
aneuploid
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.
SO:0000054
http://en.wikipedia.org/wiki/Aneuploid
sequence
wiki
http://en.wikipedia.org/wiki/Aneuploid
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.
SO:ke
hyperploid
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present.
SO:0000055
http://en.wikipedia.org/wiki/Hyperploid
sequence
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present.
SO:ke
wiki
http://en.wikipedia.org/wiki/Hyperploid
hypoploid
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing.
SO:0000056
http://en.wikipedia.org/wiki/Hypoploid
sequence
wiki
http://en.wikipedia.org/wiki/Hypoploid
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing.
SO:ke
operator
A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
SO:0000057
http://en.wikipedia.org/wiki/Operator_(biology)#Operator
operator segment
sequence
wiki
http://en.wikipedia.org/wiki/Operator_(biology)#Operator
A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.
SO:ma
assortment_derived_aneuploid
SO:0000058
assortment-derived_aneuploid
sequence
true
nuclease_binding_site
A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.
SO:0000059
nuclease binding site
sequence
A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease.
SO:cb
compound_chromosome_arm
FLAG - this term is should probably be a part of rather than an is_a.
SO:0000060
compound chromosome arm
sequence
restriction_enzyme_binding_site
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme.
A region of a molecule that binds to a restriction enzyme.
SO:0000061
restriction endonuclease binding site
restriction enzyme binding site
sequence
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme.
SO:cb
deficient_intrachromosomal_transposition
An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
SO:0000062
deficient intrachromosomal transposition
sequence
An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
FB:reference_manual
deficient_interchromosomal_transposition
An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
SO:0000063
deficient interchromosomal transposition
sequence
An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining.
SO:ke
gene_by_transcript_attribute
SO:0000064
This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.
sequence
true
free_chromosome_arm
A chromosome structure variation whereby an arm exists as an individual chromosome element.
SO:0000065
free chromosome arm
sequence
A chromosome structure variation whereby an arm exists as an individual chromosome element.
SO:ke
gene_by_polyadenylation_attribute
SO:0000066
sequence
true
gene_to_gene_feature
SO:0000067
gene to gene feature
sequence
overlapping
An attribute describing a gene that has a sequence that overlaps the sequence of another gene.
SO:0000068
sequence
An attribute describing a gene that has a sequence that overlaps the sequence of another gene.
SO:ke
inside_intron
An attribute to describe a gene when it is located within the intron of another gene.
SO:0000069
inside intron
sequence
An attribute to describe a gene when it is located within the intron of another gene.
SO:ke
inside_intron_antiparallel
An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand.
SO:0000070
inside intron antiparallel
sequence
An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand.
SO:ke
inside_intron_parallel
An attribute to describe a gene when it is located within the intron of another gene and on the same strand.
SO:0000071
inside intron parallel
sequence
An attribute to describe a gene when it is located within the intron of another gene and on the same strand.
SO:ke
end_overlapping_gene
SO:0000072
sequence
true
five_prime_three_prime_overlap
An attribute to describe a gene when the five prime region overlaps with another gene's 3' region.
SO:0000073
five prime-three prime overlap
sequence
An attribute to describe a gene when the five prime region overlaps with another gene's 3' region.
SO:ke
five_prime_five_prime_overlap
An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.
SO:0000074
five prime-five prime overlap
sequence
An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.
SO:ke
three_prime_three_prime_overlap
An attribute to describe a gene when the 3' region overlaps with another gene's 3' region.
SO:0000075
sequence
three prime-three prime overlap
An attribute to describe a gene when the 3' region overlaps with another gene's 3' region.
SO:ke
three_prime_five_prime_overlap
5' 3' overlap
An attribute to describe a gene when the 3' region overlaps with another gene's 5' region.
SO:0000076
sequence
three prime five prime overlap
An attribute to describe a gene when the 3' region overlaps with another gene's 5' region.
SO:ke
antisense
A region sequence that is complementary to a sequence of messenger RNA.
SO:0000077
http://en.wikipedia.org/wiki/Antisense
sequence
wiki
http://en.wikipedia.org/wiki/Antisense
A region sequence that is complementary to a sequence of messenger RNA.
SO:ke
polycistronic_transcript
A transcript that is polycistronic.
SO:0000078
polycistronic transcript
sequence
A transcript that is polycistronic.
SO:xp
dicistronic_transcript
A transcript that is dicistronic.
SO:0000079
dicistronic transcript
sequence
A transcript that is dicistronic.
SO:ke
operon_member
SO:0000080
operon member
sequence
gene_array_member
SO:0000081
gene array member
sequence
processed_transcript_attribute
SO:0000082
sequence
true
macronuclear_sequence
SO:0000083
macronuclear sequence
sequence
micronuclear_sequence
SO:0000084
micronuclear sequence
sequence
gene_by_genome_location
SO:0000085
sequence
true
gene_by_organelle_of_genome
SO:0000086
sequence
true
nuclear_gene
A gene from nuclear sequence.
SO:0000087
http://en.wikipedia.org/wiki/Nuclear_gene
nuclear gene
sequence
A gene from nuclear sequence.
SO:xp
wiki
http://en.wikipedia.org/wiki/Nuclear_gene
mt_gene
A gene located in mitochondrial sequence.
SO:0000088
http://en.wikipedia.org/wiki/Mitochondrial_gene
mitochondrial gene
mt gene
sequence
A gene located in mitochondrial sequence.
SO:xp
wiki
http://en.wikipedia.org/wiki/Mitochondrial_gene
kinetoplast_gene
A gene located in kinetoplast sequence.
SO:0000089
kinetoplast gene
sequence
A gene located in kinetoplast sequence.
SO:xp
plastid_gene
A gene from plastid sequence.
SO:0000090
plastid gene
sequence
A gene from plastid sequence.
SO:xp
apicoplast_gene
A gene from apicoplast sequence.
SO:0000091
apicoplast gene
sequence
A gene from apicoplast sequence.
SO:xp
ct_gene
A gene from chloroplast sequence.
SO:0000092
chloroplast gene
ct gene
sequence
A gene from chloroplast sequence.
SO:xp
chromoplast_gene
A gene from chromoplast_sequence.
SO:0000093
chromoplast gene
sequence
A gene from chromoplast_sequence.
SO:xp
cyanelle_gene
A gene from cyanelle sequence.
SO:0000094
cyanelle gene
sequence
A gene from cyanelle sequence.
SO:xp
leucoplast_gene
A plastid gene from leucoplast sequence.
SO:0000095
leucoplast gene
sequence
A plastid gene from leucoplast sequence.
SO:xp
proplastid_gene
A gene from proplastid sequence.
SO:0000096
proplastid gene
sequence
A gene from proplastid sequence.
SO:ke
nucleomorph_gene
A gene from nucleomorph sequence.
SO:0000097
nucleomorph gene
sequence
A gene from nucleomorph sequence.
SO:xp
plasmid_gene
A gene from plasmid sequence.
SO:0000098
plasmid gene
sequence
A gene from plasmid sequence.
SO:xp
proviral_gene
A gene from proviral sequence.
SO:0000099
proviral gene
sequence
A gene from proviral sequence.
SO:xp
endogenous_retroviral_gene
A proviral gene with origin endogenous retrovirus.
SO:0000100
endogenous retroviral gene
sequence
A proviral gene with origin endogenous retrovirus.
SO:xp
transposable_element
A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
SO:0000101
http://en.wikipedia.org/wiki/Transposable_element
sequence
transposable element
transposon
wiki
http://en.wikipedia.org/wiki/Transposable_element
A transposon or insertion sequence. An element that can insert in a variety of DNA sequences.
http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
expressed_sequence_match
A match to an EST or cDNA sequence.
SO:0000102
expressed sequence match
sequence
A match to an EST or cDNA sequence.
SO:ke
clone_insert_end
SO:0000103
The end of the clone insert.
clone insert end
sequence
SO:ke
The end of the clone insert.
polypeptide
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
SO:0000104
SO:0000358
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.
http://en.wikipedia.org/wiki/Polypeptide
protein
sequence
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
SO:ma
wiki
http://en.wikipedia.org/wiki/Polypeptide
chromosome_arm
A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.
SO:0000105
chromosome arm
sequence
A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.
http://www.medterms.com/script/main/art.asp?articlekey=5152
non_capped_primary_transcript
SO:0000106
sequence
true
sequencing_primer
SO:0000107
sequence
sequencing primer
mRNA_with_frameshift
An mRNA with a frameshift.
SO:0000108
frameshifted mRNA
mRNA with frameshift
sequence
An mRNA with a frameshift.
SO:xp
sequence_variant_obs
A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
SO:0000109
mutation
sequence
true
A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
SO:ke
sequence_feature
Any extent of continuous biological sequence.
SO:0000110
located sequence feature
located_sequence_feature
sequence
sequence feature
Any extent of continuous biological sequence.
LAMHDI:mb
SO:ke
transposable_element_gene
A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.
SO:0000111
sequence
transposable element gene
A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast.
SO:ke
primer
An oligo to which new deoxyribonucleotides can be added by DNA polymerase.
DNA primer
SO:0000112
http://en.wikipedia.org/wiki/Primer_(molecular_biology)
primer oligonucleotide
primer polynucleotide
primer sequence
sequence
wiki
http://en.wikipedia.org/wiki/Primer_(molecular_biology)
An oligo to which new deoxyribonucleotides can be added by DNA polymerase.
SO:ke
proviral_region
A viral sequence which has integrated into a host genome.
SO:0000113
proviral region
proviral sequence
sequence
A viral sequence which has integrated into a host genome.
SO:ke
methylated_cytosine
A methylated deoxy-cytosine.
SO:0000114
methylated C
methylated cytosine
methylated cytosine base
methylated cytosine residue
methylated_C
sequence
A methylated deoxy-cytosine.
SO:ke
transcript_feature
SO:0000115
sequence
true
edited
An attribute describing a sequence that is modified by editing.
SO:0000116
sequence
An attribute describing a sequence that is modified by editing.
SO:ke
transcript_with_readthrough_stop_codon
SO:0000117
sequence
true
transcript_with_translational_frameshift
A transcript with a translational frameshift.
SO:0000118
sequence
transcript with translational frameshift
A transcript with a translational frameshift.
SO:xp
regulated
An attribute to describe a sequence that is regulated.
SO:0000119
sequence
An attribute to describe a sequence that is regulated.
SO:ke
protein_coding_primary_transcript
A primary transcript that, at least in part, encodes one or more proteins.
May contain introns.
SO:0000120
pre mRNA
protein coding primary transcript
sequence
A primary transcript that, at least in part, encodes one or more proteins.
SO:ke
forward_primer
A single stranded oligo used for polymerase chain reaction.
DNA forward primer
SO:0000121
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
forward DNA primer
forward primer
forward primer oligo
forward primer oligonucleotide
forward primer polynucleotide
forward primer sequence
sequence
A single stranded oligo used for polymerase chain reaction.
http://mged.sourceforge.net/ontologies/MGEDontology.php
RNA_sequence_secondary_structure
A folded RNA sequence.
RNA sequence secondary structure
SO:0000122
sequence
A folded RNA sequence.
SO:ke
transcriptionally_regulated
An attribute describing a gene that is regulated at transcription.
By:<protein_id>.
SO:0000123
sequence
transcriptionally regulated
An attribute describing a gene that is regulated at transcription.
SO:ma
transcriptionally_constitutive
Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate.
SO:0000124
sequence
transcriptionally constitutive
Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate.
SO:ke
transcriptionally_induced
An inducer molecule is required for transcription to occur.
SO:0000125
sequence
transcriptionally induced
An inducer molecule is required for transcription to occur.
SO:ke
transcriptionally_repressed
A repressor molecule is required for transcription to stop.
SO:0000126
sequence
transcriptionally repressed
A repressor molecule is required for transcription to stop.
SO:ke
silenced_gene
A gene that is silenced.
SO:0000127
sequence
silenced gene
A gene that is silenced.
SO:xp
gene_silenced_by_DNA_modification
A gene that is silenced by DNA modification.
SO:0000128
gene silenced by DNA modification
sequence
A gene that is silenced by DNA modification.
SO:xp
gene_silenced_by_DNA_methylation
A gene that is silenced by DNA methylation.
SO:0000129
gene silenced by DNA methylation
methylation-silenced gene
sequence
A gene that is silenced by DNA methylation.
SO:xp
post_translationally_regulated
An attribute describing a gene that is regulated after it has been translated.
SO:0000130
post translationally regulated
post-translationally regulated
sequence
An attribute describing a gene that is regulated after it has been translated.
SO:ke
translationally_regulated
An attribute describing a gene that is regulated as it is translated.
SO:0000131
sequence
translationally regulated
An attribute describing a gene that is regulated as it is translated.
SO:ke
reverse_primer
A single stranded oligo used for polymerase chain reaction.
DNA reverse primer
SO:0000132
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
reverse DNA primer
reverse primer
reverse primer oligo
reverse primer oligonucleotide
reverse primer sequence
sequence
A single stranded oligo used for polymerase chain reaction.
http://mged.sourceforge.net/ontologies/MGEDontology.php
epigenetically_modified
SO:0000133
This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones.
epigenetically modified
sequence
SO:ke
This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones.
genomically_imprinted
Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin.
SO:0000134
genomically imprinted
http:http://en.wikipedia.org/wiki/Genomic_imprinting
imprinted
sequence
wiki
http:http://en.wikipedia.org/wiki/Genomic_imprinting
Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin.
SO:ke
maternally_imprinted
SO:0000135
The maternal copy of the gene is modified, rendering it transcriptionally silent.
maternally imprinted
sequence
SO:ke
The maternal copy of the gene is modified, rendering it transcriptionally silent.
paternally_imprinted
SO:0000136
The paternal copy of the gene is modified, rendering it transcriptionally silent.
paternally imprinted
sequence
SO:ke
The paternal copy of the gene is modified, rendering it transcriptionally silent.
allelically_excluded
Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell.
Examples are x-inactivation and immunoglobulin formation.
SO:0000137
allelically excluded
sequence
Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell.
SO:ke
gene_rearranged_at_DNA_level
An epigenetically modified gene, rearranged at the DNA level.
SO:0000138
gene rearranged at DNA level
sequence
An epigenetically modified gene, rearranged at the DNA level.
SO:xp
ribosome_entry_site
Region in mRNA where ribosome assembles.
SO:0000139
ribosome entry site
sequence
Region in mRNA where ribosome assembles.
SO:ke
attenuator
A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.
SO:0000140
attenuator sequence
http://en.wikipedia.org/wiki/Attenuator
sequence
A sequence segment located within the five prime end of an mRNA that causes premature termination of translation.
SO:as
wiki
http://en.wikipedia.org/wiki/Attenuator
terminator
SO:0000141
The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
http://en.wikipedia.org/wiki/Terminator_(genetics)
sequence
terminator sequence
wiki
http://en.wikipedia.org/wiki/Terminator_(genetics)
The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
DNA_sequence_secondary_structure
A folded DNA sequence.
DNA sequence secondary structure
SO:0000142
sequence
A folded DNA sequence.
SO:ke
assembly_component
A region of known length which may be used to manufacture a longer region.
SO:0000143
assembly component
sequence
A region of known length which may be used to manufacture a longer region.
SO:ke
primary_transcript_attribute
SO:0000144
sequence
true
recoded_codon
A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough.
SO:0000145
recoded codon
sequence
A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough.
SO:xp
capped
An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.
SO:0000146
sequence
An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.
SO:ke
exon
A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
SO:0000147
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
http://en.wikipedia.org/wiki/Exon
sequence
wiki
http://en.wikipedia.org/wiki/Exon
A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
SO:ke
supercontig
One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
SO:0000148
scaffold
sequence
One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's.
SO:ls
contig
A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
SO:0000149
http://en.wikipedia.org/wiki/Contig
sequence
A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases.
SO:ls
wiki
http://en.wikipedia.org/wiki/Contig
read
A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
SO:0000150
sequence
A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.
SO:rd
clone
A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.
SO:0000151
http:http://en.wikipedia.org/wiki/Clone_(genetics)
sequence
wiki
http:http://en.wikipedia.org/wiki/Clone_(genetics)
A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism.
SO:ke
YAC
SO:0000152
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.
sequence
yeast artificial chromosome
SO:ma
Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.
BAC
Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.
SO:0000153
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
bacterial artificial chromosome
sequence
Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.
SO:ma
PAC
P1
P1 artificial chromosome
SO:0000154
The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome.
http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome
sequence
The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells.
http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome
wiki
http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome
plasmid
A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.
SO:0000155
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
plasmid sequence
sequence
A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.
SO:ma
cosmid
A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.
Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
SO:0000156
cosmid vector
http://en.wikipedia.org/wiki/Cosmid
sequence
wiki
http://en.wikipedia.org/wiki/Cosmid
A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.
SO:ma
phagemid
A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids.
SO:0000157
http://en.wikipedia.org/wiki/Phagemid
phagemid vector
sequence
wiki
http://en.wikipedia.org/wiki/Phagemid
A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids.
SO:ma
fosmid
A cloning vector that utilizes the E. coli F factor.
Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996.
SO:0000158
fosmid vector
http://en.wikipedia.org/wiki/Fosmid
sequence
A cloning vector that utilizes the E. coli F factor.
SO:ma
wiki
http://en.wikipedia.org/wiki/Fosmid
deletion
SO:0000159
SO:1000033
The point at which one or more contiguous nucleotides were excised.
deleted_sequence
http://en.wikipedia.org/wiki/Nucleotide_deletion
loinc:LA6692-3
nucleotide deletion
nucleotide_deletion
sequence
Deletion
loinc:LA6692-3
SO:ke
The point at which one or more contiguous nucleotides were excised.
wiki
http://en.wikipedia.org/wiki/Nucleotide_deletion
lambda_clone
A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
SO:0000160
sequence
true
A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
ISBN:0-1767-2380-8
methylated_adenine
A modified base in which adenine has been methylated.
SO:0000161
methylated A
methylated adenine
methylated adenine base
methylated adenine residue
methylated_A
sequence
A modified base in which adenine has been methylated.
SO:ke
splice_site
Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
SO:0000162
With spliceosomal introns, the splice sites bind the spliceosomal machinery.
http://en.wikipedia.org/wiki/Splice_site
sequence
splice site
Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.
SO:cjm
SO:ke
wiki
http://en.wikipedia.org/wiki/Splice_site
five_prime_cis_splice_site
5' splice site
Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.
SO:0000163
donor
donor splice site
five prime splice site
sequence
splice donor site
Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron.
SO:cjm
SO:ke
http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
three_prime_cis_splice_site
3' splice site
Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.
SO:0000164
acceptor
acceptor splice site
sequence
splice acceptor site
three prime splice site
Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron.
SO:cjm
SO:ke
http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
enhancer
A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.
SO:0000165
http://en.wikipedia.org/wiki/Enhancer_(genetics)
sequence
wiki
http://en.wikipedia.org/wiki/Enhancer_(genetics)
A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
enhancer_bound_by_factor
An enhancer bound by a factor.
SO:0000166
enhancer bound by factor
sequence
An enhancer bound by a factor.
SO:xp
promoter
A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
SO:0000167
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
http://en.wikipedia.org/wiki/Promoter
promoter sequence
sequence
A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.
SO:regcreative
wiki
http://en.wikipedia.org/wiki/Promoter
restriction_enzyme_cut_site
A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.
SO:0000168
sequence
true
A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.
SO:ma
RNApol_I_promoter
A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.
RNA polymerase A promoter
RNApol I promoter
SO:0000169
pol I promoter
polymerase I promoter
sequence
A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.
SO:ke
RNApol_II_promoter
A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
RNA polymerase B promoter
RNApol II promoter
SO:0000170
pol II promoter
polymerase II promoter
sequence
A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
SO:ke
RNApol_III_promoter
A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.
RNA polymerase C promoter
RNApol III promoter
SO:0000171
pol III promoter
polymerase III promoter
sequence
A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.
SO:ke
CAAT_signal
CAAT box
CAAT signal
CAAT-box
Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT.
SO:0000172
http://en.wikipedia.org/wiki/CAAT_box
sequence
wiki
http://en.wikipedia.org/wiki/CAAT_box
Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
GC_rich_promoter_region
A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG.
GC rich promoter region
GC-rich region
SO:0000173
sequence
A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
TATA_box
A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T).
Binds TBP.
Goldstein-Hogness box
SO:0000174
TATA box
http://en.wikipedia.org/wiki/TATA_box
sequence
wiki
http://en.wikipedia.org/wiki/TATA_box
A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T).
PMID:16858867
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
minus_10_signal
-10 signal
A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70.
Pribnow Schaller box
Pribnow box
Pribnow-Schaller box
SO:0000175
http://en.wikipedia.org/wiki/Pribnow_box
minus 10 signal
sequence
wiki
http://en.wikipedia.org/wiki/Pribnow_box
A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
minus_35_signal
-35 signal
A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70.
SO:0000176
minus 35 signal
sequence
A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
cross_genome_match
A nucleotide match against a sequence from another organism.
SO:0000177
cross genome match
sequence
A nucleotide match against a sequence from another organism.
SO:ma
operon
A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.
SO:0000178
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
http://en.wikipedia.org/wiki/Operon
sequence
A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.
SO:ma
wiki
http://en.wikipedia.org/wiki/Operon
clone_insert_start
SO:0000179
The start of the clone insert.
clone insert start
sequence
SO:ke
The start of the clone insert.
retrotransposon
A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.
SO:0000180
class I
class I transposon
http://en.wikipedia.org/wiki/Retrotransposon
retrotransposon element
sequence
wiki
http://en.wikipedia.org/wiki/Retrotransposon
A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase.
http://www.dddmag.com/Glossary.aspx#r
translated_nucleotide_match
A match against a translated sequence.
SO:0000181
sequence
translated nucleotide match
A match against a translated sequence.
SO:ke
DNA_transposon
A transposon where the mechanism of transposition is via a DNA intermediate.
DNA transposon
SO:0000182
class II
class II transposon
sequence
A transposon where the mechanism of transposition is via a DNA intermediate.
SO:ke
non_transcribed_region
A region of the gene which is not transcribed.
SO:0000183
non transcribed region
non-transcribed sequence
nontranscribed region
nontranscribed sequence
sequence
A region of the gene which is not transcribed.
SO:ke
U2_intron
A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.
May have either GT-AG or AT-AG 5' and 3' boundaries.
SO:0000184
U2 intron
sequence
A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.
PMID:9428511
primary_transcript
A transcript that in its initial state requires modification to be functional.
SO:0000185
http://en.wikipedia.org/wiki/Primary_transcript
precursor RNA
primary transcript
sequence
A transcript that in its initial state requires modification to be functional.
SO:ma
wiki
http://en.wikipedia.org/wiki/Primary_transcript
LTR_retrotransposon
A retrotransposon flanked by long terminal repeat sequences.
LTR retrotransposon
SO:0000186
long terminal repeat retrotransposon
sequence
A retrotransposon flanked by long terminal repeat sequences.
SO:ke
repeat_family
A group of characterized repeat sequences.
SO:0000187
sequence
true
A group of characterized repeat sequences.
SO:ke
intron
A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
SO:0000188
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
http://en.wikipedia.org/wiki/Intron
sequence
wiki
http://en.wikipedia.org/wiki/Intron
A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
non_LTR_retrotransposon
A retrotransposon without long terminal repeat sequences.
SO:0000189
non LTR retrotransposon
sequence
A retrotransposon without long terminal repeat sequences.
SO:ke
five_prime_intron
5' intron
5' intron sequence
SO:0000190
five prime intron
sequence
interior_intron
SO:0000191
interior intron
sequence
three_prime_intron
3' intron
3' intron sequence
SO:0000192
sequence
three prime intron
RFLP_fragment
A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.
RFLP
RFLP fragment
SO:0000193
http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism
restriction fragment length polymorphism
sequence
A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme.
GOC:pj
wiki
http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism
LINE_element
A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats.
LINE
LINE element
Long interspersed element
Long interspersed nuclear element
SO:0000194
sequence
A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats.
http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
coding_exon
An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
SO:0000195
coding exon
sequence
An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).
SO:ke
five_prime_coding_exon_coding_region
SO:0000196
The sequence of the five_prime_coding_exon that codes for protein.
five prime exon coding region
sequence
SO:cjm
The sequence of the five_prime_coding_exon that codes for protein.
three_prime_coding_exon_coding_region
SO:0000197
The sequence of the three_prime_coding_exon that codes for protein.
sequence
three prime exon coding region
SO:cjm
The sequence of the three_prime_coding_exon that codes for protein.
noncoding_exon
An exon that does not contain any codons.
SO:0000198
noncoding exon
sequence
An exon that does not contain any codons.
SO:ke
translocation
A region of nucleotide sequence that has translocated to a new position.
SO:0000199
sequence
transchr
translocated sequence
A region of nucleotide sequence that has translocated to a new position.
SO:ke
http://www.ncbi.nlm.nih.gov/dbvar/
transchr
five_prime_coding_exon
5' coding exon
SO:0000200
The 5' most coding exon.
five prime coding exon
sequence
SO:ke
The 5' most coding exon.
interior_exon
An exon that is bounded by 5' and 3' splice sites.
SO:0000201
interior exon
sequence
An exon that is bounded by 5' and 3' splice sites.
PMID:10373547
three_prime_coding_exon
3' coding exon
SO:0000202
The coding exon that is most 3-prime on a given transcript.
sequence
three prime coding exon
SO:ma
The coding exon that is most 3-prime on a given transcript.
UTR
Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
SO:0000203
sequence
untranslated region
Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.
SO:ke
five_prime_UTR
5' UTR
A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
SO:0000204
five prime UTR
five_prime_untranslated_region
http://en.wikipedia.org/wiki/5'_UTR
sequence
wiki
http://en.wikipedia.org/wiki/5'_UTR
A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
three_prime_UTR
A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
SO:0000205
http://en.wikipedia.org/wiki/Three_prime_untranslated_region
sequence
three prime UTR
three prime untranslated region
A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
wiki
http://en.wikipedia.org/wiki/Three_prime_untranslated_region
SINE_element
A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element.
SINE element
SO:0000206
Short interspersed element
Short interspersed nuclear element
http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element
sequence
wiki
http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element
A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element.
SO:ke
simple_sequence_length_variation
SO:0000207
SSLP
sequence
simple sequence length polymorphism
simple sequence length variation
terminal_inverted_repeat_element
A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.
SO:0000208
TIR element
sequence
terminal inverted repeat element
A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.
http://www.genetics.org/cgi/reprint/156/4/1983.pdf
rRNA_primary_transcript
A primary transcript encoding a ribosomal RNA.
SO:0000209
rRNA primary transcript
ribosomal RNA primary transcript
sequence
A primary transcript encoding a ribosomal RNA.
SO:ke
tRNA_primary_transcript
A primary transcript encoding a transfer RNA (SO:0000253).
SO:0000210
sequence
tRNA primary transcript
A primary transcript encoding a transfer RNA (SO:0000253).
SO:ke
alanine_tRNA_primary_transcript
A primary transcript encoding alanyl tRNA.
SO:0000211
alanine tRNA primary transcript
sequence
A primary transcript encoding alanyl tRNA.
SO:ke
arginine_tRNA_primary_transcript
A primary transcript encoding arginyl tRNA (SO:0000255).
SO:0000212
arginine tRNA primary transcript
sequence
A primary transcript encoding arginyl tRNA (SO:0000255).
SO:ke
asparagine_tRNA_primary_transcript
A primary transcript encoding asparaginyl tRNA (SO:0000256).
SO:0000213
asparagine tRNA primary transcript
sequence
A primary transcript encoding asparaginyl tRNA (SO:0000256).
SO:ke
aspartic_acid_tRNA_primary_transcript
A primary transcript encoding aspartyl tRNA (SO:0000257).
SO:0000214
aspartic acid tRNA primary transcript
sequence
A primary transcript encoding aspartyl tRNA (SO:0000257).
SO:ke
cysteine_tRNA_primary_transcript
A primary transcript encoding cysteinyl tRNA (SO:0000258).
SO:0000215
cysteine tRNA primary transcript
sequence
A primary transcript encoding cysteinyl tRNA (SO:0000258).
SO:ke
glutamic_acid_tRNA_primary_transcript
A primary transcript encoding glutaminyl tRNA (SO:0000260).
SO:0000216
glutamic acid tRNA primary transcript
sequence
A primary transcript encoding glutaminyl tRNA (SO:0000260).
SO:ke
glutamine_tRNA_primary_transcript
A primary transcript encoding glutamyl tRNA (SO:0000260).
SO:0000217
glutamine tRNA primary transcript
sequence
A primary transcript encoding glutamyl tRNA (SO:0000260).
SO:ke
glycine_tRNA_primary_transcript
A primary transcript encoding glycyl tRNA (SO:0000263).
SO:0000218
glycine tRNA primary transcript
sequence
A primary transcript encoding glycyl tRNA (SO:0000263).
SO:ke
histidine_tRNA_primary_transcript
A primary transcript encoding histidyl tRNA (SO:0000262).
SO:0000219
histidine tRNA primary transcript
sequence
A primary transcript encoding histidyl tRNA (SO:0000262).
SO:ke
isoleucine_tRNA_primary_transcript
A primary transcript encoding isoleucyl tRNA (SO:0000263).
SO:0000220
isoleucine tRNA primary transcript
sequence
A primary transcript encoding isoleucyl tRNA (SO:0000263).
SO:ke
leucine_tRNA_primary_transcript
A primary transcript encoding leucyl tRNA (SO:0000264).
SO:0000221
leucine tRNA primary transcript
sequence
A primary transcript encoding leucyl tRNA (SO:0000264).
SO:ke
lysine_tRNA_primary_transcript
A primary transcript encoding lysyl tRNA (SO:0000265).
SO:0000222
lysine tRNA primary transcript
sequence
A primary transcript encoding lysyl tRNA (SO:0000265).
SO:ke
methionine_tRNA_primary_transcript
A primary transcript encoding methionyl tRNA (SO:0000266).
SO:0000223
methionine tRNA primary transcript
sequence
A primary transcript encoding methionyl tRNA (SO:0000266).
SO:ke
phenylalanine_tRNA_primary_transcript
A primary transcript encoding phenylalanyl tRNA (SO:0000267).
SO:0000224
phenylalanine tRNA primary transcript
sequence
A primary transcript encoding phenylalanyl tRNA (SO:0000267).
SO:ke
proline_tRNA_primary_transcript
A primary transcript encoding prolyl tRNA (SO:0000268).
SO:0000225
proline tRNA primary transcript
sequence
A primary transcript encoding prolyl tRNA (SO:0000268).
SO:ke
serine_tRNA_primary_transcript
A primary transcript encoding seryl tRNA (SO:000269).
SO:0000226
sequence
serine tRNA primary transcript
A primary transcript encoding seryl tRNA (SO:000269).
SO:ke
threonine_tRNA_primary_transcript
A primary transcript encoding threonyl tRNA (SO:000270).
SO:0000227
sequence
threonine tRNA primary transcript
A primary transcript encoding threonyl tRNA (SO:000270).
SO:ke
tryptophan_tRNA_primary_transcript
A primary transcript encoding tryptophanyl tRNA (SO:000271).
SO:0000228
sequence
tryptophan tRNA primary transcript
A primary transcript encoding tryptophanyl tRNA (SO:000271).
SO:ke
tyrosine_tRNA_primary_transcript
A primary transcript encoding tyrosyl tRNA (SO:000272).
SO:0000229
sequence
tyrosine tRNA primary transcript
A primary transcript encoding tyrosyl tRNA (SO:000272).
SO:ke
valine_tRNA_primary_transcript
A primary transcript encoding valyl tRNA (SO:000273).
SO:0000230
sequence
valine tRNA primary transcript
A primary transcript encoding valyl tRNA (SO:000273).
SO:ke
snRNA_primary_transcript
A primary transcript encoding a small nuclear RNA (SO:0000274).
SO:0000231
sequence
snRNA primary transcript
A primary transcript encoding a small nuclear RNA (SO:0000274).
SO:ke
snoRNA_primary_transcript
A primary transcript encoding a small nucleolar mRNA (SO:0000275).
SO:0000232
sequence
snoRNA primary transcript
A primary transcript encoding a small nucleolar mRNA (SO:0000275).
SO:ke
mature_transcript
A processed transcript cannot contain introns.
A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.
SO:0000233
http://en.wikipedia.org/wiki/Mature_transcript
mature transcript
sequence
wiki
http://en.wikipedia.org/wiki/Mature_transcript
A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.
SO:ke
mRNA
An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
SO:0000234
http://en.wikipedia.org/wiki/MRNA
messenger RNA
sequence
Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
SO:ma
wiki
http://en.wikipedia.org/wiki/MRNA
TF_binding_site
A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667].
SO:0000235
TF binding site
sequence
transcription factor binding site
A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667].
SO:ke
ORF
SO:0000236
The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.
open reading frame
sequence
SGD:rb
SO:ma
The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.
transcript_attribute
SO:0000237
sequence
transcript attribute
foldback_element
A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats.
LVR element
SO:0000238
foldback element
long inverted repeat element
sequence
A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats.
http://www.genetics.org/cgi/reprint/156/4/1983.pdf
flanking_region
SO:0000239
The sequences extending on either side of a specific region.
flanking region
sequence
SO:ke
The sequences extending on either side of a specific region.
chromosome_variation
SO:0000240
chromosome variation
sequence
internal_UTR
A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.
SO:0000241
internal UTR
sequence
A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.
SO:cjm
untranslated_region_polycistronic_mRNA
SO:0000242
The untranslated sequence separating the 'cistrons' of multicistronic mRNA.
sequence
untranslated region polycistronic mRNA
SO:ke
The untranslated sequence separating the 'cistrons' of multicistronic mRNA.
internal_ribosome_entry_site
IRES
SO:0000243
Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.
http://en.wikipedia.org/wiki/Internal_ribosome_entry_site
internal ribosomal entry sequence
internal ribosomal entry site
internal ribosome entry sequence
internal ribosome entry site
sequence
SO:ke
Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.
wiki
http://en.wikipedia.org/wiki/Internal_ribosome_entry_site
four_cutter_restriction_site
4-cutter_restriction_site
SO:0000244
four-cutter_restriction_sit
sequence
true
mRNA_by_polyadenylation_status
SO:0000245
sequence
true
polyadenylated
A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule.
SO:0000246
sequence
A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule.
SO:ke
mRNA_not_polyadenylated
SO:0000247
sequence
true
sequence_length_variation
SO:0000248
sequence
sequence length variation
six_cutter_restriction_site
6-cutter_restriction_site
SO:0000249
sequence
six-cutter_restriction_site
true
modified_RNA_base_feature
A post_transcriptionally modified base.
SO:0000250
modified RNA base feature
sequence
A post_transcriptionally modified base.
SO:ke
eight_cutter_restriction_site
8-cutter_restriction_site
SO:0000251
eight-cutter_restriction_site
sequence
true
rRNA
RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
SO:0000252
http://en.wikipedia.org/wiki/RRNA
ribosomal RNA
ribosomal ribonucleic acid
sequence
ISBN:0198506732
RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
wiki
http://en.wikipedia.org/wiki/RRNA
tRNA
SO:0000253
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.
http://en.wikipedia.org/wiki/TRNA
sequence
transfer RNA
transfer ribonucleic acid
wiki
http://en.wikipedia.org/wiki/TRNA
ISBN:0198506732
Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005
alanyl_tRNA
A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.
SO:0000254
alanyl tRNA
alanyl-transfer RNA
alanyl-transfer ribonucleic acid
sequence
A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.
SO:ke
rRNA_small_subunit_primary_transcript
A primary transcript encoding a small ribosomal subunit RNA.
SO:0000255
rRNA small subunit primary transcript
sequence
A primary transcript encoding a small ribosomal subunit RNA.
SO:ke
asparaginyl_tRNA
A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.
SO:0000256
asparaginyl tRNA
asparaginyl-transfer RNA
asparaginyl-transfer ribonucleic acid
sequence
A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.
SO:ke
aspartyl_tRNA
A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.
SO:0000257
aspartyl tRNA
aspartyl-transfer RNA
aspartyl-transfer ribonucleic acid
sequence
A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.
SO:ke
cysteinyl_tRNA
A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.
SO:0000258
cysteinyl tRNA
cysteinyl-transfer RNA
cysteinyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.
SO:ke
glutaminyl_tRNA
A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.
SO:0000259
glutaminyl tRNA
glutaminyl-transfer RNA
glutaminyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.
SO:ke
glutamyl_tRNA
A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.
SO:0000260
glutamyl tRNA
glutamyl-transfer RNA
glutamyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.
SO:ke
glycyl_tRNA
A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.
SO:0000261
glycyl tRNA
glycyl-transfer RNA
glycyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.
SO:ke
histidyl_tRNA
A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.
SO:0000262
histidyl tRNA
histidyl-transfer RNA
histidyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.
SO:ke
isoleucyl_tRNA
A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.
SO:0000263
isoleucyl tRNA
isoleucyl-transfer RNA
isoleucyl-transfer ribonucleic acid
sequence
A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.
SO:ke
leucyl_tRNA
A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.
SO:0000264
leucyl tRNA
leucyl-transfer RNA
leucyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.
SO:ke
lysyl_tRNA
A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.
SO:0000265
lysyl tRNA
lysyl-transfer RNA
lysyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.
SO:ke
methionyl_tRNA
A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.
SO:0000266
methionyl tRNA
methionyl-transfer RNA
methionyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.
SO:ke
phenylalanyl_tRNA
A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.
SO:0000267
phenylalanyl tRNA
phenylalanyl-transfer RNA
phenylalanyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.
SO:ke
prolyl_tRNA
A tRNA sequence that has a proline anticodon, and a 3' proline binding region.
SO:0000268
prolyl tRNA
prolyl-transfer RNA
prolyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a proline anticodon, and a 3' proline binding region.
SO:ke
seryl_tRNA
A tRNA sequence that has a serine anticodon, and a 3' serine binding region.
SO:0000269
sequence
seryl tRNA
seryl-transfer RNA
seryl-transfer ribonucleic acid
A tRNA sequence that has a serine anticodon, and a 3' serine binding region.
SO:ke
threonyl_tRNA
A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.
SO:0000270
sequence
threonyl tRNA
threonyl-transfer RNA
threonyl-transfer ribonucleic acid
A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.
SO:ke
tryptophanyl_tRNA
A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.
SO:0000271
sequence
tryptophanyl tRNA
tryptophanyl-transfer RNA
tryptophanyl-transfer ribonucleic acid
A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.
SO:ke
tyrosyl_tRNA
A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.
SO:0000272
sequence
tyrosyl tRNA
tyrosyl-transfer RNA
tyrosyl-transfer ribonucleic acid
A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.
SO:ke
valyl_tRNA
A tRNA sequence that has a valine anticodon, and a 3' valine binding region.
SO:0000273
sequence
valyl tRNA
valyl-transfer RNA
valyl-transfer ribonucleic acid
A tRNA sequence that has a valine anticodon, and a 3' valine binding region.
SO:ke
snRNA
A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
SO:0000274
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
http://en.wikipedia.org/wiki/SnRNA
sequence
small nuclear RNA
wiki
http://en.wikipedia.org/wiki/SnRNA
A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
PMID:11733745
WB:ems
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
snoRNA
A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.
SO:0000275
http://en.wikipedia.org/wiki/SnoRNA
sequence
small nucleolar RNA
A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.
GOC:kgc
wiki
http://en.wikipedia.org/wiki/SnoRNA
miRNA
SO:0000276
SO:0000649
Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
http://en.wikipedia.org/wiki/MiRNA
http://en.wikipedia.org/wiki/StRNA
micro RNA
microRNA
sequence
small temporal RNA
stRNA
wiki
http://en.wikipedia.org/wiki/StRNA
PMID:11081512
PMID:12592000
Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
wiki
http://en.wikipedia.org/wiki/MiRNA
bound_by_factor
An attribute describing a sequence that is bound by another molecule.
Formerly called transcript_by_bound_factor.
SO:0000277
bound by factor
sequence
An attribute describing a sequence that is bound by another molecule.
SO:ke
transcript_bound_by_nucleic_acid
A transcript that is bound by a nucleic acid.
Formerly called transcript_by_bound_nucleic_acid.
SO:0000278
sequence
transcript bound by nucleic acid
A transcript that is bound by a nucleic acid.
SO:xp
transcript_bound_by_protein
A transcript that is bound by a protein.
Formerly called transcript_by_bound_protein.
SO:0000279
sequence
transcript bound by protein
A transcript that is bound by a protein.
SO:xp
engineered_gene
A gene that is engineered.
SO:0000280
engineered gene
sequence
A gene that is engineered.
SO:xp
engineered_foreign_gene
A gene that is engineered and foreign.
SO:0000281
engineered foreign gene
sequence
A gene that is engineered and foreign.
SO:xp
mRNA_with_minus_1_frameshift
An mRNA with a minus 1 frameshift.
SO:0000282
mRNA with minus 1 frameshift
sequence
An mRNA with a minus 1 frameshift.
SO:xp
engineered_foreign_transposable_element_gene
A transposable_element that is engineered and foreign.
SO:0000283
engineered foreign transposable element gene
sequence
A transposable_element that is engineered and foreign.
SO:xp
type_I_enzyme_restriction_site
SO:0000284
The recognition site is bipartite and interrupted.
sequence
true
The recognition site is bipartite and interrupted.
http://www.promega.com
foreign_gene
A gene that is foreign.
SO:0000285
foreign gene
sequence
A gene that is foreign.
SO:xp
long_terminal_repeat
A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.
LTR
SO:0000286
direct terminal repeat
http://en.wikipedia.org/wiki/Long_terminal_repeat
long terminal repeat
sequence
A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
wiki
http://en.wikipedia.org/wiki/Long_terminal_repeat
fusion_gene
A gene that is a fusion.
SO:0000287
fusion gene
http://en.wikipedia.org/wiki/Fusion_gene
sequence
wiki
http://en.wikipedia.org/wiki/Fusion_gene
A gene that is a fusion.
SO:xp
engineered_fusion_gene
A fusion gene that is engineered.
SO:0000288
engineered fusion gene
sequence
A fusion gene that is engineered.
SO:xp
microsatellite
A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.
SO:0000289
VNTR
http://en.wikipedia.org/wiki/Microsatellite
microsatellite locus
microsatellite marker
sequence
wiki
http://en.wikipedia.org/wiki/Microsatellite
A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.
NCBI:th
http://www.informatics.jax.org/silver/glossary.shtml
dinucleotide_repeat_microsatellite_feature
SO:0000290
dinucleotide repeat microsatellite
dinucleotide repeat microsatellite feature
dinucleotide repeat microsatellite locus
dinucleotide repeat microsatellite marker
sequence
trinucleotide_repeat_microsatellite_feature
SO:0000291
dinucleotide repeat microsatellite marker
rinucleotide repeat microsatellite
sequence
trinucleotide repeat microsatellite feature
trinucleotide repeat microsatellite locus
repetitive_element
SO:0000292
sequence
true
engineered_foreign_repetitive_element
A repetitive element that is engineered and foreign.
SO:0000293
engineered foreign repetitive element
sequence
A repetitive element that is engineered and foreign.
SO:xp
inverted_repeat
SO:0000294
The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
http://en.wikipedia.org/wiki/Inverted_repeat
inverted repeat
inverted repeat sequence
sequence
wiki
http://en.wikipedia.org/wiki/Inverted_repeat
SO:ke
The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
U12_intron
A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.
May have either GT-AC or AT-AC 5' and 3' boundaries.
SO:0000295
U12 intron
U12-dependent intron
sequence
A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.
PMID:9428511
origin_of_replication
SO:0000296
The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
http://en.wikipedia.org/wiki/Origin_of_replication
ori
origin of replication
sequence
The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
wiki
http://en.wikipedia.org/wiki/Origin_of_replication
D_loop
D-loop
Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.
SO:0000297
displacement loop
http://en.wikipedia.org/wiki/D_loop
sequence
wiki
http://en.wikipedia.org/wiki/D_loop
Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
recombination_feature
SO:0000298
recombination feature
sequence
specific_recombination_site
SO:0000299
sequence
specific recombination site
recombination_feature_of_rearranged_gene
SO:0000300
recombination feature of rearranged gene
sequence
vertebrate_immune_system_gene_recombination_feature
SO:0000301
sequence
vertebrate immune system gene recombination feature
J_gene_recombination_feature
J gene recombination feature
J-RS
Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.
SO:0000302
sequence
Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
clip
Part of the primary transcript that is clipped off during processing.
SO:0000303
sequence
Part of the primary transcript that is clipped off during processing.
SO:ke
type_II_enzyme_restriction_site
SO:0000304
The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site.
sequence
true
The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site.
http://www.promega.com
modified_DNA_base
A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
Modified base:<modified_base>.
SO:0000305
modified base site
sequence
A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
methylated_DNA_base_feature
A nucleotide modified by methylation.
SO:0000306
methylated base feature
sequence
A nucleotide modified by methylation.
SO:ke
CpG_island
CG island
CpG island
Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
SO:0000307
http://en.wikipedia.org/wiki/CpG_island
sequence
Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.
SO:rd
wiki
http://en.wikipedia.org/wiki/CpG_island
sequence_feature_locating_method
SO:0000308
sequence
true
computed_feature
SO:0000309
sequence
true
predicted_ab_initio_computation
SO:0000310
sequence
true
computed_feature_by_similarity
.
SO:0000311
sequence
similar to:<sequence_id>
true
.
SO:ma
experimentally_determined
Attribute to describe a feature that has been experimentally verified.
SO:0000312
experimentally determined
sequence
Attribute to describe a feature that has been experimentally verified.
SO:ke
stem_loop
A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.
RNA_hairpin_loop
SO:0000019
SO:0000313
http://en.wikipedia.org/wiki/Stem_loop
sequence
stem loop
stem-loop
A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
wiki
http://en.wikipedia.org/wiki/Stem_loop
direct_repeat
A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA.
SO:0000314
direct repeat
http://en.wikipedia.org/wiki/Direct_repeat
sequence
wiki
http://en.wikipedia.org/wiki/Direct_repeat
A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA.
SO:ke
TSS
SO:0000315
The first base where RNA polymerase begins to synthesize the RNA transcript.
sequence
transcription start site
transcription_start_site
SO:ke
The first base where RNA polymerase begins to synthesize the RNA transcript.
CDS
A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
SO:0000316
coding sequence
coding_sequence
sequence
A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
SO:ma
cDNA_clone
Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.
SO:0000317
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
cDNA clone
sequence
Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.
http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html
start_codon
First codon to be translated by a ribosome.
SO:0000318
http://en.wikipedia.org/wiki/Start_codon
initiation codon
sequence
start codon
wiki
http://en.wikipedia.org/wiki/Start_codon
First codon to be translated by a ribosome.
SO:ke
stop_codon
In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
SO:0000319
http://en.wikipedia.org/wiki/Stop_codon
sequence
stop codon
wiki
http://en.wikipedia.org/wiki/Stop_codon
In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.
SO:ke
intronic_splice_enhancer
SO:0000320
Sequences within the intron that modulate splice site selection for some introns.
intronic splice enhancer
sequence
SO:ke
Sequences within the intron that modulate splice site selection for some introns.
mRNA_with_plus_1_frameshift
An mRNA with a plus 1 frameshift.
SO:0000321
mRNA with plus 1 frameshift
sequence
An mRNA with a plus 1 frameshift.
SO:ke
nuclease_hypersensitive_site
SO:0000322
nuclease hypersensitive site
sequence
coding_start
SO:0000323
The first base to be translated into protein.
coding start
sequence
translation initiation site
translation start
SO:ke
The first base to be translated into protein.
tag
A nucleotide sequence that may be used to identify a larger sequence.
SO:0000324
sequence
A nucleotide sequence that may be used to identify a larger sequence.
SO:ke
rRNA_large_subunit_primary_transcript
35S rRNA primary transcript
A primary transcript encoding a large ribosomal subunit RNA.
SO:0000325
rRNA large subunit primary transcript
sequence
A primary transcript encoding a large ribosomal subunit RNA.
SO:ke
SAGE_tag
A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
SAGE tag
SO:0000326
sequence
A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract
coding_end
SO:0000327
The last base to be translated into protein. It does not include the stop codon.
coding end
sequence
translation termination site
translation_end
SO:ke
The last base to be translated into protein. It does not include the stop codon.
microarray_oligo
SO:0000328
microarray oligo
microarray oligonucleotide
sequence
mRNA_with_plus_2_frameshift
An mRNA with a plus 2 frameshift.
SO:0000329
mRNA with plus 2 frameshift
sequence
An mRNA with a plus 2 frameshift.
SO:xp
conserved_region
Region of sequence similarity by descent from a common ancestor.
SO:0000330
conserved region
http://en.wikipedia.org/wiki/Conserved_region
sequence
Region of sequence similarity by descent from a common ancestor.
SO:ke
wiki
http://en.wikipedia.org/wiki/Conserved_region
STS
SO:0000331
Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
sequence
sequence tag site
Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.
http://www.biospace.com
coding_conserved_region
Coding region of sequence similarity by descent from a common ancestor.
SO:0000332
coding conserved region
sequence
Coding region of sequence similarity by descent from a common ancestor.
SO:ke
exon_junction
SO:0000333
The boundary between two exons in a processed transcript.
exon junction
sequence
SO:ke
The boundary between two exons in a processed transcript.
nc_conserved_region
Non-coding region of sequence similarity by descent from a common ancestor.
SO:0000334
nc conserved region
noncoding conserved region
sequence
Non-coding region of sequence similarity by descent from a common ancestor.
SO:ke
mRNA_with_minus_2_frameshift
A mRNA with a minus 2 frameshift.
SO:0000335
mRNA with minus 2 frameshift
sequence
A mRNA with a minus 2 frameshift.
SO:ke
pseudogene
A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog).
SO:0000336
http://en.wikipedia.org/wiki/Pseudogene
sequence
wiki
http://en.wikipedia.org/wiki/Pseudogene
A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog).
http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html
RNAi_reagent
A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
RNAi reagent
SO:0000337
sequence
A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.
SO:rd
MITE
A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins.
SO:0000338
miniature inverted repeat transposable element
sequence
A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins.
http://www.pnas.org/cgi/content/full/97/18/10083
recombination_hotspot
A region in a genome which promotes recombination.
SO:0000339
http://en.wikipedia.org/wiki/Recombination_hotspot
recombination hotspot
sequence
wiki
http://en.wikipedia.org/wiki/Recombination_hotspot
A region in a genome which promotes recombination.
SO:rd
chromosome
SO:0000340
Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
http://en.wikipedia.org/wiki/Chromosome
sequence
SO:ma
Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.
wiki
http://en.wikipedia.org/wiki/Chromosome
chromosome_band
A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
SO:0000341
chromosome band
cytoband
cytological band
http://en.wikipedia.org/wiki/Cytological_band
sequence
wiki
http://en.wikipedia.org/wiki/Cytological_band
A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.
SO:ma
site_specific_recombination_target_region
SO:0000342
sequence
site specific recombination target region
match
A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
SO:0000343
sequence
A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.
SO:ke
splice_enhancer
Region of a transcript that regulates splicing.
SO:0000344
sequence
splice enhancer
Region of a transcript that regulates splicing.
SO:ke
EST
A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
SO:0000345
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
expressed sequence tag
sequence
A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
SO:ke
loxP_site
Cre-recombination target region
SO:0000346
loxP site
sequence
nucleotide_match
A match against a nucleotide sequence.
SO:0000347
nucleotide match
sequence
A match against a nucleotide sequence.
SO:ke
nucleic_acid
An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.
SO:0000348
http://en.wikipedia.org/wiki/Nucleic_acid
nucleic acid
sequence
An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.
CHEBI:33696
RSC:cb
wiki
http://en.wikipedia.org/wiki/Nucleic_acid
protein_match
A match against a protein sequence.
SO:0000349
protein match
sequence
A match against a protein sequence.
SO:ke
FRT_site
An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.
FLP recombination target region
FRT site
SO:0000350
sequence
An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.
SO:ma
synthetic_sequence
An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.
SO:0000351
sequence
synthetic sequence
An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.
SO:ma
DNA
An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.
SO:0000352
sequence
An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.
RSC:cb
sequence_assembly
A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
SO:0000353
http://en.wikipedia.org/wiki/Sequence_assembly
sequence
sequence assembly
wiki
http://en.wikipedia.org/wiki/Sequence_assembly
A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.
SO:ma
group_1_intron_homing_endonuclease_target_region
A region of intronic nucleotide sequence targeted by a nuclease enzyme.
SO:0000354
group 1 intron homing endonuclease target region
sequence
A region of intronic nucleotide sequence targeted by a nuclease enzyme.
SO:ke
haplotype_block
A region of the genome which is co-inherited as the result of the lack of historic recombination within it.
SO:0000355
haplotype block
sequence
A region of the genome which is co-inherited as the result of the lack of historic recombination within it.
SO:ma
RNA
An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.
SO:0000356
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.
RSC:cb
flanked
An attribute describing a region that is bounded either side by a particular kind of region.
SO:0000357
sequence
An attribute describing a region that is bounded either side by a particular kind of region.
SO:ke
floxed
An attribute describing sequence that is flanked by Lox-P sites.
SO:0000359
http://en.wikipedia.org/wiki/Floxed
sequence
wiki
http://en.wikipedia.org/wiki/Floxed
An attribute describing sequence that is flanked by Lox-P sites.
SO:ke
codon
A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.
SO:0000360
http://en.wikipedia.org/wiki/Codon
sequence
A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.
SO:ke
http://www.everythingbio.com/glos/definition.php?word=codon
wiki
http://en.wikipedia.org/wiki/Codon
FRT_flanked
An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.
FRT flanked
SO:0000361
sequence
An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.
SO:ke
invalidated_by_chimeric_cDNA
A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.
SO:0000362
invalidated by chimeric cDNA
sequence
A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.
SO:ma
floxed_gene
A transgene that is floxed.
SO:0000363
floxed gene
sequence
A transgene that is floxed.
SO:xp
transposable_element_flanking_region
SO:0000364
The region of sequence surrounding a transposable element.
sequence
transposable element flanking region
SO:ke
The region of sequence surrounding a transposable element.
integron
A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.
SO:0000365
http://en.wikipedia.org/wiki/Integron
sequence
A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.
SO:as
wiki
http://en.wikipedia.org/wiki/Integron
insertion_site
SO:0000366
The junction where an insertion occurred.
insertion site
sequence
SO:ke
The junction where an insertion occurred.
attI_site
A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.
SO:0000367
attI site
sequence
A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.
SO:as
transposable_element_insertion_site
SO:0000368
The junction in a genome where a transposable_element has inserted.
sequence
transposable element insertion site
SO:ke
The junction in a genome where a transposable_element has inserted.
integrase_coding_region
SO:0000369
sequence
true
small_regulatory_ncRNA
A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
SO:0000370
sequence
small regulatory ncRNA
A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression.
SO:ma
conjugative_transposon
A transposon that encodes function required for conjugation.
SO:0000371
conjugative transposon
sequence
A transposon that encodes function required for conjugation.
http://www.sci.sdsu.edu/~smaloy/Glossary/C.html
enzymatic_RNA
An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
SO:0000372
This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts.
enzymatic RNA
sequence
An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.
RSC:cb
recombinationally_inverted_gene
A recombinationally rearranged gene by inversion.
SO:0000373
recombinationally inverted gene
sequence
A recombinationally rearranged gene by inversion.
SO:xp
ribozyme
An RNA with catalytic activity.
SO:0000374
http://en.wikipedia.org/wiki/Ribozyme
sequence
An RNA with catalytic activity.
SO:ma
wiki
http://en.wikipedia.org/wiki/Ribozyme
rRNA_5_8S
5.8S LSU rRNA
5.8S rRNA
5.8S ribosomal RNA
5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea.
SO:0000375
http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA
rRNA 5 8S
sequence
5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002
wiki
http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA
RNA_6S
6S RNA
A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.
RNA 6S
SO:0000376
http://en.wikipedia.org/wiki/6S_RNA
sequence
A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013
wiki
http://en.wikipedia.org/wiki/6S_RNA
CsrB_RsmB_RNA
An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.
CsrB RsmB RNA
CsrB-RsmB RNA
SO:0000377
sequence
An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018
DsrA_RNA
DsrA RNA
DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.
SO:0000378
http://en.wikipedia.org/wiki/DsrA_RNA
sequence
wiki
http://en.wikipedia.org/wiki/DsrA_RNA
DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014
GcvB_RNA
A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
GcvB RNA
SO:0000379
http://en.wikipedia.org/wiki/GcvB_RNA
sequence
wiki
http://en.wikipedia.org/wiki/GcvB_RNA
A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022
hammerhead_ribozyme
A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.
SO:0000380
hammerhead ribozyme
http://en.wikipedia.org/wiki/Hammerhead_ribozyme
sequence
A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.
PMID:2436805
wiki
http://en.wikipedia.org/wiki/Hammerhead_ribozyme
group_IIA_intron
SO:0000381
group IIA intron
sequence
group_IIB_intron
SO:0000382
group IIB intron
sequence
MicF_RNA
A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.
MicF RNA
SO:0000383
http://en.wikipedia.org/wiki/MicF_RNA
sequence
wiki
http://en.wikipedia.org/wiki/MicF_RNA
A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033
OxyS_RNA
A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.
OxyS RNA
SO:0000384
http://en.wikipedia.org/wiki/OxyS_RNA
sequence
A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035
wiki
http://en.wikipedia.org/wiki/OxyS_RNA
RNase_MRP_RNA
RNase MRP RNA
SO:0000385
The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
sequence
The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030
RNase_P_RNA
RNase P RNA
SO:0000386
The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
sequence
The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010
RprA_RNA
RprA RNA
SO:0000387
Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.
http://en.wikipedia.org/wiki/RprA_RNA
sequence
wiki
http://en.wikipedia.org/wiki/RprA_RNA
Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034
RRE_RNA
RRE RNA
SO:0000388
The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.
sequence
The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036
spot_42_RNA
A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.
SO:0000389
http://en.wikipedia.org/wiki/Spot_42_RNA
sequence
spot-42 RNA
wiki
http://en.wikipedia.org/wiki/Spot_42_RNA
A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021
telomerase_RNA
SO:0000390
The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
http://en.wikipedia.org/wiki/Telomerase_RNA
sequence
telomerase RNA
The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025
wiki
http://en.wikipedia.org/wiki/Telomerase_RNA
U1_snRNA
SO:0000391
U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
U1 small nuclear RNA
U1 snRNA
http://en.wikipedia.org/wiki/U1_snRNA
sequence
small nuclear RNA U1
snRNA U1
wiki
http://en.wikipedia.org/wiki/U1_snRNA
RSC:cb
U1 small nuclear RNA
RSC:cb
small nuclear RNA U1
U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003
RSC:cb
snRNA U1
U2_snRNA
SO:0000392
U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
U2 small nuclear RNA
U2 snRNA
http://en.wikipedia.org/wiki/U2_snRNA
sequence
small nuclear RNA U2
snRNA U2
RSC:CB
U2 small nuclear RNA
RSC:CB
snRNA U2
RSC:CB
small nuclear RNA U2
wiki
http://en.wikipedia.org/wiki/U2_snRNA
U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004
U4_snRNA
SO:0000393
U4 small nuclear RNA
U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
U4 snRNA
http://en.wikipedia.org/wiki/U4_snRNA
sequence
small nuclear RNA U4
snRNA U4
RSC:cb
snRNA U4
U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015
wiki
http://en.wikipedia.org/wiki/U4_snRNA
RSC:cb
U4 small nuclear RNA
RSC:cb
small nuclear RNA U4
U4atac_snRNA
An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
SO:0000394
U4atac small nuclear RNA
U4atac snRNA
sequence
small nuclear RNA U4atac
snRNA U4atac
An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).
PMID:=12409455
RSC:cb
small nuclear RNA U4atac
RSC:cb
snRNA U4atac
RSC:cb
U4atac small nuclear RNA
U5_snRNA
SO:0000395
U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
U5 small nuclear RNA
U5 snRNA
http://en.wikipedia.org/wiki/U5_snRNA
sequence
small nuclear RNA U5
snRNA U5
RSC:cb
snRNA U5
wiki
http://en.wikipedia.org/wiki/U5_snRNA
RSC:cb
U5 small nuclear RNA
U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020
RSC:cb
small nuclear RNA U5
U6_snRNA
SO:0000396
U6 small nuclear RNA
U6 snRNA
U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
http://en.wikipedia.org/wiki/U6_snRNA
sequence
small nuclear RNA U6
snRNA U6
U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015
wiki
http://en.wikipedia.org/wiki/U6_snRNA
RSC:cb
U6 small nuclear RNA
RSC:cb
small nuclear RNA U6
RSC:cb
snRNA U6
U6atac_snRNA
SO:0000397
U6atac small nuclear RNA
U6atac snRNA
U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
sequence
snRNA U6atac
RSC:cb
U6atac small nuclear RNA
U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract
RSC:cb
snRNA U6atac
RSC:cb
U6atac snRNA
U11_snRNA
SO:0000398
U11 small nuclear RNA
U11 snRNA
U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
http://en.wikipedia.org/wiki/U11_snRNA
sequence
small nuclear RNA U11
snRNA U11
RSC:cb
U11 small nuclear RNA
RSC:cb
snRNA U11
wiki
http://en.wikipedia.org/wiki/U11_snRNA
RSC:cb
small nuclear RNA U11
PMID:9622129
U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.
U12_snRNA
SO:0000399
The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
U12 small nuclear RNA
U12 snRNA
http://en.wikipedia.org/wiki/U12_snRNA
sequence
small nuclear RNA U12
snRNA U12
RSC:cb
small nuclear RNA U12
The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007
RSC:cb
U12 small nuclear RNA
RSC:cb
snRNA U12
wiki
http://en.wikipedia.org/wiki/U12_snRNA
sequence_attribute
An attribute describes a quality of sequence.
SO:0000400
sequence
sequence attribute
An attribute describes a quality of sequence.
SO:ke
gene_attribute
SO:0000401
gene attribute
sequence
enhancer_attribute
SO:0000402
sequence
true
U14_snoRNA
An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
SO:0000403
SO:0005839
U14 small nucleolar RNA
U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
U14 snoRNA
sequence
small nucleolar RNA U14
snoRNA U14
PMID:2551119
U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016
vault_RNA
A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
SO:0000404
http://en.wikipedia.org/wiki/Vault_RNA
sequence
vault RNA
A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006
wiki
http://en.wikipedia.org/wiki/Vault_RNA
Y_RNA
SO:0000405
Y RNA
Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.
http://en.wikipedia.org/wiki/Y_RNA
sequence
Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019
wiki
http://en.wikipedia.org/wiki/Y_RNA
twintron
An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.
SO:0000406
http://en.wikipedia.org/wiki/Twintron
sequence
An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.
PMID:1899376
PMID:7823908
wiki
http://en.wikipedia.org/wiki/Twintron
rRNA_18S
18S rRNA
18S ribosomal RNA
A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.
SO:0000407
http://en.wikipedia.org/wiki/18S_ribosomal_RNA
rRNA 18S
sequence
A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.
SO:ke
wiki
http://en.wikipedia.org/wiki/18S_ribosomal_RNA
site
SO:0000408
The interbase position where something (eg an aberration) occurred.
sequence
true
SO:ke
The interbase position where something (eg an aberration) occurred.
binding_site
A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.
BS:00033
SO:0000409
See GO:0005488 : binding.
binding_or_interaction_site
http://en.wikipedia.org/wiki/Binding_site
sequence
site
A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.
EBIBS:GAR
SO:ke
wiki
http://en.wikipedia.org/wiki/Binding_site
protein_binding_site
A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
SO:0000410
See GO:0042277 : peptide binding.
protein binding site
sequence
A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
SO:ke
rescue_region
A region that rescues.
SO:0000411
rescue fragment
rescue region
rescue segment
sequence
A region that rescues.
SO:xp
restriction_fragment
A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
SO:0000412
http://en.wikipedia.org/wiki/Restriction_fragment
restriction fragment
sequence
A region of polynucleotide sequence produced by digestion with a restriction endonuclease.
SO:ke
wiki
http://en.wikipedia.org/wiki/Restriction_fragment
sequence_difference
A region where the sequence differs from that of a specified sequence.
SO:0000413
sequence
sequence difference
A region where the sequence differs from that of a specified sequence.
SO:ke
invalidated_by_genomic_contamination
An attribute to describe a feature that is invalidated due to genomic contamination.
SO:0000414
invalidated by genomic contamination
sequence
An attribute to describe a feature that is invalidated due to genomic contamination.
SO:ke
invalidated_by_genomic_polyA_primed_cDNA
An attribute to describe a feature that is invalidated due to polyA priming.
SO:0000415
invalidated by genomic polyA primed cDNA
sequence
An attribute to describe a feature that is invalidated due to polyA priming.
SO:ke
invalidated_by_partial_processing
An attribute to describe a feature that is invalidated due to partial processing.
SO:0000416
invalidated by partial processing
sequence
An attribute to describe a feature that is invalidated due to partial processing.
SO:ke
polypeptide_domain
A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution.
BS:00012
BS:00134
Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
SO:0000417
SO:0001069
domain
polypeptide domain
polypeptide_structural_domain
sequence
structural domain
A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution.
EBIBS:GAR
domain
uniprot:feature_type
polypeptide_structural_domain
structural domain
signal_peptide
BS:00159
Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
SO:0000418
The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
http://en.wikipedia.org/wiki/Signal_peptide
sequence
signal
signal peptide
signal peptide coding sequence
signal
uniprot:feature_type
wiki
http://en.wikipedia.org/wiki/Signal_peptide
The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
mature_protein_region
BS:00149
SO:0000419
The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
chain
mature peptide
mature protein region
sequence
EBIBS:GAR
SO:cb
The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
chain
uniprot:feature_type
five_prime_terminal_inverted_repeat
5' TIR
SO:0000420
five prime terminal inverted repeat
sequence
three_prime_terminal_inverted_repeat
3' TIR
SO:0000421
sequence
three prime terminal inverted repeat
U5_LTR_region
SO:0000422
U5 LTR region
U5 long terminal repeat region
sequence
R_LTR_region
R LTR region
R long terminal repeat region
SO:0000423
sequence
U3_LTR_region
SO:0000424
U3 LTR region
U3 long terminal repeat region
sequence
five_prime_LTR
5' LTR
5' long terminal repeat
SO:0000425
five prime LTR
sequence
three_prime_LTR
3' LTR
3' long terminal repeat
SO:0000426
sequence
three prime LTR
R_five_prime_LTR_region
R 5' long term repeat region
R five prime LTR region
SO:0000427
sequence
U5_five_prime_LTR_region
SO:0000428
U5 5' long terminal repeat region
U5 five prime LTR region
sequence
U3_five_prime_LTR_region
SO:0000429
U3 5' long term repeat region
U3 five prime LTR region
sequence
R_three_prime_LTR_region
R 3' long terminal repeat region
R three prime LTR region
SO:0000430
sequence
U3_three_prime_LTR_region
SO:0000431
U3 3' long terminal repeat region
U3 three prime LTR region
sequence
U5_three_prime_LTR_region
SO:0000432
U5 3' long terminal repeat region
U5 three prime LTR region
sequence
non_LTR_retrotransposon_polymeric_tract
A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.
SO:0000433
non LTR retrotransposon polymeric tract
sequence
A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.
SO:ke
target_site_duplication
A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.
SO:0000434
sequence
target site duplication
A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.
http://www.koko.gov.my/CocoaBioTech/Glossaryt.html
RR_tract
A polypurine tract within an LTR_retrotransposon.
LTR retrotransposon poly purine tract
RR tract
SO:0000435
sequence
A polypurine tract within an LTR_retrotransposon.
SO:ke
ARS
A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
SO:0000436
autonomously replicating sequence
sequence
A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.
SO:ma
assortment_derived_duplication
SO:0000437
sequence
true
gene_not_polyadenylated
SO:0000438
sequence
true
inverted_ring_chromosome
SO:0000439
inverted ring chromosome
sequence
vector_replicon
A replicon that has been modified to act as a vector for foreign sequence.
SO:0000440
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
http://en.wikipedia.org/wiki/Vector_(molecular_biology)
sequence
vector
vector replicon
wiki
http://en.wikipedia.org/wiki/Vector_(molecular_biology)
A replicon that has been modified to act as a vector for foreign sequence.
SO:ma
ss_oligo
A single stranded oligonucleotide.
SO:0000441
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
sequence
single strand oligo
single strand oligonucleotide
single stranded oligonucleotide
ss oligo
ss oligonucleotide
A single stranded oligonucleotide.
SO:ke
ds_oligo
A double stranded oligonucleotide.
SO:0000442
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
double stranded oligonucleotide
ds oligo
ds-oligonucleotide
sequence
A double stranded oligonucleotide.
SO:ke
polymer_attribute
An attribute to describe the kind of biological sequence.
SO:0000443
polymer attribute
sequence
An attribute to describe the kind of biological sequence.
SO:ke
three_prime_noncoding_exon
Non-coding exon in the 3' UTR.
SO:0000444
sequence
three prime noncoding exon
Non-coding exon in the 3' UTR.
SO:ke
five_prime_noncoding_exon
5' nc exon
5' non coding exon
Non-coding exon in the 5' UTR.
SO:0000445
five prime noncoding exon
sequence
Non-coding exon in the 5' UTR.
SO:ke
UTR_intron
Intron located in the untranslated region.
SO:0000446
UTR intron
sequence
Intron located in the untranslated region.
SO:ke
five_prime_UTR_intron
An intron located in the 5' UTR.
SO:0000447
five prime UTR intron
sequence
An intron located in the 5' UTR.
SO:ke
three_prime_UTR_intron
An intron located in the 3' UTR.
SO:0000448
sequence
three prime UTR intron
An intron located in the 3' UTR.
SO:ke
random_sequence
A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components.
SO:0000449
random sequence
sequence
A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components.
SO:ma
interband
A light region between two darkly staining bands in a polytene chromosome.
SO:0000450
chromosome interband
sequence
A light region between two darkly staining bands in a polytene chromosome.
SO:ma
gene_with_polyadenylated_mRNA
A gene that encodes a polyadenylated mRNA.
SO:0000451
gene with polyadenylated mRNA
sequence
A gene that encodes a polyadenylated mRNA.
SO:xp
transgene_attribute
SO:0000452
sequence
true
chromosomal_transposition
A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type.
SO:0000453
chromosomal transposition
sequence
transposition
A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type.
FB:reference_manual
SO:ke
rasiRNA
A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
SO:0000454
http://en.wikipedia.org/wiki/RasiRNA
repeat associated small interfering RNA
sequence
wiki
http://en.wikipedia.org/wiki/RasiRNA
A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.
http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284
gene_with_mRNA_with_frameshift
A gene that encodes an mRNA with a frameshift.
SO:0000455
gene with mRNA with frameshift
sequence
A gene that encodes an mRNA with a frameshift.
SO:xp
recombinationally_rearranged_gene
A gene that is recombinationally rearranged.
SO:0000456
recombinationally rearranged gene
sequence
A gene that is recombinationally rearranged.
SO:ke
interchromosomal_duplication
A chromosome duplication involving an insertion from another chromosome.
SO:0000457
interchromosomal duplication
sequence
A chromosome duplication involving an insertion from another chromosome.
SO:ke
D_gene_segment
D gene
D-GENE
Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.
SO:0000458
sequence
Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
gene_with_trans_spliced_transcript
A gene with a transcript that is trans-spliced.
SO:0000459
gene with trans spliced transcript
sequence
A gene with a transcript that is trans-spliced.
SO:xp
vertebrate_immunoglobulin_T_cell_receptor_segment
I am using the term segment instead of gene here to avoid confusion with the region 'gene'.
SO:0000460
sequence
vertebrate immunoglobulin T cell receptor segment
vertebrate_immunoglobulin/T-cell receptor gene
inversion_derived_bipartite_deficiency
A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.
SO:0000461
inversion derived bipartite deficiency
sequence
A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.
FB:km
pseudogenic_region
A non-functional descendant of a functional entity.
SO:0000462
pseudogenic region
sequence
A non-functional descendant of a functional entity.
SO:cjm
encodes_alternately_spliced_transcripts
A gene that encodes more than one transcript.
SO:0000463
encodes alternately spliced transcripts
sequence
A gene that encodes more than one transcript.
SO:ke
decayed_exon
A non-functional descendant of an exon.
SO:0000464
decayed exon
sequence
A non-functional descendant of an exon.
SO:ke
inversion_derived_deficiency_plus_duplication
A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion.
SO:0000465
inversion derived deficiency plus duplication
sequence
A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion.
FB:km
V_gene_segment
Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.
SO:0000466
V gene
V-GENE
sequence
variable_gene
Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
post_translationally_regulated_by_protein_stability
An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein.
SO:0000467
post translationally regulated by protein stability
post-translationally regulated by protein stability
sequence
An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein.
SO:ke
golden_path_fragment
One of the pieces of sequence that make up a golden path.
SO:0000468
golden path fragment
sequence
One of the pieces of sequence that make up a golden path.
SO:rd
post_translationally_regulated_by_protein_modification
An attribute describing a gene sequence where the resulting protein is modified to regulate it.
SO:0000469
post translationally regulated by protein modification
post-translationally regulated by protein modification
sequence
An attribute describing a gene sequence where the resulting protein is modified to regulate it.
SO:ke
J_gene_segment
Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment.
J gene
J-GENE
SO:0000470
sequence
Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
autoregulated
SO:0000471
The gene product is involved in its own transcriptional regulation.
sequence
SO:ke
The gene product is involved in its own transcriptional regulation.
tiling_path
A set of regions which overlap with minimal polymorphism to form a linear sequence.
SO:0000472
sequence
tiling path
A set of regions which overlap with minimal polymorphism to form a linear sequence.
SO:cjm
negatively_autoregulated
SO:0000473
The gene product is involved in its own transcriptional regulation where it decreases transcription.
negatively autoregulated
sequence
SO:ke
The gene product is involved in its own transcriptional regulation where it decreases transcription.
tiling_path_fragment
A piece of sequence that makes up a tiling_path (SO:0000472).
SO:0000474
sequence
tiling path fragment
A piece of sequence that makes up a tiling_path (SO:0000472).
SO:ke
positively_autoregulated
SO:0000475
The gene product is involved in its own transcriptional regulation, where it increases transcription.
positively autoregulated
sequence
SO:ke
The gene product is involved in its own transcriptional regulation, where it increases transcription.
contig_read
A DNA sequencer read which is part of a contig.
SO:0000476
contig read
sequence
A DNA sequencer read which is part of a contig.
SO:ke
polycistronic_gene
A gene that is polycistronic.
SO:0000477
sequence
true
A gene that is polycistronic.
SO:ke
C_gene_segment
C gene
C_GENE
Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
SO:0000478
constant gene
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
trans_spliced_transcript
A transcript that is trans-spliced.
SO:0000479
sequence
trans spliced transcript
trans-spliced transcript
A transcript that is trans-spliced.
SO:xp
tiling_path_clone
A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly.
SO:0000480
sequence
tiling path clone
A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly.
SO:ke
terminal_inverted_repeat
An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon.
SO:0000481
TIR
sequence
terminal inverted repeat
An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon.
SO:ke
vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
SO:0000482
sequence
vertebrate immunoglobulin T cell receptor gene cluster
vertebrate_immunoglobulin/T-cell receptor gene cluster
nc_primary_transcript
A primary transcript that is never translated into a protein.
SO:0000483
nc primary transcript
noncoding primary transcript
sequence
A primary transcript that is never translated into a protein.
SO:ke
three_prime_coding_exon_noncoding_region
SO:0000484
The sequence of the 3' exon that is not coding.
sequence
three prime coding exon noncoding region
three_prime_exon_noncoding_region
SO:ke
The sequence of the 3' exon that is not coding.
DJ_J_cluster
(DJ)-J-CLUSTER
DJ J cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.
SO:0000485
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
five_prime_coding_exon_noncoding_region
SO:0000486
The sequence of the 5' exon preceding the start codon.
five prime coding exon noncoding region
five_prime_exon_noncoding_region
sequence
SO:ke
The sequence of the 5' exon preceding the start codon.
VDJ_J_C_cluster
(VDJ)-J-C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.
SO:0000487
VDJ J C cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VDJ_J_cluster
(VDJ)-J-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.
SO:0000488
VDJ J cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VJ_C_cluster
(VJ)-C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.
SO:0000489
VJ C cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VJ_J_C_cluster
(VJ)-J-C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.
SO:0000490
VJ J C cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VJ_J_cluster
(VJ)-J-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.
SO:0000491
VJ J cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D_gene_recombination_feature
D gene recombination feature
SO:0000492
sequence
three_prime_D_heptamer
3'D-HEPTAMER
7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
SO:0000493
sequence
three prime D heptamer
7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
three_prime_D_nonamer
3'D-NOMAMER
A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
SO:0000494
sequence
three prime D nonamer
A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
three_prime_D_spacer
3'D-SPACER
A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.
SO:0000495
sequence
three prime D spacer
A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
five_prime_D_heptamer
5'D-HEPTAMER
7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
SO:0000496
five prime D heptamer
sequence
7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
five_prime_D_nonamer
5'D-NONAMER
9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
SO:0000497
five prime D nonamer
sequence
9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
five_prime_D_spacer
12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
5'-SPACER
SO:0000498
five prime D spacer
five prime D-spacer
sequence
12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
virtual_sequence
A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.
SO:0000499
sequence
virtual sequence
A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.
SO:ke
Hoogsteen_base_pair
A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds.
Hoogsteen base pair
SO:0000500
http://en.wikipedia.org/wiki/Hoogsteen_base_pair
sequence
wiki
http://en.wikipedia.org/wiki/Hoogsteen_base_pair
A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds.
PMID:12177293
reverse_Hoogsteen_base_pair
A type of non-canonical base-pairing.
SO:0000501
reverse Hoogsteen base pair
sequence
A type of non-canonical base-pairing.
SO:ke
transcribed_region
A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.
SO:0000502
This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.
sequence
true
A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.
SO:ke
alternately_spliced_gene_encodeing_one_transcript
SO:0000503
sequence
true
D_DJ_C_cluster
D DJ C cluster
D-(DJ)-C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene.
SO:0000504
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D_DJ_cluster
D DJ cluster
D-(DJ)-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene.
SO:0000505
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D_DJ_J_C_cluster
D DJ J C cluster
D-(DJ)-J-C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene.
SO:0000506
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
pseudogenic_exon
A non functional descendant of an exon, part of a pseudogene.
SO:0000507
This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
pseudogenic exon
sequence
A non functional descendant of an exon, part of a pseudogene.
SO:ke
D_DJ_J_cluster
D DJ J cluster
D-(DJ)-J-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene.
SO:0000508
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D_J_C_cluster
D J C cluster
D-J-C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene.
SO:0000509
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VD_gene_segment
Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
SO:0000510
VD gene
V_D_GENE
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205).
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
J_C_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene.
J C cluster
J-C-CLUSTER
SO:0000511
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
inversion_derived_deficiency_plus_aneuploid
A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion.
SO:0000512
inversion derived deficiency plus aneuploid
sequence
A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion.
FB:km
J_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.
J cluster
J-CLUSTER
SO:0000513
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
J_nonamer
9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
J nonamer
J-NONAMER
SO:0000514
sequence
9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
J_heptamer
7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
J heptamer
J-HEPTAMER
SO:0000515
sequence
7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
pseudogenic_transcript
A non functional descendant of a transcript, part of a pseudogene.
SO:0000516
This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
pseudogenic transcript
sequence
A non functional descendant of a transcript, part of a pseudogene.
SO:ke
J_spacer
12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
J spacer
J-SPACER
SO:0000517
sequence
12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_DJ_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene.
SO:0000518
V DJ cluster
V-(DJ)-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_DJ_J_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene.
SO:0000519
V DJ J cluster
V-(DJ)-J-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_VDJ_C_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene.
SO:0000520
V VDJ C cluster
V-(VDJ)-C-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_VDJ_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene.
SO:0000521
V VDJ cluster
V-(VDJ)-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_VDJ_J_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene.
SO:0000522
V VDJ J cluster
V-(VDJ)-J-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_VJ_C_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.
SO:0000523
V VJ C cluster
V-(VJ)-C-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_VJ_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene.
SO:0000524
V VJ cluster
V-(VJ)-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_VJ_J_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene.
SO:0000525
V VJ J cluster
V-(VJ)-J-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.
SO:0000526
V cluster
V-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_D_DJ_C_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene.
SO:0000527
V D DJ C cluster
V-D-(DJ)-C-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_D_DJ_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene.
SO:0000528
V D DJ cluster
V-D-(DJ)-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_D_DJ_J_C_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene.
SO:0000529
V D DJ J C cluster
V-D-(DJ)-J-C-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_D_DJ_J_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene.
SO:0000530
V D DJ J cluster
V-D-(DJ)-J-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_D_J_C_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene.
SO:0000531
V D J C cluster
V-D-J-C-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_D_J_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene.
SO:0000532
V D J cluster
V-D-J-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_heptamer
7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
SO:0000533
V heptamer
V-HEPTAMER
sequence
7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_J_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene.
SO:0000534
V J cluster
V-J-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_J_C_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene.
SO:0000535
V J C cluster
V-J-C-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_nonamer
9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
SO:0000536
V nonamer
V-NONAMER
sequence
9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_spacer
12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
SO:0000537
V spacer
V-SPACER
sequence
12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_gene_recombination_feature
Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene.
SO:0000538
V gene recombination feature
V-RS
sequence
Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
DJ_C_cluster
(DJ)-C-CLUSTER
DJ C cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene.
SO:0000539
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
DJ_J_C_cluster
(DJ)-J-C-CLUSTER
DJ J C cluster
Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE.
SO:0000540
sequence
Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
VDJ_C_cluster
(VDJ)-C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene.
SO:0000541
VDJ C cluster
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_DJ_C_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene.
SO:0000542
V DJ C cluster
V-(DJ)-C-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
alternately_spliced_gene_encoding_greater_than_one_transcript
SO:0000543
sequence
true
helitron
A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons.
ISCR
SO:0000544
http://en.wikipedia.org/wiki/Helitron
sequence
wiki
http://en.wikipedia.org/wiki/Helitron
A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons.
http://www.pnas.org/cgi/content/full/100/11/6569
recoding_pseudoknot
SO:0000545
The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding.
recoding pseudoknot
sequence
The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937
designed_sequence
SO:0000546
designed sequence
sequence
inversion_derived_bipartite_duplication
A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion.
SO:0000547
inversion derived bipartite duplication
sequence
A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion.
FB:km
gene_with_edited_transcript
A gene that encodes a transcript that is edited.
SO:0000548
gene with edited transcript
sequence
A gene that encodes a transcript that is edited.
SO:xp
inversion_derived_duplication_plus_aneuploid
A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion.
SO:0000549
inversion derived duplication plus aneuploid
sequence
A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion.
FB:km
aneuploid_chromosome
A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking.
Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila.
SO:0000550
aneuploid chromosome
sequence
A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking.
SO:ke
polyA_signal_sequence
SO:0000551
The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
poly(A) signal
polyA signal sequence
polyadenylation termination signal
sequence
The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
Shine_Dalgarno_sequence
A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
Not found in Eukaryotic sequence.
RBS
SO:0000552
Shine Dalgarno sequence
Shine-Dalgarno sequence
five prime ribosome binding site
http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence
sequence
wiki
http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence
A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.
SO:jh
polyA_site
SO:0000553
SO:0001430
The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence.
polyA cleavage site
polyA junction
polyA site
polyA_junction
polyadenylation site
sequence
The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
assortment_derived_deficiency_plus_duplication
SO:0000554
sequence
true
five_prime_clip
5' clip
5' most region of a precursor transcript that is clipped off during processing.
SO:0000555
five prime clip
sequence
5' most region of a precursor transcript that is clipped off during processing.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
five_prime_D_recombination_signal_sequence
5'RS
Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene.
SO:0000556
five prime D recombination signal sequence
five prime D-recombination signal sequence
sequence
Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
three_prime_clip
3'-clip
3'-most region of a precursor transcript that is clipped off during processing.
SO:0000557
sequence
three prime clip
3'-most region of a precursor transcript that is clipped off during processing.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
C_cluster
C cluster
C-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.
SO:0000558
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D_cluster
D cluster
D-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene.
SO:0000559
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
D_J_cluster
D J cluster
D-J-CLUSTER
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.
SO:0000560
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
HEPTAMER
SO:0000561
Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.
heptamer of recombination feature of vertebrate immune system gene
sequence
Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
SO:0000562
nonamer of recombination feature of vertebrate immune system gene
sequence
vertebrate_immune_system_gene_recombination_spacer
SO:0000563
sequence
vertebrate immune system gene recombination spacer
V_DJ_J_C_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene.
SO:0000564
V DJ J C cluster
V-(DJ)-J-C-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_VDJ_J_C_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene.
SO:0000565
V VDJ J C cluster
V-(VDJ)-J-C-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
V_VJ_J_C_cluster
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene.
SO:0000566
V VJ J C cluster
V-(VJ)-J-C-CLUSTER
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
inversion_derived_aneuploid_chromosome
A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion.
SO:0000567
inversion derived aneuploid chromosome
sequence
A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion.
FB:km
bidirectional_promoter
An unregulated promoter that allows continuous expression.
SO:0000568
bidirectional promoter
sequence
An unregulated promoter that allows continuous expression.
SO:ke
retrotransposed
An attribute of a feature that occurred as the product of a reverse transcriptase mediated event.
GO:0003964 RNA-directed DNA polymerase activity.
SO:0000569
SO:0100042
http://en.wikipedia.org/wiki/Retrotransposed
sequence
wiki
http://en.wikipedia.org/wiki/Retrotransposed
An attribute of a feature that occurred as the product of a reverse transcriptase mediated event.
SO:ke
three_prime_D_recombination_signal_sequence
3'D-RS
Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene.
SO:0000570
sequence
three prime D recombination signal sequence
three_prime_D-recombination_signal_sequence
Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
miRNA_encoding
SO:0000571
miRNA encoding
sequence
DJ_gene_segment
D-J-GENE
DJ gene
Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment.
SO:0000572
sequence
Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment.
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
rRNA_encoding
SO:0000573
rRNA encoding
sequence
VDJ_gene_segment
Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
SO:0000574
V-D-J-GENE
VDJ gene
sequence
Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
scRNA_encoding
SO:0000575
scRNA encoding
sequence
VJ_gene_segment
Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
SO:0000576
V-J-GENE
VJ gene
sequence
Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205).
http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#
centromere
A region of chromosome where the spindle fibers attach during mitosis and meiosis.
SO:0000577
http://en.wikipedia.org/wiki/Centromere
sequence
A region of chromosome where the spindle fibers attach during mitosis and meiosis.
SO:ke
wiki
http://en.wikipedia.org/wiki/Centromere
snoRNA_encoding
SO:0000578
sequence
snoRNA encoding
edited_transcript_feature
A locatable feature on a transcript that is edited.
SO:0000579
edited transcript feature
sequence
A locatable feature on a transcript that is edited.
SO:ma
methylation_guide_snoRNA_primary_transcript
A primary transcript encoding a methylation guide small nucleolar RNA.
SO:0000580
methylation guide snoRNA primary transcript
sequence
A primary transcript encoding a methylation guide small nucleolar RNA.
SO:ke
cap
A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.
SO:0000581
http://en.wikipedia.org/wiki/5%27_cap
sequence
A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA.
http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html
wiki
http://en.wikipedia.org/wiki/5%27_cap
rRNA_cleavage_snoRNA_primary_transcript
A primary transcript encoding an rRNA cleavage snoRNA.
SO:0000582
rRNA cleavage snoRNA primary transcript
sequence
A primary transcript encoding an rRNA cleavage snoRNA.
SO:ke
pre_edited_region
SO:0000583
The region of a transcript that will be edited.
pre edited region
pre-edited region
sequence
The region of a transcript that will be edited.
http://dna.kdna.ucla.edu/rna/index.aspx
tmRNA
10Sa RNA
A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes.
SO:0000584
http://en.wikipedia.org/wiki/TmRNA
sequence
ssrA
wiki
http://en.wikipedia.org/wiki/TmRNA
A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023
C_D_box_snoRNA_encoding
C/D box snoRNA encoding
SO:0000585
sequence
tmRNA_primary_transcript
10Sa RNA primary transcript
A primary transcript encoding a tmRNA (SO:0000584).
SO:0000586
sequence
ssrA RNA primary transcript
tmRNA primary transcript
A primary transcript encoding a tmRNA (SO:0000584).
SO:ke
group_I_intron
GO:0000372.
Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions.
SO:0000587
group I intron
http://en.wikipedia.org/wiki/Group_I_intron
sequence
wiki
http://en.wikipedia.org/wiki/Group_I_intron
Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028
autocatalytically_spliced_intron
A self spliced intron.
SO:0000588
autocatalytically spliced intron
sequence
A self spliced intron.
SO:ke
SRP_RNA_primary_transcript
A primary transcript encoding a signal recognition particle RNA.
SO:0000589
SRP RNA primary transcript
sequence
A primary transcript encoding a signal recognition particle RNA.
SO:ke
SRP_RNA
7S RNA
SO:0000590
SRP RNA
The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
sequence
signal recognition particle RNA
The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017
pseudoknot
A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop.
SO:0000591
http://en.wikipedia.org/wiki/Pseudoknot
sequence
wiki
http://en.wikipedia.org/wiki/Pseudoknot
A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop.
RSC:cb
H_pseudoknot
A pseudoknot which contains two stems and at least two loops.
H pseudoknot
H-pseudoknot
H-type pseudoknot
SO:0000592
classical pseudoknot
hairpin-type pseudoknot
sequence
A pseudoknot which contains two stems and at least two loops.
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract
C_D_box_snoRNA
C D box snoRNA
C/D box snoRNA
Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.
SO:0000593
box C/D snoRNA
sequence
Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
H_ACA_box_snoRNA
H ACA box snoRNA
H/ACA box snoRNA
Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.
SO:0000594
box H/ACA snoRNA
sequence
Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
C_D_box_snoRNA_primary_transcript
A primary transcript encoding a small nucleolar RNA of the box C/D family.
C/D box snoRNA primary transcript
SO:0000595
sequence
A primary transcript encoding a small nucleolar RNA of the box C/D family.
SO:ke
H_ACA_box_snoRNA_primary_transcript
A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
H ACA box snoRNA primary transcript
SO:0000596
sequence
A primary transcript encoding a small nucleolar RNA of the box H/ACA family.
SO:ke
transcript_edited_by_U_insertion/deletion
SO:0000597
The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
sequence
true
The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
http://www.rna.ucla.edu/index.html
edited_by_C_insertion_and_dinucleotide_insertion
SO:0000598
sequence
transcript_edited_by_C-insertion_and_dinucleotide_insertion
true
edited_by_C_to_U_substitution
SO:0000599
sequence
true
edited_by_A_to_I_substitution
SO:0000600
sequence
true
edited_by_G_addition
SO:0000601
sequence
true
guide_RNA
A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.
SO:0000602
gRNA
guide RNA
http://en.wikipedia.org/wiki/Guide_RNA
sequence
wiki
http://en.wikipedia.org/wiki/Guide_RNA
A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.
http://www.rna.ucla.edu/index.html
group_II_intron
GO:0000373.
Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
SO:0000603
group II intron
http://en.wikipedia.org/wiki/Group_II_intron
sequence
Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.
http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml
wiki
http://en.wikipedia.org/wiki/Group_II_intron
editing_block
Edited mRNA sequence mediated by a single guide RNA (SO:0000602).
SO:0000604
editing block
sequence
Edited mRNA sequence mediated by a single guide RNA (SO:0000602).
http://dna.kdna.ucla.edu/rna/index.aspx
intergenic_region
A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
SO:0000605
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
http://en.wikipedia.org/wiki/Intergenic_region
intergenic region
sequence
wiki
http://en.wikipedia.org/wiki/Intergenic_region
A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.
SO:cjm
editing_domain
Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
SO:0000606
editing domain
sequence
Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).
http://dna.kdna.ucla.edu/rna/index.aspx
unedited_region
SO:0000607
The region of an edited transcript that will not be edited.
sequence
unedited region
The region of an edited transcript that will not be edited.
http://dna.kdna.ucla.edu/rna/index.aspx
H_ACA_box_snoRNA_encoding
H ACA box snoRNA encoding
SO:0000608
sequence
oligo_U_tail
SO:0000609
The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).
oligo U tail
sequence
The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).
http://www.rna.ucla.edu/
polyA_sequence
SO:0000610
Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
polyA sequence
sequence
SO:ke
Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.
branch_site
A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
SO:0000611
branch point
branch site
branch_point
sequence
A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.
SO:ke
polypyrimidine_tract
SO:0000612
The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
http://en.wikipedia.org/wiki/Polypyrimidine_tract
polypyrimidine tract
sequence
The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.
http://nar.oupjournals.org/cgi/content/full/25/4/888
wiki
http://en.wikipedia.org/wiki/Polypyrimidine_tract
bacterial_RNApol_promoter
A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
SO:0000613
bacterial RNApol promoter
sequence
A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
SO:ke
bacterial_terminator
A terminator signal for bacterial transcription.
SO:0000614
bacterial terminator
sequence
A terminator signal for bacterial transcription.
SO:ke
terminator_of_type_2_RNApol_III_promoter
A terminator signal for RNA polymerase III transcription.
SO:0000615
sequence
terminator of type 2 RNApol III promoter
A terminator signal for RNA polymerase III transcription.
SO:ke
transcription_end_site
SO:0000616
The base where transcription ends.
sequence
transcription end site
SO:ke
The base where transcription ends.
RNApol_III_promoter_type_1
RNApol III promoter type 1
SO:0000617
sequence
RNApol_III_promoter_type_2
RNApol III promoter type 2
SO:0000618
sequence
tRNA promoter
A_box
A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG.
A-box
Binds TFIIIC.
SO:0000619
http://en.wikipedia.org/wiki/A-box
sequence
A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG.
SO:ke
wiki
http://en.wikipedia.org/wiki/A-box
B_box
A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC.
B-box
Binds TFIIIC.
SO:0000620
sequence
A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC.
SO:ke
RNApol_III_promoter_type_3
RNApol III promoter type 3
SO:0000621
sequence
C_box
An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn.
C-box
SO:0000622
sequence
An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn.
SO:ke
snRNA_encoding
SO:0000623
sequence
snRNA encoding
telomere
A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
SO:0000624
http://en.wikipedia.org/wiki/Telomere
sequence
telomeric DNA
telomeric sequence
wiki
http://en.wikipedia.org/wiki/Telomere
A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
SO:ma
silencer
A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
SO:0000625
http://en.wikipedia.org/wiki/Silencer_(DNA)
sequence
A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
SO:ke
wiki
http://en.wikipedia.org/wiki/Silencer_(DNA)
chromosomal_regulatory_element
SO:0000626
chromosomal regulatory element
sequence
insulator
A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
SO:0000627
http://en.wikipedia.org/wiki/Insulator_(genetics)
insulator element
sequence
wiki
http://en.wikipedia.org/wiki/Insulator_(genetics)
A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression.
SO:regcreative
chromosomal_structural_element
SO:0000628
chromosomal structural element
sequence
five_prime_open_reading_frame
SO:0000629
five prime open reading frame
sequence
upstream_AUG_codon
A start codon upstream of the ORF.
SO:0000630
sequence
upstream AUG codon
A start codon upstream of the ORF.
SO:ke
polycistronic_primary_transcript
A primary transcript encoding for more than one gene product.
SO:0000631
polycistronic primary transcript
sequence
A primary transcript encoding for more than one gene product.
SO:ke
monocistronic_primary_transcript
A primary transcript encoding for one gene product.
SO:0000632
monocistronic primary transcript
sequence
A primary transcript encoding for one gene product.
SO:ke
monocistronic_mRNA
An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
SO:0000633
http://en.wikipedia.org/wiki/Monocistronic_mRNA
monocistronic mRNA
monocistronic processed transcript
sequence
An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.
SO:rd
wiki
http://en.wikipedia.org/wiki/Monocistronic_mRNA
polycistronic_mRNA
An mRNA that encodes multiple proteins from at least two non-overlapping regions.
SO:0000634
http://en.wikipedia.org/wiki/Polycistronic_mRNA
polycistronic mRNA
polycistronic processed transcript
sequence
An mRNA that encodes multiple proteins from at least two non-overlapping regions.
SO:rd
wiki
http://en.wikipedia.org/wiki/Polycistronic_mRNA
mini_exon_donor_RNA
A primary transcript that donates the spliced leader to other mRNA.
SO:0000635
mini exon donor RNA
mini-exon donor RNA
sequence
A primary transcript that donates the spliced leader to other mRNA.
SO:ke
spliced_leader_RNA
SO:0000636
mini-exon
sequence
spliced leader RNA
engineered_plasmid
A plasmid that is engineered.
SO:0000637
engineered plasmid
engineered plasmid gene
sequence
A plasmid that is engineered.
SO:xp
transcribed_spacer_region
Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
SO:0000638
sequence
transcribed spacer region
Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.
http://oregonstate.edu/instruction/bb492/general/glossary.html
internal_transcribed_spacer_region
Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.
SO:0000639
internal transcribed spacer region
sequence
Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.
SO:ke
external_transcribed_spacer_region
Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
SO:0000640
external transcribed spacer region
sequence
Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.
SO:ke
tetranucleotide_repeat_microsatellite_feature
SO:0000641
sequence
tetranucleotide repeat microsatellite feature
SRP_RNA_encoding
SO:0000642
SRP RNA encoding
sequence
minisatellite
A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.
SO:0000643
http://en.wikipedia.org/wiki/Minisatellite
sequence
wiki
http://en.wikipedia.org/wiki/Minisatellite
A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.
http://www.informatics.jax.org/silver/glossary.shtml
antisense_RNA
Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
SO:0000644
antisense RNA
http://en.wikipedia.org/wiki/Antisense_RNA
sequence
Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
SO:ke
wiki
http://en.wikipedia.org/wiki/Antisense_RNA
antisense_primary_transcript
SO:0000645
The reverse complement of the primary transcript.
antisense primary transcript
sequence
SO:ke
The reverse complement of the primary transcript.
siRNA
A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.
SO:0000646
http://en.wikipedia.org/wiki/SiRNA
sequence
small interfering RNA
A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.
PMID:12592000
wiki
http://en.wikipedia.org/wiki/SiRNA
miRNA_primary_transcript
A primary transcript encoding a micro RNA.
SO:0000647
SO:0000648
miRNA primary transcript
micro RNA primary transcript
sequence
small temporal RNA primary transcript
stRNA primary transcript
stRNA_primary_transcript
A primary transcript encoding a micro RNA.
SO:ke
small_subunit_rRNA
Ribosomal RNA transcript that structures the small subunit of the ribosome.
SO:0000650
SSU RNA
SSU rRNA
sequence
small subunit rRNA
RSC:cb
SSU RNA
RSC:cb
SSU rRNA
Ribosomal RNA transcript that structures the small subunit of the ribosome.
SO:ke
large_subunit_rRNA
LSU RNA
LSU rRNA
Ribosomal RNA transcript that structures the large subunit of the ribosome.
SO:0000651
large subunit rRNA
sequence
Ribosomal RNA transcript that structures the large subunit of the ribosome.
SO:ke
LSU rRNA
RSC:cb
LSU RNA
RSC:cb
rRNA_5S
5S LSU rRNA
5S rRNA
5S ribosomal RNA
5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription.
SO:0000652
http://en.wikipedia.org/wiki/5S_ribosomal_RNA
rRNA 5S
sequence
5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001
wiki
http://en.wikipedia.org/wiki/5S_ribosomal_RNA
rRNA_28S
28S LSU rRNA
28S rRNA
28S ribosomal RNA
A component of the large ribosomal subunit.
SO:0000653
http://en.wikipedia.org/wiki/28S_ribosomal_RNA
rRNA 28S
sequence
wiki
http://en.wikipedia.org/wiki/28S_ribosomal_RNA
A component of the large ribosomal subunit.
SO:ke
maxicircle_gene
A mitochondrial gene located in a maxicircle.
SO:0000654
maxi-circle gene
maxicircle gene
sequence
A mitochondrial gene located in a maxicircle.
SO:xp
ncRNA
A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
SO:0000655
http://en.wikipedia.org/wiki/NcRNA
noncoding RNA
sequence
An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
SO:ke
wiki
http://en.wikipedia.org/wiki/NcRNA
stRNA_encoding
SO:0000656
sequence
stRNA encoding
repeat_region
A region of sequence containing one or more repeat units.
SO:0000657
repeat region
sequence
A region of sequence containing one or more repeat units.
SO:ke
dispersed_repeat
A repeat that is located at dispersed sites in the genome.
SO:0000658
dispersed repeat
http://en.wikipedia.org/wiki/Interspersed_repeat
interspersed repeat
sequence
A repeat that is located at dispersed sites in the genome.
SO:ke
wiki
http://en.wikipedia.org/wiki/Interspersed_repeat
tmRNA_encoding
SO:0000659
sequence
tmRNA encoding
DNA_invertase_target_sequence
SO:0000660
sequence
true
intron_attribute
SO:0000661
sequence
true
spliceosomal_intron
An intron which is spliced by the spliceosome.
GO:0000398.
SO:0000662
sequence
spliceosomal intron
An intron which is spliced by the spliceosome.
SO:ke
tRNA_encoding
SO:0000663
sequence
tRNA encoding
introgressed_chromosome_region
SO:0000664
introgressed chromosome region
sequence
monocistronic_transcript
A transcript that is monocistronic.
SO:0000665
monocistronic transcript
sequence
A transcript that is monocistronic.
SO:xp
mobile_intron
An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.
SO:0000666
mobile intron
sequence
An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.
SO:ke
insertion
SO:0000667
SO:1000034
The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
insertion
loinc:LA6687-3
nucleotide insertion
nucleotide_insertion
sequence
http://www.ncbi.nlm.nih.gov/dbvar/
insertion
SO:ke
The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.
Insertion
loinc:LA6687-3
EST_match
A match against an EST sequence.
EST match
SO:0000668
sequence
A match against an EST sequence.
SO:ke
sequence_rearrangement_feature
SO:0000669
sequence
sequence rearrangement feature
chromosome_breakage_sequence
A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.
SO:0000670
chromosome breakage sequence
sequence
A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.
SO:ma
internal_eliminated_sequence
A sequence eliminated from the genome of ciliates during nuclear differentiation.
SO:0000671
internal eliminated sequence
sequence
A sequence eliminated from the genome of ciliates during nuclear differentiation.
SO:ma
macronucleus_destined_segment
A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.
SO:0000672
macronucleus destined segment
sequence
A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.
SO:ma
transcript
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
SO:0000673
http://en.wikipedia.org/wiki/RNA
sequence
wiki
http://en.wikipedia.org/wiki/RNA
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
SO:ma
non_canonical_splice_site
A splice site where the donor and acceptor sites differ from the canonical form.
SO:0000674
SO:0000678
SO:0000679
non canonical splice site
non-canonical splice site
sequence
true
A splice site where the donor and acceptor sites differ from the canonical form.
SO:ke
canonical_splice_site
SO:0000675
SO:0000676
SO:0000677
The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.
canonical splice site
sequence
true
SO:ke
The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.
canonical_three_prime_splice_site
SO:0000676
The canonical 3' splice site has the sequence "AG".
canonical 3' splice site
canonical three prime splice site
sequence
SO:ke
The canonical 3' splice site has the sequence "AG".
canonical_five_prime_splice_site
SO:0000677
The canonical 5' splice site has the sequence "GT".
canonical 5' splice site
canonical five prime splice site
sequence
SO:ke
The canonical 5' splice site has the sequence "GT".
non_canonical_three_prime_splice_site
A 3' splice site that does not have the sequence "AG".
SO:0000678
non canonical 3' splice site
non canonical three prime splice site
non-canonical three prime splice site
sequence
A 3' splice site that does not have the sequence "AG".
SO:ke
non_canonical_five_prime_splice_site
A 5' splice site which does not have the sequence "GT".
SO:0000679
non canonical 5' splice site
non canonical five prime splice site
non-canonical five prime splice site
sequence
A 5' splice site which does not have the sequence "GT".
SO:ke
non_canonical_start_codon
A start codon that is not the usual AUG sequence.
SO:0000680
non ATG start codon
non canonical start codon
non-canonical start codon
sequence
A start codon that is not the usual AUG sequence.
SO:ke
aberrant_processed_transcript
A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.
SO:0000681
aberrant processed transcript
sequence
A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons.
SO:ke
splicing_feature
SO:0000682
sequence
true
exonic_splice_enhancer
Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.
SO:0000683
exonic splice enhancer
sequence
Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract
nuclease_sensitive_site
A region of nucleotide sequence targeted by a nuclease enzyme.
SO:0000684
nuclease sensitive site
sequence
A region of nucleotide sequence targeted by a nuclease enzyme.
SO:ma
DNAseI_hypersensitive_site
DHS
DNAseI hypersensitive site
SO:0000685
sequence
translocation_element
A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations.
SO:0000686
sequence
translocation element
A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations.
SO:ma
deletion_junction
SO:0000687
The space between two bases in a sequence which marks the position where a deletion has occurred.
deletion junction
sequence
SO:ke
The space between two bases in a sequence which marks the position where a deletion has occurred.
golden_path
A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
SO:0000688
golden path
sequence
A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.
SO:ls
cDNA_match
A match against cDNA sequence.
SO:0000689
cDNA match
sequence
A match against cDNA sequence.
SO:ke
gene_with_polycistronic_transcript
A gene that encodes a polycistronic transcript.
SO:0000690
gene with polycistronic transcript
sequence
A gene that encodes a polycistronic transcript.
SO:xp
cleaved_initiator_methionine
BS:00067
SO:0000691
The initiator methionine that has been cleaved from a mature polypeptide sequence.
cleaved initiator methionine
init_met
initiator methionine
sequence
EBIBS:GAR
The initiator methionine that has been cleaved from a mature polypeptide sequence.
init_met
uniprot:feature_type
gene_with_dicistronic_transcript
A gene that encodes a dicistronic transcript.
SO:0000692
gene with dicistronic transcript
sequence
A gene that encodes a dicistronic transcript.
SO:xp
gene_with_recoded_mRNA
A gene that encodes an mRNA that is recoded.
SO:0000693
gene with recoded mRNA
sequence
A gene that encodes an mRNA that is recoded.
SO:xp
SNP
SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.
SO:0000694
sequence
single nucleotide polymorphism
SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.
SO:cb
reagent
A sequence used in experiment.
Requested by Lynn Crosby, jan 2006.
SO:0000695
sequence
A sequence used in experiment.
SO:ke
oligo
A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
SO:0000696
http://en.wikipedia.org/wiki/Oligonucleotide
oligonucleotide
sequence
A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.
SO:ma
wiki
http://en.wikipedia.org/wiki/Oligonucleotide
gene_with_stop_codon_read_through
A gene that encodes a transcript with stop codon readthrough.
SO:0000697
gene with stop codon read through
sequence
A gene that encodes a transcript with stop codon readthrough.
SO:xp
gene_with_stop_codon_redefined_as_pyrrolysine
A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.
SO:0000698
gene with stop codon redefined as pyrrolysine
sequence
A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.
SO:xp
junction
A junction is a boundary between regions. A boundary has an extent of zero.
A sequence_feature with an extent of zero.
SO:0000699
boundary
breakpoint
sequence
A sequence_feature with an extent of zero.
SO:ke
remark
A comment about the sequence.
SO:0000700
sequence
A comment about the sequence.
SO:ke
possible_base_call_error
A region of sequence where the validity of the base calling is questionable.
SO:0000701
possible base call error
sequence
A region of sequence where the validity of the base calling is questionable.
SO:ke
possible_assembly_error
A region of sequence where there may have been an error in the assembly.
SO:0000702
possible assembly error
sequence
A region of sequence where there may have been an error in the assembly.
SO:ke
experimental_result_region
A region of sequence implicated in an experimental result.
SO:0000703
experimental result region
sequence
A region of sequence implicated in an experimental result.
SO:ke
gene
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
SO:0000704
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
http://en.wikipedia.org/wiki/Gene
sequence
wiki
http://en.wikipedia.org/wiki/Gene
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
SO:immuno_workshop
tandem_repeat
SO:0000705
Two or more adjacent copies of a region (of length greater than 1).
http://en.wikipedia.org/wiki/Tandem_repeat
http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
sequence
tandem repeat
wiki
http://en.wikipedia.org/wiki/Tandem_repeat
SO:ke
Two or more adjacent copies of a region (of length greater than 1).
trans_splice_acceptor_site
3' trans splice site
SO:0000706
The 3' splice site of the acceptor primary transcript.
This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.
sequence
trans splice acceptor site
SO:ke
The 3' splice site of the acceptor primary transcript.
trans_splice_donor_site
5 prime trans splice site
SL RNA contains a donor site.
SO:0000707
The 5' five prime splice site region of the donor RNA.
sequence
trans splice donor site
trans-splice donor site
SO:ke
The 5' five prime splice site region of the donor RNA.
SL1_acceptor_site
A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.
SL1 acceptor site
SO:0000708
sequence
A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.
SO:nlw
SL2_acceptor_site
A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SL2 acceptor site
SO:0000709
sequence
A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
gene_with_stop_codon_redefined_as_selenocysteine
A gene encoding an mRNA that has the stop codon redefined as selenocysteine.
SO:0000710
gene with stop codon redefined as selenocysteine
sequence
A gene encoding an mRNA that has the stop codon redefined as selenocysteine.
SO:xp
gene_with_mRNA_recoded_by_translational_bypass
A gene with mRNA recoded by translational bypass.
SO:0000711
gene with mRNA recoded by translational bypass
sequence
A gene with mRNA recoded by translational bypass.
SO:xp
gene_with_transcript_with_translational_frameshift
A gene encoding a transcript that has a translational frameshift.
SO:0000712
gene with transcript with translational frameshift
sequence
A gene encoding a transcript that has a translational frameshift.
SO:xp
DNA_motif
A motif that is active in the DNA form of the sequence.
DNA motif
SO:0000713
http://en.wikipedia.org/wiki/DNA_motif
sequence
A motif that is active in the DNA form of the sequence.
SO:ke
wiki
http://en.wikipedia.org/wiki/DNA_motif
nucleotide_motif
A region of nucleotide sequence corresponding to a known motif.
SO:0000714
nucleotide motif
sequence
A region of nucleotide sequence corresponding to a known motif.
SO:ke
RNA_motif
A motif that is active in RNA sequence.
RNA motif
SO:0000715
sequence
A motif that is active in RNA sequence.
SO:ke
dicistronic_mRNA
An mRNA that has the quality dicistronic.
SO:0000716
dicistronic mRNA
dicistronic processed transcript
sequence
An mRNA that has the quality dicistronic.
SO:ke
reading_frame
A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.
SO:0000717
This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
http://en.wikipedia.org/wiki/Reading_frame
reading frame
sequence
wiki
http://en.wikipedia.org/wiki/Reading_frame
A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.
SGD:rb
blocked_reading_frame
A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons.
SO:0000718
Term requested by Rama from SGD.
blocked reading frame
sequence
A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons.
SGD:rb
ultracontig
An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.
SO:0000719
sequence
superscaffold
An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.
FB:WG
foreign_transposable_element
A transposable element that is foreign.
SO:0000720
foreign transposable element
requested by Michael on 19 Nov 2004.
sequence
A transposable element that is foreign.
SO:ke
gene_with_dicistronic_primary_transcript
A gene that encodes a dicistronic primary transcript.
Requested by Michael, 19 nov 2004.
SO:0000721
gene with dicistronic primary transcript
sequence
A gene that encodes a dicistronic primary transcript.
SO:xp
gene_with_dicistronic_mRNA
A gene that encodes a polycistronic mRNA.
Requested by MA nov 19 2004.
SO:0000722
gene with dicistronic mRNA
gene with dicistronic processed transcript
sequence
A gene that encodes a polycistronic mRNA.
SO:xp
iDNA
Genomic sequence removed from the genome, as a normal event, by a process of recombination.
SO:0000723
http://en.wikipedia.org/wiki/IDNA
intervening DNA
sequence
wiki
http://en.wikipedia.org/wiki/IDNA
Genomic sequence removed from the genome, as a normal event, by a process of recombination.
SO:ma
oriT
A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
SO:0000724
http://en.wikipedia.org/wiki/Origin_of_transfer
origin of transfer
sequence
A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
wiki
http://en.wikipedia.org/wiki/Origin_of_transfer
transit_peptide
Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.
BS:00055
SO:0000725
The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).
sequence
signal
transit
transit peptide
transit
uniprot:feature_type
The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
repeat_unit
Added to comply with the feature table. A single repeat.
SO:0000726
The simplest repeated component of a repeat region. A single repeat.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
repeat unit
sequence
SO:ke
The simplest repeated component of a repeat region. A single repeat.
CRM
A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network.
Requested by Stephen Grossmann Dec 2004.
SO:0000727
TF module
cis regulatory module
sequence
transcription factor module
A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network.
PMID:19660565
SO:SG
intein
A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.
Intein-mediated protein splicing occurs after mRNA has been translated into a protein.
SO:0000728
http://en.wikipedia.org/wiki/Intein
protein intron
sequence
A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.
SO:ke
wiki
http://en.wikipedia.org/wiki/Intein
intein_containing
An attribute of protein-coding genes where the initial protein product contains an intein.
SO:0000729
intein containing
sequence
An attribute of protein-coding genes where the initial protein product contains an intein.
SO:ke
gap
A gap in the sequence of known length. The unknown bases are filled in with N's.
SO:0000730
sequence
A gap in the sequence of known length. The unknown bases are filled in with N's.
SO:ke
fragmentary
An attribute to describe a feature that is incomplete.
SO:0000731
Term added because of request by MO people.
fragment
sequence
An attribute to describe a feature that is incomplete.
SO:ke
predicted
An attribute describing an unverified region.
SO:0000732
http://en.wikipedia.org/wiki/Predicted
sequence
An attribute describing an unverified region.
SO:ke
wiki
http://en.wikipedia.org/wiki/Predicted
feature_attribute
An attribute describing a located_sequence_feature.
SO:0000733
feature attribute
sequence
An attribute describing a located_sequence_feature.
SO:ke
exemplar_mRNA
Added for the MO people.
An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.
SO:0000734
exemplar mRNA
sequence
An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.
http://mged.sourceforge.net/ontologies/MGEDontology.php
sequence_location
SO:0000735
sequence
sequence location
organelle_sequence
SO:0000736
organelle sequence
sequence
mitochondrial_sequence
SO:0000737
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
mitochondrial sequence
sequence
nuclear_sequence
SO:0000738
nuclear sequence
sequence
nucleomorphic_sequence
SO:0000739
nucleomorphic sequence
sequence
plastid_sequence
SO:0000740
plastid sequence
sequence
kinetoplast
A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species.
SO:0000741
SO:0000826
http://en.wikipedia.org/wiki/Kinetoplast
kinetoplast_chromosome
sequence
A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species.
PMID:8395055
wiki
http://en.wikipedia.org/wiki/Kinetoplast
maxicircle
A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method.
SO:0000742
SO:0000827
maxicircle_chromosome
sequence
A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method.
PMID:8395055
apicoplast_sequence
SO:0000743
apicoplast sequence
sequence
chromoplast_sequence
SO:0000744
chromoplast sequence
sequence
chloroplast_sequence
SO:0000745
chloroplast sequence
sequence
cyanelle_sequence
SO:0000746
cyanelle sequence
sequence
leucoplast_sequence
SO:0000747
leucoplast sequence
sequence
proplastid_sequence
SO:0000748
proplastid sequence
sequence
plasmid_location
SO:0000749
plasmid location
sequence
amplification_origin
An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.
SO:0000750
amplification origin
sequence
An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.
SO:ma
proviral_location
SO:0000751
proviral location
sequence
gene_group_regulatory_region
SO:0000752
gene group regulatory region
sequence
clone_insert
SO:0000753
The region of sequence that has been inserted and is being propagated by the clone.
clone insert
sequence
SO:ke
The region of sequence that has been inserted and is being propagated by the clone.
lambda_vector
SO:0000754
The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
lambda vector
sequence
ISBN:0-1767-2380-8
The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.
plasmid_vector
SO:0000755
http://en.wikipedia.org/wiki/Plasmid_vector#Vectors
plasmid vector
sequence
wiki
http://en.wikipedia.org/wiki/Plasmid_vector#Vectors
cDNA
DNA synthesized by reverse transcriptase using RNA as a template.
SO:0000756
complementary DNA
http://en.wikipedia.org/wiki/CDNA
sequence
DNA synthesized by reverse transcriptase using RNA as a template.
SO:ma
wiki
http://en.wikipedia.org/wiki/CDNA
single_stranded_cDNA
SO:0000757
sequence
single strand cDNA
single stranded cDNA
single-strand cDNA
double_stranded_cDNA
SO:0000758
double strand cDNA
double stranded cDNA
double-strand cDNA
sequence
plasmid_clone
SO:0000759
sequence
true
YAC_clone
SO:0000760
sequence
true
phagemid_clone
SO:0000761
sequence
true
PAC_clone
P1_clone
SO:0000762
sequence
true
fosmid_clone
SO:0000763
sequence
true
BAC_clone
SO:0000764
sequence
true
cosmid_clone
SO:0000765
sequence
true
pyrrolysyl_tRNA
A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.
SO:0000766
pyrrolysyl tRNA
pyrrolysyl-transfer RNA
pyrrolysyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.
SO:ke
clone_insert_start
SO:0000767
sequence
true
episome
A plasmid that may integrate with a chromosome.
SO:0000768
sequence
A plasmid that may integrate with a chromosome.
SO:ma
tmRNA_coding_piece
Added in response to comment from Kelly Williams from Indiana. Nov 2005.
SO:0000769
The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
sequence
tmRNA coding piece
Indiana:kw
The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
doi:10.1093/nar/gkh795
issn:1362-4962
tmRNA_acceptor_piece
Added in response to Kelly Williams from Indiana. Date: Nov 2005.
SO:0000770
The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
sequence
tmRNA acceptor piece
Indiana:kw
The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.
doi:10.1093/nar/gkh795
QTL
A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
Added in respose to request by Simon Twigger November 14th 2005.
SO:0000771
quantitative trait locus
sequence
A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.
http://rgd.mcw.edu/tu/qtls/
genomic_island
A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.
Genomic islands are transmissible elements characterized by large size (>10kb).
SO:0000772
genomic island
http://en.wikipedia.org/wiki/Genomic_island
sequence
A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.
Phigo:at
SO:ke
wiki
http://en.wikipedia.org/wiki/Genomic_island
pathogenic_island
Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.
Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
SO:0000773
pathogenic island
sequence
Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.
SO:ke
metabolic_island
A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.
Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands.
SO:0000774
metabolic island
sequence
A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.
SO:ke
adaptive_island
An adaptive island is a genomic island that provides an adaptive advantage to the host.
SO:0000775
The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
adaptive island
sequence
An adaptive island is a genomic island that provides an adaptive advantage to the host.
SO:ke
symbiosis_island
A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.
Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149.
SO:0000776
sequence
symbiosis island
A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.
SO:ke
pseudogenic_rRNA
A non functional descendant of an rRNA.
Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
SO:0000777
pseudogenic rRNA
sequence
A non functional descendant of an rRNA.
SO:ke
pseudogenic_tRNA
A non functional descendent of a tRNA.
Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
SO:0000778
pseudogenic tRNA
sequence
A non functional descendent of a tRNA.
SO:ke
engineered_episome
An episome that is engineered.
Requested by Lynn Crosby Jan 2006.
SO:0000779
engineered episome
sequence
An episome that is engineered.
SO:xp
transposable_element_attribute
Added by KE Jan 2006 to capture the kinds of attributes of TEs
SO:0000780
sequence
true
transgenic
Attribute describing sequence that has been integrated with foreign sequence.
SO:0000781
sequence
Attribute describing sequence that has been integrated with foreign sequence.
SO:ke
natural
An attribute describing a feature that occurs in nature.
SO:0000782
sequence
An attribute describing a feature that occurs in nature.
SO:ke
engineered
An attribute to describe a region that was modified in vitro.
SO:0000783
sequence
An attribute to describe a region that was modified in vitro.
SO:ke
foreign
An attribute to describe a region from another species.
SO:0000784
sequence
An attribute to describe a region from another species.
SO:ke
cloned_region
Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.
SO:0000785
cloned region
cloned segment
sequence
reagent_attribute
Added jan 2006 by KE.
SO:0000786
reagent attribute
sequence
true
clone_attribute
SO:0000787
sequence
true
cloned
SO:0000788
sequence
true
validated
An attribute to describe a feature that has been proven.
SO:0000789
sequence
An attribute to describe a feature that has been proven.
SO:ke
invalidated
An attribute describing a feature that is invalidated.
SO:0000790
sequence
An attribute describing a feature that is invalidated.
SO:ke
cloned_genomic
SO:0000791
sequence
true
cloned_cDNA
SO:0000792
sequence
true
engineered_DNA
SO:0000793
sequence
true
engineered_rescue_region
A rescue region that is engineered.
SO:0000794
engineered rescue fragment
engineered rescue region
engineered rescue segment
sequence
A rescue region that is engineered.
SO:xp
rescue_mini_gene
A mini_gene that rescues.
SO:0000795
rescue mini gene
rescue mini-gene
sequence
A mini_gene that rescues.
SO:xp
transgenic_transposable_element
Modified as requested by Lynn - FB. May 2007.
SO:0000796
TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.
sequence
transgenic transposable element
FB:mc
TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.
natural_transposable_element
SO:0000797
TE that exists (or existed) in nature.
natural transposable element
sequence
FB:mc
TE that exists (or existed) in nature.
engineered_transposable_element
SO:0000798
TE that has been modified by manipulations in vitro.
engineered transposable element
sequence
FB:mc
TE that has been modified by manipulations in vitro.
engineered_foreign_transposable_element
A transposable_element that is engineered and foreign.
SO:0000799
engineered foreign transposable element
sequence
A transposable_element that is engineered and foreign.
FB:mc
assortment_derived_duplication
A multi-chromosome duplication aberration generated by reassortment of other aberration components.
SO:0000800
assortment derived duplication
sequence
A multi-chromosome duplication aberration generated by reassortment of other aberration components.
FB:gm
assortment_derived_deficiency_plus_duplication
A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.
SO:0000801
assortment derived deficiency plus duplication
sequence
A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.
FB:gm
assortment_derived_deficiency
A multi-chromosome deficiency aberration generated by reassortment of other aberration components.
SO:0000802
assortment-derived deficiency
sequence
A multi-chromosome deficiency aberration generated by reassortment of other aberration components.
FB:gm
assortment_derived_aneuploid
A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.
SO:0000803
assortment derived aneuploid
sequence
A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.
FB:gm
engineered_region
A region that is engineered.
SO:0000804
construct
engineered region
engineered sequence
sequence
A region that is engineered.
SO:xp
engineered_foreign_region
A region that is engineered and foreign.
SO:0000805
engineered foreign region
sequence
A region that is engineered and foreign.
SO:xp
fusion
SO:0000806
sequence
engineered_tag
A tag that is engineered.
SO:0000807
engineered tag
sequence
A tag that is engineered.
SO:xp
validated_cDNA_clone
A cDNA clone that has been validated.
SO:0000808
sequence
validated cDNA clone
A cDNA clone that has been validated.
SO:xp
invalidated_cDNA_clone
A cDNA clone that is invalid.
SO:0000809
invalidated cDNA clone
sequence
A cDNA clone that is invalid.
SO:xp
chimeric_cDNA_clone
A cDNA clone invalidated because it is chimeric.
SO:0000810
chimeric cDNA clone
sequence
A cDNA clone invalidated because it is chimeric.
SO:xp
genomically_contaminated_cDNA_clone
A cDNA clone invalidated by genomic contamination.
SO:0000811
genomically contaminated cDNA clone
sequence
A cDNA clone invalidated by genomic contamination.
SO:xp
polyA_primed_cDNA_clone
A cDNA clone invalidated by polyA priming.
SO:0000812
polyA primed cDNA clone
sequence
A cDNA clone invalidated by polyA priming.
SO:xp
partially_processed_cDNA_clone
A cDNA invalidated clone by partial processing.
SO:0000813
partially processed cDNA clone
sequence
A cDNA invalidated clone by partial processing.
SO:xp
rescue
An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.
SO:0000814
sequence
An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.
SO:ke
mini_gene
By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA.
SO:0000815
mini gene
sequence
By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA.
PMID:15992143
rescue_gene
A gene that rescues.
SO:0000816
rescue gene
sequence
A gene that rescues.
SO:xp
wild_type
An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.
SO:0000817
http://en.wikipedia.org/wiki/Wild_type
loinc:LA9658-1
sequence
wild type
wiki
http://en.wikipedia.org/wiki/Wild_type
wild type
loinc:LA9658-1
An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.
SO:ke
wild_type_rescue_gene
A gene that rescues.
SO:0000818
sequence
wild type rescue gene
A gene that rescues.
SO:xp
mitochondrial_chromosome
A chromosome originating in a mitochondria.
SO:0000819
mitochondrial chromosome
sequence
A chromosome originating in a mitochondria.
SO:xp
chloroplast_chromosome
A chromosome originating in a chloroplast.
SO:0000820
chloroplast chromosome
sequence
A chromosome originating in a chloroplast.
SO:xp
chromoplast_chromosome
A chromosome originating in a chromoplast.
SO:0000821
chromoplast chromosome
sequence
A chromosome originating in a chromoplast.
SO:xp
cyanelle_chromosome
A chromosome originating in a cyanelle.
SO:0000822
cyanelle chromosome
sequence
A chromosome originating in a cyanelle.
SO:xp
leucoplast_chromosome
A chromosome with origin in a leucoplast.
SO:0000823
leucoplast chromosome
sequence
A chromosome with origin in a leucoplast.
SO:xp
macronuclear_chromosome
A chromosome originating in a macronucleus.
SO:0000824
macronuclear chromosome
sequence
A chromosome originating in a macronucleus.
SO:xp
micronuclear_chromosome
A chromosome originating in a micronucleus.
SO:0000825
micronuclear chromosome
sequence
A chromosome originating in a micronucleus.
SO:xp
nuclear_chromosome
A chromosome originating in a nucleus.
SO:0000828
nuclear chromosome
sequence
A chromosome originating in a nucleus.
SO:xp
nucleomorphic_chromosome
A chromosome originating in a nucleomorph.
SO:0000829
nucleomorphic chromosome
sequence
A chromosome originating in a nucleomorph.
SO:xp
chromosome_part
A region of a chromosome.
SO:0000830
This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
chromosome part
sequence
A region of a chromosome.
SO:ke
gene_member_region
A manufactured term used to allow the parts of a gene to have an is_a path to the root.
A region of a gene.
SO:0000831
gene member region
sequence
A region of a gene.
SO:ke
promoter_region
A region of sequence which is part of a promoter.
SO:0000832
This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.
sequence
true
A region of sequence which is part of a promoter.
SO:ke
transcript_region
A region of a transcript.
SO:0000833
This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.
sequence
transcript region
A region of a transcript.
SO:ke
mature_transcript_region
A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
A region of a mature transcript.
SO:0000834
mature transcript region
sequence
A region of a mature transcript.
SO:ke
primary_transcript_region
A part of a primary transcript.
SO:0000835
This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.
primary transcript region
sequence
A part of a primary transcript.
SO:ke
mRNA_region
A region of an mRNA.
SO:0000836
This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.
mRNA region
sequence
A region of an mRNA.
SO:cb
UTR_region
A region of UTR.
A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.
SO:0000837
UTR region
sequence
A region of UTR.
SO:ke
rRNA_primary_transcript_region
A region of an rRNA primary transcript.
SO:0000838
To allow transcribed_spacer_region to have a path to the root.
rRNA primary transcript region
sequence
A region of an rRNA primary transcript.
SO:ke
polypeptide_region
Added to allow the polypeptide regions to have is_a paths back to the root.
BS:00124
BS:00331
Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
SO:0000839
positional
positional polypeptide feature
region
region or site annotation
sequence
site
Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
SO:GAR
SO:ke
region
uniprot:feature_type
site
uniprot:feature_type
repeat_component
A manufactured to group the parts of repeats, to give them an is_a path back to the root.
A region of a repeated sequence.
SO:0000840
repeat component
sequence
A region of a repeated sequence.
SO:ke
spliceosomal_intron_region
A region within an intron.
A terms added to allow the parts of introns to have is_a paths to the root.
SO:0000841
sequence
spliceosomal intron region
A region within an intron.
SO:ke
gene_component_region
SO:0000842
gene component region
sequence
bacterial_RNApol_promoter_region
A region which is part of a bacterial RNA polymerase promoter.
SO:0000843
This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.
sequence
true
A region which is part of a bacterial RNA polymerase promoter.
SO:ke
RNApol_II_promoter_region
A region of sequence which is a promoter for RNA polymerase II.
SO:0000844
This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.
sequence
true
A region of sequence which is a promoter for RNA polymerase II.
SO:ke
RNApol_III_promoter_type_1_region
A region of sequence which is a promoter for RNA polymerase III type 1.
SO:0000845
This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root.
sequence
true
A region of sequence which is a promoter for RNA polymerase III type 1.
SO:ke
RNApol_III_promoter_type_2_region
A region of sequence which is a promoter for RNA polymerase III type 2.
SO:0000846
This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root.
sequence
true
A region of sequence which is a promoter for RNA polymerase III type 2.
SO:ke
tmRNA_region
A region of a tmRNA.
SO:0000847
This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root.
sequence
tmRNA region
A region of a tmRNA.
SO:cb
LTR_component
LTR component
SO:0000848
long term repeat component
sequence
three_prime_LTR_component
3' long terminal repeat component
SO:0000849
sequence
three prime LTR component
five_prime_LTR_component
5' long term repeat component
SO:0000850
five prime LTR component
sequence
CDS_region
A region of a CDS.
CDS region
SO:0000851
sequence
A region of a CDS.
SO:cb
exon_region
A region of an exon.
SO:0000852
exon region
sequence
A region of an exon.
RSC:cb
homologous_region
A region that is homologous to another region.
SO:0000853
homolog
homologous region
homologue
http://en.wikipedia.org/wiki/Homology_(biology)
sequence
A region that is homologous to another region.
SO:ke
wiki
http://en.wikipedia.org/wiki/Homology_(biology)
paralogous_region
A homologous_region that is paralogous to another region.
A term to be used in conjunction with the paralogous_to relationship.
SO:0000854
http://en.wikipedia.org/wiki/Paralog#Paralogy
paralog
paralogous region
paralogue
sequence
A homologous_region that is paralogous to another region.
SO:ke
wiki
http://en.wikipedia.org/wiki/Paralog#Paralogy
orthologous_region
A homologous_region that is orthologous to another region.
SO:0000855
This term should be used in conjunction with the similarity relationships defined in SO.
http://en.wikipedia.org/wiki/Ortholog#Orthology
ortholog
orthologous region
orthologue
sequence
A homologous_region that is orthologous to another region.
SO:ke
wiki
http://en.wikipedia.org/wiki/Ortholog#Orthology
conserved
SO:0000856
sequence
homologous
SO:0000857
Similarity due to common ancestry.
sequence
SO:ke
Similarity due to common ancestry.
orthologous
An attribute describing a kind of homology where divergence occurred after a speciation event.
SO:0000858
sequence
An attribute describing a kind of homology where divergence occurred after a speciation event.
SO:ke
paralogous
An attribute describing a kind of homology where divergence occurred after a duplication event.
SO:0000859
sequence
An attribute describing a kind of homology where divergence occurred after a duplication event.
SO:ke
syntenic
Attribute describing sequence regions occurring in same order on chromosome of different species.
SO:0000860
http://en.wikipedia.org/wiki/Syntenic
sequence
Attribute describing sequence regions occurring in same order on chromosome of different species.
SO:ke
wiki
http://en.wikipedia.org/wiki/Syntenic
capped_primary_transcript
A primary transcript that is capped.
SO:0000861
capped primary transcript
sequence
A primary transcript that is capped.
SO:xp
capped_mRNA
An mRNA that is capped.
SO:0000862
capped mRNA
sequence
An mRNA that is capped.
SO:xp
mRNA_attribute
An attribute describing an mRNA feature.
SO:0000863
mRNA attribute
sequence
An attribute describing an mRNA feature.
SO:ke
exemplar
An attribute describing a sequence is representative of a class of similar sequences.
SO:0000864
sequence
An attribute describing a sequence is representative of a class of similar sequences.
SO:ke
frameshift
An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.
SO:0000865
http://en.wikipedia.org/wiki/Frameshift
sequence
An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.
SO:ke
wiki
http://en.wikipedia.org/wiki/Frameshift
minus_1_frameshift
A frameshift caused by deleting one base.
SO:0000866
minus 1 frameshift
sequence
A frameshift caused by deleting one base.
SO:ke
minus_2_frameshift
A frameshift caused by deleting two bases.
SO:0000867
minus 2 frameshift
sequence
A frameshift caused by deleting two bases.
SO:ke
plus_1_frameshift
A frameshift caused by inserting one base.
SO:0000868
plus 1 frameshift
sequence
A frameshift caused by inserting one base.
SO:ke
plus_2_framshift
A frameshift caused by inserting two bases.
SO:0000869
plus 2 framshift
sequence
A frameshift caused by inserting two bases.
SO:ke
trans_spliced
An attribute describing transcript sequence that is created by splicing exons from diferent genes.
SO:0000870
sequence
trans-spliced
An attribute describing transcript sequence that is created by splicing exons from diferent genes.
SO:ke
polyadenylated_mRNA
An mRNA that is polyadenylated.
SO:0000871
polyadenylated mRNA
sequence
An mRNA that is polyadenylated.
SO:xp
trans_spliced_mRNA
An mRNA that is trans-spliced.
SO:0000872
sequence
trans-spliced mRNA
An mRNA that is trans-spliced.
SO:xp
edited_transcript
A transcript that is edited.
SO:0000873
edited transcript
sequence
A transcript that is edited.
SO:ke
edited_transcript_by_A_to_I_substitution
A transcript that has been edited by A to I substitution.
SO:0000874
edited transcript by A to I substitution
sequence
A transcript that has been edited by A to I substitution.
SO:ke
bound_by_protein
An attribute describing a sequence that is bound by a protein.
SO:0000875
bound by protein
sequence
An attribute describing a sequence that is bound by a protein.
SO:ke
bound_by_nucleic_acid
An attribute describing a sequence that is bound by a nucleic acid.
SO:0000876
bound by nucleic acid
sequence
An attribute describing a sequence that is bound by a nucleic acid.
SO:ke
alternatively_spliced
An attribute describing a situation where a gene may encode for more than 1 transcript.
SO:0000877
alternatively spliced
sequence
An attribute describing a situation where a gene may encode for more than 1 transcript.
SO:ke
monocistronic
An attribute describing a sequence that contains the code for one gene product.
SO:0000878
sequence
An attribute describing a sequence that contains the code for one gene product.
SO:ke
dicistronic
An attribute describing a sequence that contains the code for two gene products.
SO:0000879
sequence
An attribute describing a sequence that contains the code for two gene products.
SO:ke
polycistronic
An attribute describing a sequence that contains the code for more than one gene product.
SO:0000880
sequence
An attribute describing a sequence that contains the code for more than one gene product.
SO:ke
recoded
An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations.
SO:0000881
sequence
An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations.
SO:ke
codon_redefined
An attribute describing the alteration of codon meaning.
SO:0000882
codon redefined
sequence
An attribute describing the alteration of codon meaning.
SO:ke
stop_codon_read_through
A stop codon redefined to be a new amino acid.
SO:0000883
sequence
stop codon read through
stop codon readthrough
A stop codon redefined to be a new amino acid.
SO:ke
stop_codon_redefined_as_pyrrolysine
A stop codon redefined to be the new amino acid, pyrrolysine.
SO:0000884
sequence
stop codon redefined as pyrrolysine
A stop codon redefined to be the new amino acid, pyrrolysine.
SO:ke
stop_codon_redefined_as_selenocysteine
A stop codon redefined to be the new amino acid, selenocysteine.
SO:0000885
sequence
stop codon redefined as selenocysteine
A stop codon redefined to be the new amino acid, selenocysteine.
SO:ke
recoded_by_translational_bypass
Recoded mRNA where a block of nucleotides is not translated.
SO:0000886
recoded by translational bypass
sequence
Recoded mRNA where a block of nucleotides is not translated.
SO:ke
translationally_frameshifted
Recoding by frameshifting a particular site.
SO:0000887
sequence
translationally frameshifted
Recoding by frameshifting a particular site.
SO:ke
maternally_imprinted_gene
A gene that is maternally_imprinted.
SO:0000888
maternally imprinted gene
sequence
A gene that is maternally_imprinted.
SO:xp
paternally_imprinted_gene
A gene that is paternally imprinted.
SO:0000889
paternally imprinted gene
sequence
A gene that is paternally imprinted.
SO:xp
post_translationally_regulated_gene
A gene that is post translationally regulated.
SO:0000890
post translationally regulated gene
sequence
A gene that is post translationally regulated.
SO:xp
negatively_autoregulated_gene
A gene that is negatively autoreguated.
SO:0000891
negatively autoregulated gene
sequence
A gene that is negatively autoreguated.
SO:xp
positively_autoregulated_gene
A gene that is positively autoregulated.
SO:0000892
positively autoregulated gene
sequence
A gene that is positively autoregulated.
SO:xp
silenced
An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level.
SO:0000893
http://en.wikipedia.org/wiki/Silenced
sequence
wiki
http://en.wikipedia.org/wiki/Silenced
An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level.
SO:ke
silenced_by_DNA_modification
An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription.
SO:0000894
sequence
silenced by DNA modification
An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription.
SO:ke
silenced_by_DNA_methylation
An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription.
SO:0000895
sequence
silenced by DNA methylation
An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription.
SO:ke
translationally_regulated_gene
A gene that is translationally regulated.
SO:0000896
sequence
translationally regulated gene
A gene that is translationally regulated.
SO:xp
allelically_excluded_gene
A gene that is allelically_excluded.
SO:0000897
allelically excluded gene
sequence
A gene that is allelically_excluded.
SO:xp
epigenetically_modified_gene
A gene that is epigenetically modified.
SO:0000898
epigenetically modified gene
sequence
A gene that is epigenetically modified.
SO:ke
nuclear_mitochondrial
An attribute describing a nuclear pseudogene of a mitochndrial gene.
SO:0000899
nuclear mitochondrial
sequence
true
An attribute describing a nuclear pseudogene of a mitochndrial gene.
SO:ke
processed
An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail.
SO:0000900
sequence
true
An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail.
SO:ke
unequally_crossed_over
An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.
SO:0000901
sequence
true
unequally crossed over
An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.
SO:ke
transgene
A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.
SO:0000902
http://en.wikipedia.org/wiki/Transgene
sequence
wiki
http://en.wikipedia.org/wiki/Transgene
A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.
SO:xp
endogenous_retroviral_sequence
SO:0000903
endogenous retroviral sequence
sequence
rearranged_at_DNA_level
An attribute to describe the sequence of a feature, where the DNA is rearranged.
SO:0000904
rearranged at DNA level
sequence
An attribute to describe the sequence of a feature, where the DNA is rearranged.
SO:ke
status
An attribute describing the status of a feature, based on the available evidence.
SO:0000905
This term is the hypernym of attributes and should not be annotated to.
sequence
An attribute describing the status of a feature, based on the available evidence.
SO:ke
independently_known
Attribute to describe a feature that is independently known - not predicted.
SO:0000906
independently known
sequence
Attribute to describe a feature that is independently known - not predicted.
SO:ke
supported_by_sequence_similarity
An attribute to describe a feature that has been predicted using sequence similarity techniques.
SO:0000907
sequence
supported by sequence similarity
An attribute to describe a feature that has been predicted using sequence similarity techniques.
SO:ke
supported_by_domain_match
An attribute to describe a feature that has been predicted using sequence similarity of a known domain.
SO:0000908
sequence
supported by domain match
An attribute to describe a feature that has been predicted using sequence similarity of a known domain.
SO:ke
supported_by_EST_or_cDNA
An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data.
SO:0000909
sequence
supported by EST or cDNA
An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data.
SO:ke
orphan
SO:0000910
sequence
predicted_by_ab_initio_computation
An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity.
SO:0000911
predicted by ab initio computation
sequence
An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity.
SO:ke
asx_turn
A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
BS:00203
SO:0000912
asx turn
sequence
A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
http://www.ebi.ac.uk/msd-srv/msdmotif/
cloned_cDNA_insert
A clone insert made from cDNA.
SO:0000913
cloned cDNA insert
sequence
A clone insert made from cDNA.
SO:xp
cloned_genomic_insert
A clone insert made from genomic DNA.
SO:0000914
cloned genomic insert
sequence
A clone insert made from genomic DNA.
SO:xp
engineered_insert
A clone insert that is engineered.
SO:0000915
engineered insert
sequence
A clone insert that is engineered.
SO:xp
edit_operation
SO:0000916
edit operation
sequence
true
insert_U
An edit to insert a U.
SO:0000917
The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
insert U
sequence
true
An edit to insert a U.
SO:ke
delete_U
An edit to delete a uridine.
SO:0000918
The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
delete U
sequence
true
An edit to delete a uridine.
SO:ke
substitute_A_to_I
An edit to substitute an I for an A.
SO:0000919
sequence
substitute A to I
true
An edit to substitute an I for an A.
SO:ke
insert_C
An edit to insert a cytidine.
SO:0000920
insert C
sequence
true
An edit to insert a cytidine.
SO:ke
insert_dinucleotide
An edit to insert a dinucleotide.
SO:0000921
insert dinucleotide
sequence
true
An edit to insert a dinucleotide.
SO:ke
substitute_C_to_U
An edit to substitute an U for a C.
SO:0000922
sequence
substitute C to U
true
An edit to substitute an U for a C.
SO:ke
insert_G
An edit to insert a G.
SO:0000923
insert G
sequence
true
An edit to insert a G.
SO:ke
insert_GC
An edit to insert a GC dinucleotide.
SO:0000924
The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
insert GC
sequence
true
An edit to insert a GC dinucleotide.
SO:ke
insert_GU
An edit to insert a GU dinucleotide.
SO:0000925
The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
insert GU
sequence
true
An edit to insert a GU dinucleotide.
SO:ke
insert_CU
An edit to insert a CU dinucleotide.
SO:0000926
The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
insert CU
sequence
true
An edit to insert a CU dinucleotide.
SO:ke
insert_AU
An edit to insert a AU dinucleotide.
SO:0000927
The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
insert AU
sequence
true
An edit to insert a AU dinucleotide.
SO:ke
insert_AA
An edit to insert a AA dinucleotide.
SO:0000928
The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
insert AA
sequence
true
An edit to insert a AA dinucleotide.
SO:ke
edited_mRNA
An mRNA that is edited.
SO:0000929
edited mRNA
sequence
An mRNA that is edited.
SO:xp
guide_RNA_region
A region of guide RNA.
SO:0000930
guide RNA region
sequence
A region of guide RNA.
SO:ma
anchor_region
A region of a guide_RNA that base-pairs to a target mRNA.
SO:0000931
anchor region
sequence
A region of a guide_RNA that base-pairs to a target mRNA.
SO:jk
pre_edited_mRNA
SO:0000932
pre-edited mRNA
sequence
intermediate
An attribute to describe a feature between stages of processing.
SO:0000933
sequence
An attribute to describe a feature between stages of processing.
SO:ke
miRNA_target_site
A miRNA target site is a binding site where the molecule is a micro RNA.
SO:0000934
miRNA target site
sequence
A miRNA target site is a binding site where the molecule is a micro RNA.
FB:cds
edited_CDS
A CDS that is edited.
SO:0000935
edited CDS
sequence
A CDS that is edited.
SO:xp
vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
SO:0000936
sequence
vertebrate immunoglobulin T cell receptor rearranged segment
vertebrate_immune_system_feature
SO:0000937
sequence
true
vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
SO:0000938
sequence
vertebrate immunoglobulin T cell receptor rearranged gene cluster
vertebrate_immune_system_gene_recombination_signal_feature
SO:0000939
sequence
vertebrate immune system gene recombination signal feature
recombinationally_rearranged
SO:0000940
recombinationally rearranged
sequence
recombinationally_rearranged_vertebrate_immune_system_gene
A recombinationally rearranged gene of the vertebrate immune system.
SO:0000941
recombinationally rearranged vertebrate immune system gene
sequence
A recombinationally rearranged gene of the vertebrate immune system.
SO:xp
attP_site
An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome.
SO:0000942
attP site
sequence
An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome.
SO:as
attB_site
An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.
SO:0000943
attB site
sequence
An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.
SO:as
attL_site
A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site.
SO:0000944
attBP'
attL site
sequence
A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site.
SO:as
attR_site
A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site.
SO:0000945
attPB'
attR site
sequence
A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site.
SO:as
integration_excision_site
A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site.
SO:0000946
attachment site
integration excision site
sequence
A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site.
SO:as
resolution_site
A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles.
SO:0000947
res site
resolution site
sequence
A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles.
SO:as
inversion_site
A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites.
A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
SO:0000948
inversion site
sequence
A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites.
SO:ma
dif_site
A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase.
SO:0000949
dif site
sequence
A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase.
SO:as
attC_site
An attC site is a sequence required for the integration of a DNA of an integron.
SO:0000950
attC site
sequence
An attC site is a sequence required for the integration of a DNA of an integron.
SO:as
eukaryotic_terminator
SO:0000951
eukaryotic terminator
sequence
oriV
An origin of vegetative replication in plasmids and phages.
SO:0000952
origin of vegetative replication
sequence
An origin of vegetative replication in plasmids and phages.
SO:as
oriC
An origin of bacterial chromosome replication.
SO:0000953
origin of bacterial chromosome replication
sequence
An origin of bacterial chromosome replication.
SO:as
DNA_chromosome
DNA chromosome
SO:0000954
Structural unit composed of a self-replicating, DNA molecule.
sequence
SO:ma
Structural unit composed of a self-replicating, DNA molecule.
double_stranded_DNA_chromosome
SO:0000955
Structural unit composed of a self-replicating, double-stranded DNA molecule.
double stranded DNA chromosome
sequence
SO:ma
Structural unit composed of a self-replicating, double-stranded DNA molecule.
single_stranded_DNA_chromosome
SO:0000956
Structural unit composed of a self-replicating, single-stranded DNA molecule.
sequence
single stranded DNA chromosome
SO:ma
Structural unit composed of a self-replicating, single-stranded DNA molecule.
linear_double_stranded_DNA_chromosome
SO:0000957
Structural unit composed of a self-replicating, double-stranded, linear DNA molecule.
linear double stranded DNA chromosome
sequence
SO:ma
Structural unit composed of a self-replicating, double-stranded, linear DNA molecule.
circular_double_stranded_DNA_chromosome
SO:0000958
Structural unit composed of a self-replicating, double-stranded, circular DNA molecule.
circular double stranded DNA chromosome
sequence
SO:ma
Structural unit composed of a self-replicating, double-stranded, circular DNA molecule.
linear_single_stranded_DNA_chromosome
SO:0000959
Structural unit composed of a self-replicating, single-stranded, linear DNA molecule.
linear single stranded DNA chromosome
sequence
SO:ma
Structural unit composed of a self-replicating, single-stranded, linear DNA molecule.
circular_single_stranded_DNA_chromosome
SO:0000960
Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
circular single stranded DNA chromosome
sequence
SO:ma
Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
RNA_chromosome
RNA chromosome
SO:0000961
Structural unit composed of a self-replicating, RNA molecule.
sequence
SO:ma
Structural unit composed of a self-replicating, RNA molecule.
single_stranded_RNA_chromosome
SO:0000962
Structural unit composed of a self-replicating, single-stranded RNA molecule.
sequence
single stranded RNA chromosome
SO:ma
Structural unit composed of a self-replicating, single-stranded RNA molecule.
linear_single_stranded_RNA_chromosome
SO:0000963
Structural unit composed of a self-replicating, single-stranded, linear RNA molecule.
linear single stranded RNA chromosome
sequence
SO:ma
Structural unit composed of a self-replicating, single-stranded, linear RNA molecule.
linear_double_stranded_RNA_chromosome
SO:0000964
Structural unit composed of a self-replicating, double-stranded, linear RNA molecule.
linear double stranded RNA chromosome
sequence
SO:ma
Structural unit composed of a self-replicating, double-stranded, linear RNA molecule.
double_stranded_RNA_chromosome
SO:0000965
Structural unit composed of a self-replicating, double-stranded RNA molecule.
double stranded RNA chromosome
sequence
SO:ma
Structural unit composed of a self-replicating, double-stranded RNA molecule.
circular_single_stranded_RNA_chromosome
SO:0000966
Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
circular single stranded RNA chromosome
sequence
SO:ma
Structural unit composed of a self-replicating, single-stranded, circular DNA molecule.
circular_double_stranded_RNA_chromosome
SO:0000967
Structural unit composed of a self-replicating, double-stranded, circular RNA molecule.
circular double stranded RNA chromosome
sequence
SO:ma
Structural unit composed of a self-replicating, double-stranded, circular RNA molecule.
sequence_replication_mode
SO:0000968
This has been obsoleted as it represents a process. replaced_by: GO:0034961.
sequence
sequence replication mode
true
rolling_circle
SO:0000969
This has been obsoleted as it represents a process. replaced_by: GO:0070581.
http://en.wikipedia.org/wiki/Rolling_circle
rolling circle
sequence
true
wiki
http://en.wikipedia.org/wiki/Rolling_circle
theta_replication
SO:0000970
This has been obsoleted as it represents a process. replaced_by: GO:0070582
sequence
theta replication
true
DNA_replication_mode
DNA replication mode
SO:0000971
This has been obsoleted as it represents a process. replaced_by: GO:0006260.
sequence
true
RNA_replication_mode
RNA replication mode
SO:0000972
This has been obsoleted as it represents a process. replaced_by: GO:0034961.
sequence
true
insertion_sequence
A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats.
IS
SO:0000973
http://en.wikipedia.org/wiki/Insertion_sequence
insertion sequence
sequence
A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats.
SO:as
wiki
http://en.wikipedia.org/wiki/Insertion_sequence
minicircle_gene
SO:0000975
minicircle gene
sequence
cryptic
A feature_attribute describing a feature that is not manifest under normal conditions.
SO:0000976
sequence
A feature_attribute describing a feature that is not manifest under normal conditions.
SO:ke
anchor_binding_site
Part of an edited transcript only.
SO:0000977
anchor binding site
sequence
template_region
A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.
SO:0000978
information region
sequence
template region
A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA.
SO:jk
gRNA_encoding
A non-protein_coding gene that encodes a guide_RNA.
SO:0000979
gRNA encoding
sequence
A non-protein_coding gene that encodes a guide_RNA.
SO:ma
minicircle
A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs.
SO:0000974
SO:0000980
http://en.wikipedia.org/wiki/Minicircle
minicircle_chromosome
sequence
wiki
http://en.wikipedia.org/wiki/Minicircle
A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs.
PMID:8395055
rho_dependent_bacterial_terminator
SO:0000981
rho dependent bacterial terminator
sequence
rho_independent_bacterial_terminator
SO:0000982
rho independent bacterial terminator
sequence
strand_attribute
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
SO:0000983
sequence
strand attribute
single
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
SO:0000984
sequence
double
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
SO:0000985
sequence
topology_attribute
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
SO:0000986
sequence
topology attribute
linear
A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
SO:0000987
sequence
two-ended
A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.
SO:cb
circular
A quality of a nucleotide polymer that has no terminal nucleotide residues.
Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
SO:0000988
sequence
zero-ended
A quality of a nucleotide polymer that has no terminal nucleotide residues.
SO:cb
class_II_RNA
SO:0000989
Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
class II RNA
sequence
PMID:15333696
Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
class_I_RNA
Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.
SO:0000990
Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
class I RNA
sequence
PMID:15333696
Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.
genomic_DNA
SO:0000991
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
genomic DNA
sequence
BAC_cloned_genomic_insert
BAC cloned genomic insert
Requested by Andy Schroder - Flybase Harvard, Nov 2006.
SO:0000992
sequence
consensus
SO:0000993
Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA.
sequence
consensus_region
DO not obsolete without considering MGED mapping.
SO:0000994
consensus region
sequence
consensus_mRNA
DO not obsolete without considering MGED mapping.
SO:0000995
consensus mRNA
sequence
predicted_gene
SO:0000996
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
predicted gene
sequence
gene_fragment
SO:0000997
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
gene fragment
sequence
recursive_splice_site
A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons.
SO:0000998
recursive splice site
sequence
A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons.
http://www.genetics.org/cgi/content/full/170/2/661
BAC_end
A region of sequence from the end of a BAC clone that may provide a highly specific marker.
BAC end
BAC end sequence
BES
Requested by Keith Boroevich December, 2006.
SO:0000999
sequence
A region of sequence from the end of a BAC clone that may provide a highly specific marker.
SO:ke
rRNA_16S
16S SSU RNA
16S rRNA
16S ribosomal RNA
A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.
SO:0001000
http://en.wikipedia.org/wiki/16S_ribosomal_RNA
rRNA 16S
sequence
wiki
http://en.wikipedia.org/wiki/16S_ribosomal_RNA
A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.
SO:ke
rRNA_23S
23S LSU rRNA
23S rRNA
23S ribosomal RNA
A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.
SO:0001001
rRNA 23S
sequence
A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.
SO:ke
rRNA_25S
25S LSU rRNA
25S rRNA
25S ribosomal RNA
A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.
SO:0001002
rRNA 25S
sequence
A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.
RSC:cb
solo_LTR
A recombination product between the 2 LTR of the same element.
Requested by Hadi Quesneville January 2007.
SO:0001003
sequence
solo LTR
A recombination product between the 2 LTR of the same element.
SO:ke
low_complexity
SO:0001004
low complexity
sequence
low_complexity_region
SO:0001005
low complexity region
sequence
prophage
A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island".
SO:0001006
http://en.wikipedia.org/wiki/Prophage
sequence
wiki
http://en.wikipedia.org/wiki/Prophage
A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island".
GOC:jl
cryptic_prophage
A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes.
SO:0001007
This is not cryptic in the same sense as a cryptic gene or cryptic splice site.
cryptic prophage
http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w
sequence
A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes.
GOC:jl
tetraloop
A base-paired stem with loop of 4 non-hydrogen bonded nucleotides.
SO:0001008
http://en.wikipedia.org/wiki/Tetraloop
sequence
A base-paired stem with loop of 4 non-hydrogen bonded nucleotides.
SO:ke
wiki
http://en.wikipedia.org/wiki/Tetraloop
DNA_constraint_sequence
A double-stranded DNA used to control macromolecular structure and function.
DNA constraint
DNA constraint sequence
SO:0001009
sequence
A double-stranded DNA used to control macromolecular structure and function.
http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au]&dispmax=50
i_motif
A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.
SO:0001010
i motif
sequence
short intercalated motif
A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.
PMID:9753739
PNA_oligo
PNA oligo
Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
SO:0001011
http://en.wikipedia.org/wiki/Peptide_nucleic_acid
peptide nucleic acid
sequence
Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
SO:ke
wiki
http://en.wikipedia.org/wiki/Peptide_nucleic_acid
DNAzyme
A DNA sequence with catalytic activity.
Added by request from Colin Batchelor.
DNA enzyme
SO:0001012
catalytic DNA
deoxyribozyme
sequence
A DNA sequence with catalytic activity.
SO:cb
MNP
A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.
SO:0001013
multiple nucleotide polymorphism
sequence
A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.
http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431
intron_domain
Requested by Colin Batchelor, Feb 2007.
SO:0001014
intron domain
sequence
wobble_base_pair
A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C.
SO:0001015
http://en.wikipedia.org/wiki/Wobble_base_pair
sequence
wobble base pair
wobble pair
wiki
http://en.wikipedia.org/wiki/Wobble_base_pair
A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C.
PMID:11256617
internal_guide_sequence
A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity.
IGS
SO:0001016
internal guide sequence
sequence
A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity.
SO:cb
silent_mutation
A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation.
Added in March 2007 in after meeting with PharmGKB. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc.
SO:0001017
http://en.wikipedia.org/wiki/Silent_mutation
loinc:LA6700-4
sequence
silent mutation
A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation.
SO:ke
wiki
http://en.wikipedia.org/wiki/Silent_mutation
Silent
loinc:LA6700-4
epitope
A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells.
Requested by Trish Whetzel.
SO:0001018
http://en.wikipedia.org/wiki/Epitope
sequence
A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells.
SO:cb
http://en.wikipedia.org/wiki/Epitope
wiki
http://en.wikipedia.org/wiki/Epitope
copy_number_variation
A variation that increases or decreases the copy number of a given region.
CNP
CNV
SO:0001019
copy number polymorphism
copy number variation
http://en.wikipedia.org/wiki/Copy_number_variation
sequence
A variation that increases or decreases the copy number of a given region.
SO:ke
wiki
http://en.wikipedia.org/wiki/Copy_number_variation
sequence_variant_affecting_copy_number
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001020
SO:0001563
mutation affecting copy number
sequence
sequence variant affecting copy number
true
chromosome_breakpoint
SO:0001021
SO:0001242
aberration breakpoint
aberration_junction
chromosome breakpoint
sequence
inversion_breakpoint
SO:0001022
The point within a chromosome where an inversion begins or ends.
inversion breakpoint
sequence
SO:cb
The point within a chromosome where an inversion begins or ends.
allele
An allele is one of a set of coexisting sequence variants of a gene.
SO:0001023
allelomorph
http://en.wikipedia.org/wiki/Allele
sequence
An allele is one of a set of coexisting sequence variants of a gene.
SO:immuno_workshop
wiki
http://en.wikipedia.org/wiki/Allele
haplotype
A haplotype is one of a set of coexisting sequence variants of a haplotype block.
SO:0001024
http://en.wikipedia.org/wiki/Haplotype
sequence
wiki
http://en.wikipedia.org/wiki/Haplotype
A haplotype is one of a set of coexisting sequence variants of a haplotype block.
SO:immuno_workshop
polymorphic_sequence_variant
A sequence variant that is segregating in one or more natural populations of a species.
SO:0001025
polymorphic sequence variant
sequence
A sequence variant that is segregating in one or more natural populations of a species.
SO:immuno_workshop
genome
A genome is the sum of genetic material within a cell or virion.
SO:0001026
http://en.wikipedia.org/wiki/Genome
sequence
A genome is the sum of genetic material within a cell or virion.
SO:immuno_workshop
wiki
http://en.wikipedia.org/wiki/Genome
genotype
A genotype is a variant genome, complete or incomplete.
SO:0001027
http://en.wikipedia.org/wiki/Genotype
sequence
wiki
http://en.wikipedia.org/wiki/Genotype
A genotype is a variant genome, complete or incomplete.
SO:immuno_workshop
diplotype
A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known.
SO:0001028
sequence
A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known.
SO:immuno_workshop
direction_attribute
SO:0001029
direction attribute
sequence
forward
Forward is an attribute of the feature, where the feature is in the 5' to 3' direction.
SO:0001030
sequence
Forward is an attribute of the feature, where the feature is in the 5' to 3' direction.
SO:ke
reverse
Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.
SO:0001031
sequence
Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.
SO:ke
mitochondrial_DNA
SO:0001032
This terms is used by MO.
http://en.wikipedia.org/wiki/Mitochondrial_DNA
mitochondrial DNA
mtDNA
sequence
wiki
http://en.wikipedia.org/wiki/Mitochondrial_DNA
chloroplast_DNA
SO:0001033
This term is used by MO.
chloroplast DNA
sequence
miRtron
A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.
Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns.
SO:0001034
sequence
A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.
PMID:17589500
SO:ma
piRNA
A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
SO:0001035
http://en.wikipedia.org/wiki/PiRNA
piwi-associated RNA
sequence
A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
SO:ke
wiki
http://en.wikipedia.org/wiki/PiRNA
arginyl_tRNA
A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.
SO:0001036
arginyl tRNA
sequence
A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.
SO:ke
mobile_genetic_element
A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
MGE
SO:0001037
http://en.wikipedia.org/wiki/Mobile_genetic_element
mobile genetic element
sequence
wiki
http://en.wikipedia.org/wiki/Mobile_genetic_element
A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome.
PMID:14681355
extrachromosomal_mobile_genetic_element
An MGE that is not integrated into the host chromosome.
SO:0001038
extrachromosomal mobile genetic element
sequence
An MGE that is not integrated into the host chromosome.
SO:ke
integrated_mobile_genetic_element
An MGE that is integrated into the host chromosome.
SO:0001039
integrated mobile genetic element
sequence
An MGE that is integrated into the host chromosome.
SO:ke
integrated_plasmid
A plasmid sequence that is integrated within the host chromosome.
SO:0001040
integrated plasmid
sequence
A plasmid sequence that is integrated within the host chromosome.
SO:ke
viral_sequence
SO:0001041
The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct.
The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.
sequence
viral sequence
virus sequence
SO:ke
The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.
phage_sequence
SO:0001042
The nucleotide sequence of a virus that infects bacteria.
bacteriophage
http://en.wikipedia.org/wiki/Bacteriophage
phage
phage sequence
sequence
SO:ke
The nucleotide sequence of a virus that infects bacteria.
wiki
http://en.wikipedia.org/wiki/Bacteriophage
attCtn_site
An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.
SO:0001043
attCtn site
sequence
An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.
Phigo:at
nuclear_mt_pseudogene
A nuclear pseudogene of either coding or non-coding mitochondria derived sequence.
Definition change requested by Val, 3172757.
NUMT
SO:0001044
http://en.wikipedia.org/wiki/Numt
nuclear mitochondrial pseudogene
nuclear mt pseudogene
sequence
A nuclear pseudogene of either coding or non-coding mitochondria derived sequence.
SO:xp
wikipedia
http://en.wikipedia.org/wiki/Numt
cointegrated_plasmid
A MGE region consisting of two fused plasmids resulting from a replicative transposition event.
SO:0001045
cointegrated plasmid
cointegrated replicon
sequence
A MGE region consisting of two fused plasmids resulting from a replicative transposition event.
phigo:at
IRLinv_site
Component of the inversion site located at the left of a region susceptible to site-specific inversion.
IRLinv site
SO:0001046
sequence
Component of the inversion site located at the left of a region susceptible to site-specific inversion.
Phigo:at
IRRinv_site
Component of the inversion site located at the right of a region susceptible to site-specific inversion.
IRRinv site
SO:0001047
sequence
Component of the inversion site located at the right of a region susceptible to site-specific inversion.
Phigo:at
inversion_site_part
A region located within an inversion site.
A term created to allow the parts of an inversion site have an is_a path back to the root.
SO:0001048
inversion site part
sequence
A region located within an inversion site.
SO:ke
defective_conjugative_transposon
An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.
SO:0001049
defective conjugative transposon
sequence
An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.
Phigo:ariane
repeat_fragment
A portion of a repeat, interrupted by the insertion of another element.
Requested by Chris Smith, and others at Flybase to help annotate nested repeats.
SO:0001050
repeat fragment
sequence
A portion of a repeat, interrupted by the insertion of another element.
SO:ke
nested_region
SO:0001051
sequence
true
nested_repeat
SO:0001052
sequence
true
nested_transposon
SO:0001053
sequence
true
transposon_fragment
A portion of a transposon, interrupted by the insertion of another element.
SO:0001054
sequence
transposon fragment
A portion of a transposon, interrupted by the insertion of another element.
SO:ke
transcriptional_cis_regulatory_region
A regulatory_region that modulates the transcription of a gene or genes.
SO:0001055
sequence
transcription-control region
transcriptional cis regulatory region
A regulatory_region that modulates the transcription of a gene or genes.
PMID:9679020
SO:regcreative
splicing_regulatory_region
A regulatory_region that modulates splicing.
SO:0001056
sequence
splicing regulatory region
A regulatory_region that modulates splicing.
SO:ke
enhanceosome
SO:0001057
sequence
true
promoter_targeting_sequence
A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.
SO:0001058
promoter targeting sequence
sequence
A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.
SO:regcreative
sequence_alteration
A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
Merged with partially characterized change in nucleotide sequence.
SO:0001059
SO:1000004
SO:1000007
partially characterised change in DNA sequence
partially_characterised_change_in_DNA_sequence
sequence
sequence alteration
sequence variation
uncharacterised_change_in_nucleotide_sequence
A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
SO:ke
sequence_variant
A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
ANNOVAR:unknown
SO:0001060
VAAST:sequence_variant
sequence
sequence variant
ANNOVAR:unknown
http://www.openbioinformatics.org/annovar/annovar_download.html
A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
SO:ke
VAAST:sequence_variant
propeptide_cleavage_site
BS:00063
Discrete.
SO:0001061
The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs.
propeptide cleavage site
sequence
EBIBS:GAR
The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs.
propeptide
BS:00077
Part of a peptide chain which is cleaved off during the formation of the mature protein.
Range.
SO:0001062
http://en.wikipedia.org/wiki/Propeptide
propep
sequence
EBIBS:GAR
Part of a peptide chain which is cleaved off during the formation of the mature protein.
propep
uniprot:feature_type
wiki
http://en.wikipedia.org/wiki/Propeptide
immature_peptide_region
An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
BS:00129
Range.
SO:0001063
immature peptide region
sequence
An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.
EBIBS:GAR
active_peptide
Active peptides are proteins which are biologically active, released from a precursor molecule.
BS:00076
Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.
SO:0001064
active peptide
http://en.wikipedia.org/wiki/Peptide
peptide
sequence
peptide
uniprot:feature_type
wiki
http://en.wikipedia.org/wiki/Peptide
Active peptides are proteins which are biologically active, released from a precursor molecule.
EBIBS:GAR
UniProt:curation_manual
compositionally_biased_region_of_peptide
BS:00068
Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length.
Range.
SO:0001066
compbias
compositional bias
compositionally biased
compositionally biased region of peptide
compositionally_biased_region
sequence
compbias
uniprot:feature_type
EBIBS:GAR
Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length.
UniProt:curation_manual
polypeptide_motif
A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.).
BS:00032
Range.
SO:0001067
motif
polypeptide motif
sequence
motif
uniprot:feature_type
A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.).
EBIBS:GAR
UniProt:curation_manual
polypeptide_repeat
A polypeptide_repeat is a single copy of an internal sequence repetition.
BS:00070
Range.
SO:0001068
polypeptide repeat
repeat
sequence
repeat
uniprot:feature_type
A polypeptide_repeat is a single copy of an internal sequence repetition.
EBIBS:GAR
polypeptide_structural_region
BS:00337
Range.
Region of polypeptide with a given structural property.
SO:0001070
polypeptide structural region
sequence
structural_region
EBIBS:GAR
Region of polypeptide with a given structural property.
SO:cb
membrane_structure
Arrangement of the polypeptide with respect to the lipid bilayer.
BS:00128
Range.
SO:0001071
membrane structure
sequence
Arrangement of the polypeptide with respect to the lipid bilayer.
EBIBS:GAR
extramembrane_polypeptide_region
BS:00154
Polypeptide region that is localized outside of a lipid bilayer.
Range.
SO:0001072
extramembrane
extramembrane polypeptide region
extramembrane_region
sequence
topo_dom
topo_dom
uniprot:feature_type
extramembrane_region
EBIBS:GAR
Polypeptide region that is localized outside of a lipid bilayer.
SO:cb
extramembrane
cytoplasmic_polypeptide_region
BS:00145
Polypeptide region that is localized inside the cytoplasm.
SO:0001073
cytoplasm_location
cytoplasmic polypeptide region
inside
sequence
EBIBS:GAR
Polypeptide region that is localized inside the cytoplasm.
SO:cb
inside
cytoplasm_location
non_cytoplasmic_polypeptide_region
BS:00144
Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm.
SO:0001074
This could be inside an organelle within the cell.
non cytoplasmic polypeptide region
non_cytoplasm_location
outside
sequence
outside
non_cytoplasm_location
EBIBS:GAR
Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm.
SO:cb
intramembrane_polypeptide_region
BS:00156
Polypeptide region present in the lipid bilayer.
SO:0001075
intramembrane
intramembrane polypeptide region
sequence
intramembrane
EBIBS:GAR
Polypeptide region present in the lipid bilayer.
membrane_peptide_loop
BS:00155
Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane.
SO:0001076
membrane peptide loop
membrane_loop
sequence
EBIBS:GAR
Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane.
SO:cb
membrane_loop
transmembrane_polypeptide_region
BS:00158
Polypeptide region traversing the lipid bilayer.
SO:0001077
sequence
transmem
transmembrane
transmembrane polypeptide region
EBIBS:GAR
Polypeptide region traversing the lipid bilayer.
UniProt:curator_manual
transmem
uniprot:feature_type
transmembrane
polypeptide_secondary_structure
2nary structure
A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain.
BS:00003
Biosapien term was secondary_structure.
SO:0001078
http://en.wikipedia.org/wiki/Secondary_structure
polypeptide secondary structure
secondary structure
secondary structure region
secondary_structure
sequence
secondary structure region
wiki
http://en.wikipedia.org/wiki/Secondary_structure
secondary structure
A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain.
EBIBS:GAR
2nary structure
secondary_structure
polypeptide_structural_motif
BS:0000338
Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit.
SO:0001079
http://en.wikipedia.org/wiki/Structural_motif
polypeptide structural motif
sequence
structural_motif
structural_motif
EBIBS:GAR
Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit.
wiki
http://en.wikipedia.org/wiki/Structural_motif
coiled_coil
A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope.
BS:00041
Range.
SO:0001080
coiled
coiled coil
http://en.wikipedia.org/wiki/Coiled_coil
sequence
wiki
http://en.wikipedia.org/wiki/Coiled_coil
A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope.
EBIBS:GAR
UniProt:curation_manual
coiled
uniprot:feature_type
helix_turn_helix
A motif comprising two helices separated by a turn.
BS:00147
HTH
SO:0001081
helix turn helix
helix-turn-helix
sequence
HTH
A motif comprising two helices separated by a turn.
EBIBS:GAR
polypeptide_sequencing_information
BS:00125
Incompatibility in the sequence due to some experimental problem.
Range.
SO:0001082
sequence
sequencing_information
EBIBS:GAR
Incompatibility in the sequence due to some experimental problem.
non_adjacent_residues
BS:00182
Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them.
SO:0001083
non consecutive
non_cons
sequence
EBIBS:GAR
Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them.
UniProt:curation_manual
non_cons
uniprot:feature_type
non_terminal_residue
BS:00072
Discrete.
SO:0001084
The residue at an extremity of the sequence is not the terminal residue.
non terminal
non_ter
sequence
non_ter
uniprot:feature_type
EBIBS:GAR
The residue at an extremity of the sequence is not the terminal residue.
UniProt:curation_manual
sequence_conflict
BS:00069
Different sources report differing sequences.
Discrete.
SO:0001085
conflict
sequence
Different sources report differing sequences.
EBIBS:GAR
UniProt:curation_manual
conflict
uniprot:feature_type
sequence_uncertainty
BS:00181
Describes the positions in a sequence where the authors are unsure about the sequence assignment.
SO:0001086
sequence
unsure
Describes the positions in a sequence where the authors are unsure about the sequence assignment.
EBIBS:GAR
UniProt:curation_manual
uniprot:feature_type
unsure
cross_link
BS:00178
Posttranslationally formed amino acid bonds.
SO:0001087
cross link
crosslink
sequence
true
EBIBS:GAR
Posttranslationally formed amino acid bonds.
UniProt:curation_manual
disulfide_bond
2 discreet & joined.
BS:00028
SO:0001088
The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules.
disulfid
disulfide
disulfide bond
disulphide
disulphide bond
sequence
true
EBIBS:GAR
The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules.
UniProt:curation_manual
post_translationally_modified_region
A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein.
BS:00052
Discrete.
SO:0001089
http://en.wikipedia.org/wiki/Post_translational_modification
mod_res
modified residue
post_translational_modification
sequence
wiki
http://en.wikipedia.org/wiki/Post_translational_modification
mod_res
uniprot:feature_type
A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein.
EBIBS:GAR
UniProt:curation_manual
covalent_binding_site
BS:00246
Binding involving a covalent bond.
SO:0001090
covalent binding site
sequence
true
Binding involving a covalent bond.
EBIBS:GAR
non_covalent_binding_site
BS:00029
Binding site for any chemical group (co-enzyme, prosthetic group, etc.).
Discrete.
SO:0001091
binding
binding site
non covalent binding site
sequence
true
binding
uniprot:curation
Binding site for any chemical group (co-enzyme, prosthetic group, etc.).
EBIBS:GAR
polypeptide_metal_contact
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions.
BS:00027
Residue is part of a binding site for a metal ion.
SO:0001092
metal_binding
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions.
EBIBS:GAR
SO:cb
UniProt:curation_manual
protein_protein_contact
A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues.
BS:00131
SO:0001093
http://en.wikipedia.org/wiki/Protein_protein_interaction
protein protein contact
protein protein contact site
protein_protein_interaction
sequence
wiki
http://en.wikipedia.org/wiki/Protein_protein_interaction
A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues.
EBIBS:GAR
UniProt:Curation_manual
polypeptide_calcium_ion_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions.
BS:00186
Ca_contact_site
Residue involved in contact with calcium.
SO:0001094
ca bind
ca_bind
polypeptide calcium ion contact site
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions.
EBIBS:GAR
ca_bind
uniprot:feature_type
polypeptide_cobalt_ion_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions.
BS:00136
Co_contact_site
SO:0001095
polypeptide cobalt ion contact site
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions.
EBIBS:GAR
SO:cb
polypeptide_copper_ion_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions.
BS:00146
Cu_contact_site
SO:0001096
polypeptide copper ion contact site
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions.
EBIBS:GAR
SO:cb
polypeptide_iron_ion_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions.
BS:00137
Fe_contact_site
SO:0001097
polypeptide iron ion contact site
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions.
EBIBS:GAR
SO:cb
polypeptide_magnesium_ion_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions.
BS:00187
Mg_contact_site
SO:0001098
polypeptide magnesium ion contact site
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions.
EBIBS:GAR
SO:cb
polypeptide_manganese_ion_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions.
BS:00140
Mn_contact_site
SO:0001099
polypeptide manganese ion contact site
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions.
EBIBS:GAR
SO:cb
polypeptide_molybdenum_ion_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions.
BS:00141
Mo_contact_site
SO:0001100
polypeptide molybdenum ion contact site
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions.
EBIBS:GAR
SO:cb
polypeptide_nickel_ion_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions.
BS:00142
Ni_contact_site
SO:0001101
polypeptide nickel ion contact site
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions.
EBIBS:GAR
polypeptide_tungsten_ion_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions.
BS:00143
SO:0001102
W_contact_site
polypeptide tungsten ion contact site
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions.
EBIBS:GAR
SO:cb
polypeptide_zinc_ion_contact_site
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions.
BS:00185
SO:0001103
Zn_contact_site
polypeptide zinc ion contact site
sequence
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions.
EBIBS:GAR
SO:cb
catalytic_residue
Amino acid involved in the activity of an enzyme.
BS:00026
Discrete.
SO:0001104
act_site
active site residue
catalytic residue
sequence
act_site
uniprot:feature_type
Amino acid involved in the activity of an enzyme.
EBIBS:GAR
UniProt:curation_manual
polypeptide_ligand_contact
BS:00157
Residues which interact with a ligand.
SO:0001105
polypeptide ligand contact
protein-ligand interaction
sequence
EBIBS:GAR
Residues which interact with a ligand.
asx_motif
A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
BS:00202
SO:0001106
asx motif
sequence
A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_bulge
A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.
BS:00208
SO:0001107
beta bulge
http://en.wikipedia.org/wiki/Beta_bulge
sequence
wiki
http://en.wikipedia.org/wiki/Beta_bulge
A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_bulge_loop
A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins.
BS:00209
SO:0001108
beta bulge loop
sequence
A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins.
EBIBS:GAR
Http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_bulge_loop_five
A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3.
BS:00210
SO:0001109
beta bulge loop five
sequence
A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_bulge_loop_six
A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4.
BS:00211
SO:0001110
beta bulge loop six
sequence
A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_strand
A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array.
BS:00042
Range.
SO:0001111
http://en.wikipedia.org/wiki/Beta_sheet
sequence
strand
wiki
http://en.wikipedia.org/wiki/Beta_sheet
A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array.
EBIBS:GAR
UniProt:curation_manual
strand
uniprot:feature_type
antiparallel_beta_strand
A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets.
BS:0000341
Range.
SO:0001112
antiparallel beta strand
sequence
A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets.
EBIBS:GAR
UniProt:curation_manual
parallel_beta_strand
A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets.
BS:00151
Range.
SO:0001113
parallel beta strand
sequence
A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets.
EBIBS:GAR
UniProt:curation_manual
peptide_helix
A helix is a secondary_structure conformation where the peptide backbone forms a coil.
BS:00152
Range.
SO:0001114
helix
sequence
helix
A helix is a secondary_structure conformation where the peptide backbone forms a coil.
EBIBS:GAR
left_handed_peptide_helix
A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.
BS:00222
SO:0001115
helix-l
left handed helix
sequence
A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.
EBIBS:GAR
right_handed_peptide_helix
A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.
BS:0000339
SO:0001116
helix
right handed helix
sequence
A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.
EBIBS:GAR
helix
alpha_helix
BS:00040
Range.
SO:0001117
The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
a-helix
helix
http://en.wikipedia.org/wiki/Alpha_helix
sequence
wiki
http://en.wikipedia.org/wiki/Alpha_helix
EBIBS:GAR
The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
a-helix
helix
uniprot:feature_type
pi_helix
BS:00153
Range.
SO:0001118
The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
http://en.wikipedia.org/wiki/Pi_helix
pi helix
sequence
wiki
http://en.wikipedia.org/wiki/Pi_helix
EBIBS:GAR
The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
three_ten_helix
3(10) helix
3-10 helix
310 helix
BS:0000340
Range.
SO:0001119
The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
http://en.wikipedia.org/wiki/310_helix
sequence
three ten helix
wiki
http://en.wikipedia.org/wiki/310_helix
EBIBS:GAR
The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
polypeptide_nest_motif
A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops.
BS:00223
SO:0001120
nest
nest_motif
polypeptide nest motif
sequence
nest
A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
polypeptide_nest_left_right_motif
A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
BS:00224
SO:0001121
nest_left_right
nest_lr
polypeptide nest left right motif
sequence
A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
polypeptide_nest_right_left_motif
A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
BS:00225
SO:0001122
nest_right_left
nest_rl
polypeptide nest right left motif
sequence
A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
schellmann_loop
A motif of six or seven consecutive residues that contains two H-bonds.
BS:00226
SO:0001123
paperclip
paperclip loop
schellmann loop
sequence
A motif of six or seven consecutive residues that contains two H-bonds.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
paperclip
schellmann_loop_seven
BS:00228
SO:0001124
Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).
schellmann loop seven
sequence
seven-residue schellmann loop
EBIBS:GAR
Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).
http://www.ebi.ac.uk/msd-srv/msdmotif/
schellmann_loop_six
BS:00227
Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4).
SO:0001125
schellmann loop six
sequence
six-residue schellmann loop
Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4).
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
serine_threonine_motif
A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
BS:00229
SO:0001126
sequence
serine/threonine motif
st motif
st_motif
A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
serine_threonine_staple_motif
A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative.
BS:00230
SO:0001127
sequence
serine threonine staple motif
st_staple
A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
polypeptide_turn_motif
A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues.
BS:00148
Range.
SO:0001128
sequence
turn
turn
A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues.
EBIBS:GAR
uniprot:feature_type
asx_turn_left_handed_type_one
BS:00206
Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
SO:0001129
asx turn left handed type one
asx_turn_il
sequence
EBIBS:GAR
Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
asx_turn_left_handed_type_two
BS:00204
Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
SO:0001130
asx turn left handed type two
asx_turn_iil
sequence
EBIBS:GAR
Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
asx_turn_right_handed_type_two
BS:00205
Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
SO:0001131
asx turn right handed type two
asx_turn_iir
sequence
EBIBS:GAR
Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
asx_turn_right_handed_type_one
BS:00207
Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
SO:0001132
asx turn type right handed type one
asx_turn_ir
sequence
EBIBS:GAR
Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_turn
A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization.
BS:00212
SO:0001133
beta turn
sequence
A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_turn_left_handed_type_one
BS:00215
Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.
SO:0001134
beta turn left handed type one
beta_turn_il
sequence
type I' beta turn
type I' turn
EBIBS:GAR
Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_turn_left_handed_type_two
BS:00213
Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees.
SO:0001135
beta turn left handed type two
beta_turn_iil
sequence
type II' beta turn
type II' turn
EBIBS:GAR
Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_turn_right_handed_type_one
BS:00216
Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
SO:0001136
beta turn right handed type one
beta_turn_ir
sequence
type I beta turn
type I turn
EBIBS:GAR
Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
beta_turn_right_handed_type_two
BS:00214
Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
SO:0001137
beta turn right handed type two
beta_turn_iir
sequence
type II beta turn
type II turn
EBIBS:GAR
Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
gamma_turn
BS:00219
Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.
SO:0001138
gamma turn
sequence
EBIBS:GAR
Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
gamma_turn_classic
BS:00220
Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.
SO:0001139
classic gamma turn
gamma turn classic
sequence
EBIBS:GAR
Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.
http://www.ebi.ac.uk/msd-srv/msdmotif/
gamma_turn_inverse
BS:00221
Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.
SO:0001140
gamma turn inverse
sequence
EBIBS:GAR
Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.
http://www.ebi.ac.uk/msd-srv/msdmotif/
serine_threonine_turn
A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
BS:00231
SO:0001141
sequence
serine/threonine turn
st_turn
A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
st_turn_left_handed_type_one
BS:00234
SO:0001142
The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
sequence
st turn left handed type one
st_turn_il
EBIBS:GAR
The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
st_turn_left_handed_type_two
BS:00232
SO:0001143
The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
sequence
st turn left handed type two
st_turn_iil
EBIBS:GAR
The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
st_turn_right_handed_type_one
BS:00235
SO:0001144
The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
sequence
st turn right handed type one
st_turn_ir
EBIBS:GAR
The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
st_turn_right_handed_type_two
BS:00233
SO:0001145
The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
sequence
st turn right handed type two
st_turn_iir
EBIBS:GAR
The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.
http://www.ebi.ac.uk/msd-srv/msdmotif/
polypeptide_variation_site
A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis.
BS:00336
For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.
SO:0001146
sequence
sequence_variations
A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis.
EBIBS:GAR
SO:ke
natural_variant_site
BS:00071
Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.
Discrete.
SO:0001147
natural_variant
sequence
sequence variation
variant
Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.
EBIBS:GAR
UniProt:curation_manual
uniprot:feature_type
variant
mutated_variant_site
BS:00036
Discrete.
SO:0001148
Site which has been experimentally altered.
mutagen
mutagenesis
mutated_site
sequence
EBIBS:GAR
Site which has been experimentally altered.
UniProt:curation_manual
mutagen
uniprot:feature_type
alternate_sequence_site
BS:00073
Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
Discrete.
SO:0001065
SO:0001149
alternative_sequence
isoform
sequence
sequence variation
var_seq
varsplic
Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.
EBIBS:GAR
UniProt:curation_manual
uniprot:feature_type
var_seq
beta_turn_type_six
A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.
SO:0001150
beta turn type six
cis-proline loop
sequence
type VI beta turn
type VI turn
A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.
SO:cb
beta_turn_type_six_a
A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.
SO:0001151
beta turn type six a
sequence
type VIa beta turn
type VIa turn
A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.
PMID:2371257
SO:cb
beta_turn_type_six_a_one
SO:0001152
beta turn type six a one
sequence
type VIa1 beta turn
type VIa1 turn
beta_turn_type_six_a_two
SO:0001153
beta turn type six a two
sequence
type VIa2 beta turn
type VIa2 turn
beta_turn_type_six_b
A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.
SO:0001154
beta turn type six b
sequence
type VIb beta turn
type VIb turn
A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.
PMID:2371257
SO:cb
beta_turn_type_eight
A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.
SO:0001155
beta turn type eight
sequence
type VIII beta turn
type VIII turn
A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.
PMID:2371257
SO:cb
DRE_motif
A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.
DRE motif
NDM4
SO:0001156
This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.
WATCGATW_motif
sequence
A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.
PMID:12537576
DMv4_motif
A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).
DMv4
DMv4 motif
SO:0001157
YGGTCACATR
directional motif v4
motif 1 element
promoter motif 1
sequence
A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).
PMID:16827941:12537576
E_box_motif
A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).
AWCAGCTGWT
E box motif
NDM5
SO:0001158
generic E box motif
sequence
A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).
PMID:12537576:16827941
DMv5_motif
A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
DMv5
DMv5 motif
KTYRGTATWTTT
SO:0001159
directional motif v5
promoter motif 6
sequence
A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
PMID:12537576:16827941
DMv3_motif
A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).
DMv3
DMv3 motif
KNNCAKCNCTRNY
SO:0001160
directional motif v3
promoter motif 7
sequence
A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).
PMID:12537576:16827941
DMv2_motif
A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
DMv2
DMv2 motif
MKSYGGCARCGSYSS
SO:0001161
directional motif v2
promoter motif 8
sequence
A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).
PMID:12537576:16827941
MTE
A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).
CSARCSSAACGS
SO:0001162
motif ten element
motif_ten_element
sequence
A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).
PMID:12537576:15231738
PMID:16858867
INR1_motif
A promoter motif with consensus sequence TCATTCG.
DMp3
INR1 motif
SO:0001163
directional motif p3
directional promoter motif 3
sequence
A promoter motif with consensus sequence TCATTCG.
PMID:16827941
DPE1_motif
A promoter motif with consensus sequence CGGACGT.
DMp5
DPE1 motif
SO:0001164
directional motif 5
directional promoter motif 5
sequence
A promoter motif with consensus sequence CGGACGT.
PMID:16827941
DMv1_motif
A promoter motif with consensus sequence CARCCCT.
DMv1
DMv1 motif
SO:0001165
directional promoter motif v1
sequence
A promoter motif with consensus sequence CARCCCT.
PMID:16827941
GAGA_motif
A non directional promoter motif with consensus sequence GAGAGCG.
GAGA
GAGA motif
NDM1
SO:0001166
sequence
A non directional promoter motif with consensus sequence GAGAGCG.
PMID:16827941
NDM2_motif
A non directional promoter motif with consensus CGMYGYCR.
NDM2
NDM2 motif
SO:0001167
non directional promoter motif 2
sequence
A non directional promoter motif with consensus CGMYGYCR.
PMID:16827941
NDM3_motif
A non directional promoter motif with consensus sequence GAAAGCT.
NDM3
NDM3 motif
SO:0001168
non directional motif 3
sequence
A non directional promoter motif with consensus sequence GAAAGCT.
PMID:16827941
ds_RNA_viral_sequence
A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.
SO:0001169
double stranded RNA virus sequence
ds RNA viral sequence
sequence
A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.
SO:ke
polinton
A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.
SO:0001170
maverick element
sequence
A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.
PMID:16537396
rRNA_21S
21S LSU rRNA
21S rRNA
21S ribosomal RNA
A component of the large ribosomal subunit in mitochondrial rRNA.
SO:0001171
rRNA 21S
sequence
A component of the large ribosomal subunit in mitochondrial rRNA.
RSC:cb
tRNA_region
A region of a tRNA.
SO:0001172
sequence
tRNA region
A region of a tRNA.
RSC:cb
anticodon_loop
A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.
SO:0001173
anti-codon loop
anticodon loop
sequence
A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.
ISBN:0716719207
anticodon
A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
SO:0001174
anti-codon
http://en.wikipedia.org/wiki/Anticodon
sequence
A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.
RSC:cb
wiki
http://en.wikipedia.org/wiki/Anticodon
CCA_tail
Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.
CCA sequence
CCA tail
SO:0001175
sequence
Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.
ISBN:0716719207
DHU_loop
D loop
DHU loop
Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.
SO:0001176
sequence
ISBN:071671920
Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.
T_loop
Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
SO:0001177
T loop
TpsiC loop
sequence
ISBN:0716719207
Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.
pyrrolysine_tRNA_primary_transcript
A primary transcript encoding pyrrolysyl tRNA (SO:0000766).
SO:0001178
pyrrolysine tRNA primary transcript
sequence
A primary transcript encoding pyrrolysyl tRNA (SO:0000766).
RSC:cb
U3_snoRNA
SO:0001179
The definition is most of the old definition for snoRNA (SO:0000275).
U3 small nucleolar RNA
U3 snoRNA
U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.
http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3
sequence
small nucleolar RNA U3
snoRNA U3
U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012
wiki
http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3
AU_rich_element
A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.
ARE
AU rich element
AU-rich element
SO:0001180
http://en.wikipedia.org/wiki/AU-rich_element
sequence
wiki
http://en.wikipedia.org/wiki/AU-rich_element
A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.
PMID:7892223
Bruno_response_element
A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.
BRE
Bruno response element
Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.
SO:0001181
sequence
A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.
PMID:10893231
iron_responsive_element
A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.
IRE
SO:0001182
http://en.wikipedia.org/wiki/Iron_responsive_element
iron responsive element
sequence
A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.
PMID:3198610
PMID:8710843
wiki
http://en.wikipedia.org/wiki/Iron_responsive_element
morpholino_backbone
An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.
Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.
SO:0001183
http://en.wikipedia.org/wiki/Morpholino
morpholino backbone
sequence
An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.
RSC:cb
wiki
http://en.wikipedia.org/wiki/Morpholino
PNA
An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.
SO:0001184
peptide nucleic acid
sequence
An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.
RSC:cb
enzymatic
An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.
Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.
SO:0001185
sequence
An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.
RSC:cb
ribozymic
An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.
Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.
SO:0001186
sequence
An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.
RSC:cb
pseudouridylation_guide_snoRNA
A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
Has RNA pseudouridylation guide activity (GO:0030558).
SO:0001187
pseudouridylation guide snoRNA
sequence
A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.
GOC:mah
PMID:12457565
LNA
An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.
Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.
SO:0001188
sequence
An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.
CHEBI:48010
LNA_oligo
An oligo composed of LNA residues.
LNA oligo
SO:0001189
http://en.wikipedia.org/wiki/Locked_nucleic_acid
locked nucleic acid
sequence
An oligo composed of LNA residues.
RSC:cb
wiki
http://en.wikipedia.org/wiki/Locked_nucleic_acid
TNA
An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.
Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.
SO:0001190
sequence
An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.
CHEBI:48019
TNA_oligo
An oligo composed of TNA residues.
SO:0001191
TNA oligo
http://en.wikipedia.org/wiki/Threose_nucleic_acid
sequence
threose nucleic acid
wiki
http://en.wikipedia.org/wiki/Threose_nucleic_acid
An oligo composed of TNA residues.
RSC:cb
GNA
An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.
Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.
SO:0001192
sequence
An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.
CHEBI:48015
GNA_oligo
An oligo composed of GNA residues.
GNA oligo
SO:0001193
glycerol nucleic acid
glycol nucleic acid
http://en.wikipedia.org/wiki/Glycerol_nucleic_acid
sequence
An oligo composed of GNA residues.
RSC:cb
wiki
http://en.wikipedia.org/wiki/Glycerol_nucleic_acid
R_GNA
An attribute describing a GNA sequence in the (R)-GNA enantiomer.
Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.
R GNA
SO:0001194
sequence
An attribute describing a GNA sequence in the (R)-GNA enantiomer.
CHEBI:48016
R_GNA_oligo
(R)-glycerol nucleic acid
(R)-glycol nucleic acid
An oligo composed of (R)-GNA residues.
R GNA oligo
SO:0001195
sequence
An oligo composed of (R)-GNA residues.
RSC:cb
S_GNA
An attribute describing a GNA sequence in the (S)-GNA enantiomer.
Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.
S GNA
SO:0001196
sequence
An attribute describing a GNA sequence in the (S)-GNA enantiomer.
CHEBI:48017
S_GNA_oligo
(S)-glycerol nucleic acid
(S)-glycol nucleic acid
An oligo composed of (S)-GNA residues.
S GNA oligo
SO:0001197
sequence
An oligo composed of (S)-GNA residues.
RSC:cb
ds_DNA_viral_sequence
A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.
SO:0001198
double stranded DNA virus
ds DNA viral sequence
sequence
A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.
SO:ke
ss_RNA_viral_sequence
A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.
SO:0001199
sequence
single strand RNA virus
ss RNA viral sequence
A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.
SO:ke
negative_sense_ssRNA_viral_sequence
A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.
SO:0001200
negative sense single stranded RNA virus
negative sense ssRNA viral sequence
sequence
A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.
SO:ke
positive_sense_ssRNA_viral_sequence
A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.
SO:0001201
positive sense single stranded RNA virus
positive sense ssRNA viral sequence
sequence
A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.
SO:ke
ambisense_ssRNA_viral_sequence
A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.
SO:0001202
ambisense single stranded RNA virus
ambisense ssRNA viral sequence
sequence
A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.
SO:ke
RNA_polymerase_promoter
A region (DNA) to which RNA polymerase binds, to begin transcription.
RNA polymerase promoter
SO:0001203
sequence
A region (DNA) to which RNA polymerase binds, to begin transcription.
xenbase:jb
Phage_RNA_Polymerase_Promoter
A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
Phage RNA Polymerase Promoter
SO:0001204
sequence
A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
xenbase:jb
SP6_RNA_Polymerase_Promoter
A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.
SO:0001205
SP6 RNA Polymerase Promoter
sequence
A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.
xenbase:jb
T3_RNA_Polymerase_Promoter
A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.
SO:0001206
T3 RNA Polymerase Promoter
sequence
A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.
xenbase:jb
T7_RNA_Polymerase_Promoter
A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.
SO:0001207
T7 RNA Polymerase Promoter
sequence
A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.
xenbase:jb
five_prime_EST
5' EST
An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family.
SO:0001208
five prime EST
sequence
An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family.
http://www.ncbi.nlm.nih.gov/About/primer/est.html
three_prime_EST
3' EST
An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs).
SO:0001209
sequence
three prime EST
An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs).
http://www.ncbi.nlm.nih.gov/About/primer/est.html
translational_frameshift
SO:0001210
The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
http://en.wikipedia.org/wiki/Translational_frameshift
ribosomal frameshift
sequence
translational frameshift
wiki
http://en.wikipedia.org/wiki/Translational_frameshift
SO:ke
The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
plus_1_translational_frameshift
SO:0001211
The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
plus 1 ribosomal frameshift
plus 1 translational frameshift
sequence
SO:ke
The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
plus_2_translational_frameshift
SO:0001212
The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
plus 2 ribosomal frameshift
plus 2 translational frameshift
sequence
SO:ke
The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.
group_III_intron
GO:0000374.
Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile.
SO:0001213
group III intron
http://en.wikipedia.org/wiki/Group_III_intron
sequence
wiki
http://en.wikipedia.org/wiki/Group_III_intron
Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile.
PMID:11377794
noncoding_region_of_exon
An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.
SO:0001214
The maximal intersection of exon and UTR.
noncoding region of exon
sequence
SO:ke
The maximal intersection of exon and UTR.
coding_region_of_exon
An exon containing either a start or stop codon will be partially coding and partially non coding.
SO:0001215
The region of an exon that encodes for protein sequence.
coding region of exon
sequence
SO:ke
The region of an exon that encodes for protein sequence.
endonuclease_spliced_intron
An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.
SO:0001216
endonuclease spliced intron
sequence
An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.
SO:ke
protein_coding_gene
SO:0001217
protein coding gene
sequence
transgenic_insertion
An insertion that derives from another organism, via the use of recombinant DNA technology.
SO:0001218
sequence
transgenic insertion
An insertion that derives from another organism, via the use of recombinant DNA technology.
SO:bm
retrogene
SO:0001219
sequence
silenced_by_RNA_interference
An attribute describing an epigenetic process where a gene is inactivated by RNA interference.
RNA interference is GO:0016246.
SO:0001220
sequence
silenced by RNA interference
An attribute describing an epigenetic process where a gene is inactivated by RNA interference.
RSC:cb
silenced_by_histone_modification
An attribute describing an epigenetic process where a gene is inactivated by histone modification.
Histone modification is GO:0016570.
SO:0001221
sequence
silenced by histone modification
An attribute describing an epigenetic process where a gene is inactivated by histone modification.
RSC:cb
silenced_by_histone_methylation
An attribute describing an epigenetic process where a gene is inactivated by histone methylation.
Histone methylation is GO:0016571.
SO:0001222
sequence
silenced by histone methylation
An attribute describing an epigenetic process where a gene is inactivated by histone methylation.
RSC:cb
silenced_by_histone_deacetylation
An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.
Histone deacetylation is GO:0016573.
SO:0001223
sequence
silenced by histone deacetylation
An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.
RSC:cb
gene_silenced_by_RNA_interference
A gene that is silenced by RNA interference.
RNA interference silenced gene
RNAi silenced gene
SO:0001224
gene silenced by RNA interference
sequence
A gene that is silenced by RNA interference.
SO:xp
gene_silenced_by_histone_modification
A gene that is silenced by histone modification.
SO:0001225
gene silenced by histone modification
sequence
A gene that is silenced by histone modification.
SO:xp
gene_silenced_by_histone_methylation
A gene that is silenced by histone methylation.
SO:0001226
gene silenced by histone methylation
sequence
A gene that is silenced by histone methylation.
SO:xp
gene_silenced_by_histone_deacetylation
A gene that is silenced by histone deacetylation.
SO:0001227
gene silenced by histone deacetylation
sequence
A gene that is silenced by histone deacetylation.
SO:xp
dihydrouridine
A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.
D
RNAMOD:051
SO:0001228
http://en.wikipedia.org/wiki/Dihydrouridine
sequence
D
wiki
http://en.wikipedia.org/wiki/Dihydrouridine
A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.
RSC:cb
pseudouridine
A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.
RNAMOD:050
SO:0001229
The free molecule is CHEBI:17802.
Y
http://en.wikipedia.org/wiki/Pseudouridine
sequence
Y
wiki
http://en.wikipedia.org/wiki/Pseudouridine
A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.
RSC:cb
inosine
A modified RNA base in which hypoxanthine is bound to the ribose ring.
I
RNAMOD:017
SO:0001230
The free molecule is CHEBI:17596.
http://en.wikipedia.org/wiki/Inosine
sequence
wiki
http://en.wikipedia.org/wiki/Inosine
A modified RNA base in which hypoxanthine is bound to the ribose ring.
RSC:cb
http://library.med.utah.edu/RNAmods/
seven_methylguanine
7-methylguanine
A modified RNA base in which guanine is methylated at the 7- position.
SO:0001231
The free molecule is CHEBI:2274.
sequence
seven methylguanine
A modified RNA base in which guanine is methylated at the 7- position.
RSC:cb
ribothymidine
A modified RNA base in which thymine is bound to the ribose ring.
SO:0001232
The free molecule is CHEBI:30832.
sequence
A modified RNA base in which thymine is bound to the ribose ring.
RSC:cb
methylinosine
A modified RNA base in which methylhypoxanthine is bound to the ribose ring.
SO:0001233
sequence
A modified RNA base in which methylhypoxanthine is bound to the ribose ring.
RSC:cb
mobile
An attribute describing a feature that has either intra-genome or intracellular mobility.
SO:0001234
http://en.wikipedia.org/wiki/Mobile
sequence
An attribute describing a feature that has either intra-genome or intracellular mobility.
RSC:cb
wiki
http://en.wikipedia.org/wiki/Mobile
replicon
A region containing at least one unique origin of replication and a unique termination site.
SO:0001235
http://en.wikipedia.org/wiki/Replicon_(genetics)
sequence
wiki
http://en.wikipedia.org/wiki/Replicon_(genetics)
A region containing at least one unique origin of replication and a unique termination site.
ISBN:0716719207
base
A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
SO:0001236
http://en.wikipedia.org/wiki/Nucleobase
sequence
A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
SO:ke
wiki
http://en.wikipedia.org/wiki/Nucleobase
amino_acid
A sequence feature that corresponds to a single amino acid residue in a polypeptide.
Probably in the future this will cross reference to Chebi.
SO:0001237
amino acid
http://en.wikipedia.org/wiki/Amino_acid
sequence
wiki
http://en.wikipedia.org/wiki/Amino_acid
A sequence feature that corresponds to a single amino acid residue in a polypeptide.
RSC:cb
major_TSS
SO:0001238
major TSS
major transcription start site
sequence
minor_TSS
SO:0001239
minor TSS
sequence
TSS_region
SO:0001240
TSS region
The region of a gene from the 5' most TSS to the 3' TSS.
sequence
BBOP:nw
The region of a gene from the 5' most TSS to the 3' TSS.
encodes_alternate_transcription_start_sites
SO:0001241
encodes alternate transcription start sites
sequence
miRNA_primary_transcript_region
A part of an miRNA primary_transcript.
SO:0001243
miRNA primary transcript region
sequence
A part of an miRNA primary_transcript.
SO:ke
pre_miRNA
SO:0001244
The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.
pre-miRNA
sequence
SO:ke
The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.
miRNA_stem
SO:0001245
The stem of the hairpin loop formed by folding of the pre-miRNA.
miRNA stem
sequence
SO:ke
The stem of the hairpin loop formed by folding of the pre-miRNA.
miRNA_loop
SO:0001246
The loop of the hairpin loop formed by folding of the pre-miRNA.
miRNA loop
sequence
SO:ke
The loop of the hairpin loop formed by folding of the pre-miRNA.
synthetic_oligo
An oligo composed of synthetic nucleotides.
SO:0001247
sequence
synthetic oligo
An oligo composed of synthetic nucleotides.
SO:ke
assembly
A region of the genome of known length that is composed by ordering and aligning two or more different regions.
SO:0001248
http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly
sequence
A region of the genome of known length that is composed by ordering and aligning two or more different regions.
SO:ke
wiki
http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly
fragment_assembly
A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths.
SO:0001249
fragment assembly
physical map
sequence
A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths.
SO:ke
fingerprint_map
A fingerprint_map is a physical map composed of restriction fragments.
BACmap
FPC
FPCmap
SO:0001250
fingerprint map
restriction map
sequence
A fingerprint_map is a physical map composed of restriction fragments.
SO:ke
STS_map
An STS map is a physical map organized by the unique STS landmarks.
SO:0001251
STS map
sequence
An STS map is a physical map organized by the unique STS landmarks.
SO:ke
RH_map
A radiation hybrid map is a physical map.
RH map
SO:0001252
radiation hybrid map
sequence
A radiation hybrid map is a physical map.
SO:ke
sonicate_fragment
A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments.
SO:0001253
sequence
sonicate fragment
A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments.
SO:ke
polyploid
A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number.
SO:0001254
http://en.wikipedia.org/wiki/Polyploid
sequence
A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number.
SO:ke
wiki
http://en.wikipedia.org/wiki/Polyploid
autopolyploid
A polyploid where the multiple chromosome set was derived from the same organism.
SO:0001255
http://en.wikipedia.org/wiki/Autopolyploid
sequence
A polyploid where the multiple chromosome set was derived from the same organism.
SO:ke
wiki
http://en.wikipedia.org/wiki/Autopolyploid
allopolyploid
A polyploid where the multiple chromosome set was derived from a different organism.
SO:0001256
http://en.wikipedia.org/wiki/Allopolyploid
sequence
wiki
http://en.wikipedia.org/wiki/Allopolyploid
A polyploid where the multiple chromosome set was derived from a different organism.
SO:ke
homing_endonuclease_binding_site
SO:0001257
The binding site (recognition site) of a homing endonuclease. The binding site is typically large.
homing endonuclease binding site
sequence
SO:ke
The binding site (recognition site) of a homing endonuclease. The binding site is typically large.
octamer_motif
A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors.
Nature. 1986 Oct 16-22;323(6089):640-3.
SO:0001258
octamer motif
sequence
A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors.
GOC:dh
PMID:3095662
apicoplast_chromosome
A chromosome originating in an apicoplast.
SO:0001259
apicoplast chromosome
sequence
A chromosome originating in an apicoplast.
SO:xp
sequence_collection
A collection of discontinuous sequences.
SO:0001260
sequence
sequence collection
A collection of discontinuous sequences.
SO:ke
overlapping_feature_set
A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature.
SO:0001261
This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA.
overlapping feature set
sequence
A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature.
SO:ke
overlapping_EST_set
A continous experimental result region extending the length of multiple overlapping EST's.
SO:0001262
overlapping EST set
sequence
A continous experimental result region extending the length of multiple overlapping EST's.
SO:ke
ncRNA_gene
SO:0001263
ncRNA gen
ncRNA gene
non-coding RNA gene
sequence
gRNA_gene
SO:0001264
gRNA gene
sequence
miRNA_gene
SO:0001265
SO:0001270
miRNA gene
sequence
stRNA gene
stRNA_gene
scRNA_gene
SO:0001266
scRNA gene
sequence
snoRNA_gene
SO:0001267
sequence
snoRNA gene
snRNA_gene
SO:0001268
sequence
snRNA gene
SRP_RNA_gene
SO:0001269
SRP RNA gene
sequence
tmRNA_gene
SO:0001271
sequence
tmRNA gene
tRNA_gene
SO:0001272
sequence
tRNA gene
modified_adenosine
A modified adenine is an adenine base feature that has been altered.
SO:0001273
modified adenosine
sequence
A modified adenine is an adenine base feature that has been altered.
SO:ke
modified_inosine
A modified inosine is an inosine base feature that has been altered.
SO:0001274
modified inosine
sequence
A modified inosine is an inosine base feature that has been altered.
SO:ke
modified_cytidine
A modified cytidine is a cytidine base feature which has been altered.
SO:0001275
modified cytidine
sequence
A modified cytidine is a cytidine base feature which has been altered.
SO:ke
modified_guanosine
SO:0001276
modified guanosine
sequence
modified_uridine
SO:0001277
modified uridine
sequence
one_methylinosine
1-methylinosine
1-methylinosine is a modified inosine.
RNAMOD:018
SO:0001278
m1I
one methylinosine
sequence
1-methylinosine is a modified inosine.
http://library.med.utah.edu/RNAmods/
m1I
one_two_prime_O_dimethylinosine
1,2'-O-dimethylinosine
1,2'-O-dimethylinosine is a modified inosine.
RNAMOD:019
SO:0001279
m'Im
one two prime O dimethylinosine
sequence
1,2'-O-dimethylinosine is a modified inosine.
http://library.med.utah.edu/RNAmods/
m'Im
two_prime_O_methylinosine
2'-O-methylinosine
2'-O-methylinosine is a modified inosine.
Im
RNAMOD:081
SO:0001280
sequence
two prime O methylinosine
Im
2'-O-methylinosine is a modified inosine.
http://library.med.utah.edu/RNAmods/
three_methylcytidine
3-methylcytidine
3-methylcytidine is a modified cytidine.
RNAMOD:020
SO:0001281
m3C
sequence
three methylcytidine
3-methylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
m3C
five_methylcytidine
5-methylcytidine
5-methylcytidine is a modified cytidine.
RNAMOD:021
SO:0001282
five methylcytidine
m5C
sequence
m5C
5-methylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
two_prime_O_methylcytidine
2'-O-methylcytidine
2'-O-methylcytidine is a modified cytidine.
Cm
RNAMOD:022
SO:0001283
sequence
two prime O methylcytidine
2'-O-methylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
Cm
two_thiocytidine
2-thiocytidine
2-thiocytidine is a modified cytidine.
RNAMOD:023
SO:0001284
s2C
sequence
two thiocytidine
s2C
2-thiocytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
N4_acetylcytidine
N4 acetylcytidine
N4-acetylcytidine
N4-acetylcytidine is a modified cytidine.
RNAMOD:024
SO:0001285
ac4C
sequence
N4-acetylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
ac4C
five_formylcytidine
5-formylcytidine
5-formylcytidine is a modified cytidine.
RNAMOD:025
SO:0001286
f5C
five formylcytidine
sequence
f5C
5-formylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
five_two_prime_O_dimethylcytidine
5,2'-O-dimethylcytidine
5,2'-O-dimethylcytidine is a modified cytidine.
RNAMOD:026
SO:0001287
five two prime O dimethylcytidine
m5Cm
sequence
m5Cm
5,2'-O-dimethylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
N4_acetyl_2_prime_O_methylcytidine
N4 acetyl 2 prime O methylcytidine
N4-acetyl-2'-O-methylcytidine
N4-acetyl-2'-O-methylcytidine is a modified cytidine.
RNAMOD:027
SO:0001288
ac4Cm
sequence
N4-acetyl-2'-O-methylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
ac4Cm
lysidine
Lysidine is a modified cytidine.
RNAMOD:028
SO:0001289
http://en.wikipedia.org/wiki/Lysidine
k2C
sequence
wiki
http://en.wikipedia.org/wiki/Lysidine
Lysidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
k2C
N4_methylcytidine
N4 methylcytidine
N4-methylcytidine
N4-methylcytidine is a modified cytidine.
RNAMOD:082
SO:0001290
m4C
sequence
m4C
N4-methylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
N4_2_prime_O_dimethylcytidine
N4 2 prime O dimethylcytidine
N4,2'-O-dimethylcytidine
N4,2'-O-dimethylcytidine is a modified cytidine.
RNAMOD:083
SO:0001291
m4Cm
sequence
m4Cm
N4,2'-O-dimethylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
five_hydroxymethylcytidine
5-hydroxymethylcytidine
5-hydroxymethylcytidine is a modified cytidine.
RNAMOD:084
SO:0001292
five hydroxymethylcytidine
hm5C
sequence
hm5C
5-hydroxymethylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
five_formyl_two_prime_O_methylcytidine
5-formyl-2'-O-methylcytidine
5-formyl-2'-O-methylcytidine is a modified cytidine.
RNAMOD:095
SO:0001293
f5Cm
five formyl two prime O methylcytidine
sequence
5-formyl-2'-O-methylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
f5Cm
N4_N4_2_prime_O_trimethylcytidine
N4,N4,2'-O-trimethylcytidine
N4_N4_2_prime_O_trimethylcytidine is a modified cytidine.
RNAMOD:107
SO:0001294
m42Cm
sequence
N4_N4_2_prime_O_trimethylcytidine is a modified cytidine.
http://library.med.utah.edu/RNAmods/
m42Cm
one_methyladenosine
1-methyladenosine
1_methyladenosine is a modified adenosine.
RNAMOD:001
SO:0001295
m1A
one methyladenosine
sequence
m1A
1_methyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
two_methyladenosine
2-methyladenosine
2_methyladenosine is a modified adenosine.
RNAMOD:002
SO:0001296
m2A
sequence
two methyladenosine
m2A
2_methyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
N6_methyladenosine
N6 methyladenosine
N6-methyladenosine
N6_methyladenosine is a modified adenosine.
RNAMOD:003
SO:0001297
m6A
sequence
m6A
N6_methyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
two_prime_O_methyladenosine
2'-O-methyladenosine
2prime_O_methyladenosine is a modified adenosine.
Am
RNAMOD:004
SO:0001298
sequence
two prime O methyladenosine
2prime_O_methyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
Am
two_methylthio_N6_methyladenosine
2-methylthio-N6-methyladenosine
2_methylthio_N6_methyladenosine is a modified adenosine.
RNAMOD:005
SO:0001299
ms2m6A
sequence
two methylthio N6 methyladenosine
ms2m6A
2_methylthio_N6_methyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
N6_isopentenyladenosine
N6 isopentenyladenosine
N6-isopentenyladenosine
N6_isopentenyladenosine is a modified adenosine.
RNAMOD:006
SO:0001300
i6A
sequence
N6_isopentenyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
i6A
two_methylthio_N6_isopentenyladenosine
2-methylthio-N6-isopentenyladenosine
2_methylthio_N6_isopentenyladenosine is a modified adenosine.
RNAMOD:007
SO:0001301
ms2i6A
sequence
two methylthio N6 isopentenyladenosine
2_methylthio_N6_isopentenyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
ms2i6A
N6_cis_hydroxyisopentenyl_adenosine
N6 cis hydroxyisopentenyl adenosine
N6-(cis-hydroxyisopentenyl)adenosine
N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.
RNAMOD:008
SO:0001302
io6A
sequence
N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
io6A
two_methylthio_N6_cis_hydroxyisopentenyl_adenosine
2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine
2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.
RNAMOD:009
SO:0001303
ms2io6A
sequence
two methylthio N6 cis hydroxyisopentenyl adenosine
ms2io6A
2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
N6_glycinylcarbamoyladenosine
N6 glycinylcarbamoyladenosine
N6-glycinylcarbamoyladenosine
N6_glycinylcarbamoyladenosine is a modified adenosine.
RNAMOD:010
SO:0001304
g6A
sequence
g6A
N6_glycinylcarbamoyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
N6_threonylcarbamoyladenosine
N6 threonylcarbamoyladenosine
N6-threonylcarbamoyladenosine
N6_threonylcarbamoyladenosine is a modified adenosine.
RNAMOD:011
SO:0001305
sequence
t6A
t6A
N6_threonylcarbamoyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
two_methylthio_N6_threonyl_carbamoyladenosine
2-methylthio-N6-threonyl carbamoyladenosine
2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine.
RNAMOD:012
SO:0001306
ms2t6A
sequence
two methylthio N6 threonyl carbamoyladenosine
2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
ms2t6A
N6_methyl_N6_threonylcarbamoyladenosine
N6 methyl N6 threonylcarbamoyladenosine
N6-methyl-N6-threonylcarbamoyladenosine
N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine.
RNAMOD:013
SO:0001307
m6t6A
sequence
m6t6A
N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
N6_hydroxynorvalylcarbamoyladenosine
N6 hydroxynorvalylcarbamoyladenosine
N6-hydroxynorvalylcarbamoyladenosine
N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine.
RNAMOD:014
SO:0001308
hn6A
sequence
N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
hn6A
two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine
2-methylthio-N6-hydroxynorvalyl carbamoyladenosine
2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine.
RNAMOD:015
SO:0001309
ms2hn6A
sequence
two methylthio N6 hydroxynorvalyl carbamoyladenosine
2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
ms2hn6A
two_prime_O_ribosyladenosine_phosphate
2'-O-ribosyladenosine (phosphate)
2prime_O_ribosyladenosine_phosphate is a modified adenosine.
Ar(p)
RNAMOD:016
SO:0001310
sequence
two prime O ribosyladenosine phosphate
2prime_O_ribosyladenosine_phosphate is a modified adenosine.
http://library.med.utah.edu/RNAmods/
Ar(p)
N6_N6_dimethyladenosine
N6,N6-dimethyladenosine
N6_N6_dimethyladenosine is a modified adenosine.
RNAMOD:080
SO:0001311
m62A
sequence
m62A
N6_N6_dimethyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
N6_2_prime_O_dimethyladenosine
N6 2 prime O dimethyladenosine
N6,2'-O-dimethyladenosine
N6_2prime_O_dimethyladenosine is a modified adenosine.
RNAMOD:088
SO:0001312
m6Am
sequence
N6_2prime_O_dimethyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
m6Am
N6_N6_2_prime_O_trimethyladenosine
N6,N6,2'-O-trimethyladenosine
N6_N6_2prime_O_trimethyladenosine is a modified adenosine.
RNAMOD:089
SO:0001313
m62Am
sequence
m62Am
N6_N6_2prime_O_trimethyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
one_two_prime_O_dimethyladenosine
1,2'-O-dimethyladenosine
1,2'-O-dimethyladenosine is a modified adenosine.
RNAMOD:097
SO:0001314
m1Am
one two prime O dimethyladenosine
sequence
m1Am
1,2'-O-dimethyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
N6_acetyladenosine
N6 acetyladenosine
N6-acetyladenosine
N6_acetyladenosine is a modified adenosine.
RNAMOD:102
SO:0001315
ac6A
sequence
N6_acetyladenosine is a modified adenosine.
http://library.med.utah.edu/RNAmods/
ac6A
seven_deazaguanosine
7-deazaguanosine
7-deazaguanosine is a modified guanosine.
SO:0001316
sequence
seven deazaguanosine
7-deazaguanosine is a modified guanosine.
http://library.med.utah.edu/RNAmods/
queuosine
Q
Queuosine is a modified 7-deazoguanosine.
RNAMOD:043
SO:0001317
http://en.wikipedia.org/wiki/Queuosine
sequence
wiki
http://en.wikipedia.org/wiki/Queuosine
Q
Queuosine is a modified 7-deazoguanosine.
http://library.med.utah.edu/RNAmods/
epoxyqueuosine
Epoxyqueuosine is a modified 7-deazoguanosine.
RNAMOD:044
SO:0001318
eQ
sequence
eQ
Epoxyqueuosine is a modified 7-deazoguanosine.
http://library.med.utah.edu/RNAmods/
galactosyl_queuosine
Galactosyl_queuosine is a modified 7-deazoguanosine.
RNAMOD:045
SO:0001319
galQ
galactosyl queuosine
galactosyl-queuosine
sequence
galQ
Galactosyl_queuosine is a modified 7-deazoguanosine.
http://library.med.utah.edu/RNAmods/
mannosyl_queuosine
Mannosyl_queuosine is a modified 7-deazoguanosine.
RNAMOD:046
SO:0001320
manQ
mannosyl queuosine
mannosyl-queuosine
sequence
manQ
Mannosyl_queuosine is a modified 7-deazoguanosine.
http://library.med.utah.edu/RNAmods/
seven_cyano_seven_deazaguanosine
7-cyano-7-deazaguanosine
7_cyano_7_deazaguanosine is a modified 7-deazoguanosine.
RNAMOD:047
SO:0001321
preQ0
sequence
seven cyano seven deazaguanosine
preQ0
7_cyano_7_deazaguanosine is a modified 7-deazoguanosine.
http://library.med.utah.edu/RNAmods/
seven_aminomethyl_seven_deazaguanosine
7-aminomethyl-7-deazaguanosine
7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine.
RNAMOD:048
SO:0001322
preQ1
sequence
seven aminomethyl seven deazaguanosine
preQ1
7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine.
http://library.med.utah.edu/RNAmods/
archaeosine
Archaeosine is a modified 7-deazoguanosine.
G+
RNAMOD:049
SO:0001323
sequence
Archaeosine is a modified 7-deazoguanosine.
http://library.med.utah.edu/RNAmods/
G+
one_methylguanosine
1-methylguanosine
1_methylguanosine is a modified guanosine base feature.
RNAMOD:029
SO:0001324
m1G
one methylguanosine
sequence
1_methylguanosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
m1G
N2_methylguanosine
N2 methylguanosine
N2-methylguanosine
N2_methylguanosine is a modified guanosine base feature.
RNAMOD:030
SO:0001325
m2G
sequence
N2_methylguanosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
m2G
seven_methylguanosine
7-methylguanosine
7_methylguanosine is a modified guanosine base feature.
RNAMOD:031
SO:0001326
m7G
sequence
seven methylguanosine
m7G
7_methylguanosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
two_prime_O_methylguanosine
2'-O-methylguanosine
2prime_O_methylguanosine is a modified guanosine base feature.
Gm
RNAMOD:032
SO:0001327
sequence
two prime O methylguanosine
Gm
2prime_O_methylguanosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
N2_N2_dimethylguanosine
N2,N2-dimethylguanosine
N2_N2_dimethylguanosine is a modified guanosine base feature.
RNAMOD:033
SO:0001328
m22G
sequence
N2_N2_dimethylguanosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
m22G
N2_2_prime_O_dimethylguanosine
N2 2 prime O dimethylguanosine
N2,2'-O-dimethylguanosine
N2_2prime_O_dimethylguanosine is a modified guanosine base feature.
RNAMOD:034
SO:0001329
m2Gm
sequence
m2Gm
N2_2prime_O_dimethylguanosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
N2_N2_2_prime_O_trimethylguanosine
N2,N2,2'-O-trimethylguanosine
N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature.
RNAMOD:035
SO:0001330
m22Gmv
sequence
m22Gmv
N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
two_prime_O_ribosylguanosine_phosphate
2'-O-ribosylguanosine (phosphate)
2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature.
Gr(p)
RNAMOD:036
SO:0001331
sequence
two prime O ribosylguanosine phosphate
2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
Gr(p)
wybutosine
RNAMOD:037
SO:0001332
Wybutosine is a modified guanosine base feature.
sequence
yW
yW
Wybutosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
peroxywybutosine
Peroxywybutosine is a modified guanosine base feature.
RNAMOD:038
SO:0001333
o2yW
sequence
Peroxywybutosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
o2yW
hydroxywybutosine
Hydroxywybutosine is a modified guanosine base feature.
OHyW
RNAMOD:039
SO:0001334
sequence
Hydroxywybutosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
OHyW
undermodified_hydroxywybutosine
OHyW*
RNAMOD:040
SO:0001335
Undermodified_hydroxywybutosine is a modified guanosine base feature.
sequence
undermodified hydroxywybutosine
OHyW*
Undermodified_hydroxywybutosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
wyosine
IMG
RNAMOD:041
SO:0001336
Wyosine is a modified guanosine base feature.
sequence
IMG
Wyosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
methylwyosine
Methylwyosine is a modified guanosine base feature.
RNAMOD:042
SO:0001337
mimG
sequence
mimG
Methylwyosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
N2_7_dimethylguanosine
N2 7 dimethylguanosine
N2,7-dimethylguanosine
N2_7_dimethylguanosine is a modified guanosine base feature.
RNAMOD:090
SO:0001338
m2,7G
sequence
m2,7G
N2_7_dimethylguanosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
N2_N2_7_trimethylguanosine
N2,N2,7-trimethylguanosine
N2_N2_7_trimethylguanosine is a modified guanosine base feature.
RNAMOD:091
SO:0001339
m2,2,7G
sequence
m2,2,7G
N2_N2_7_trimethylguanosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
one_two_prime_O_dimethylguanosine
1,2'-O-dimethylguanosine
1_2prime_O_dimethylguanosine is a modified guanosine base feature.
RNAMOD:096
SO:0001340
m1Gm
one two prime O dimethylguanosine
sequence
1_2prime_O_dimethylguanosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
m1Gm
four_demethylwyosine
4-demethylwyosine
4_demethylwyosine is a modified guanosine base feature.
RNAMOD:100
SO:0001341
four demethylwyosine
imG-14
sequence
imG-14
4_demethylwyosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
isowyosine
Isowyosine is a modified guanosine base feature.
RNAMOD:101
SO:0001342
imG2
sequence
Isowyosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
imG2
N2_7_2prirme_O_trimethylguanosine
N2 7 2prirme O trimethylguanosine
N2,7,2'-O-trimethylguanosine
N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature.
RNAMOD:106
SO:0001343
m2,7Gm
sequence
m2,7Gm
N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature.
http://library.med.utah.edu/RNAmods/
five_methyluridine
5-methyluridine
5_methyluridine is a modified uridine base feature.
RNAMOD:052
SO:0001344
five methyluridine
http://en.wikipedia.org/wiki/5-methyluridine
m5U
sequence
m5U
wiki
http://en.wikipedia.org/wiki/5-methyluridine
5_methyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
two_prime_O_methyluridine
2'-O-methyluridine
2prime_O_methyluridine is a modified uridine base feature.
RNAMOD:053
SO:0001345
Um
sequence
two prime O methyluridine
2prime_O_methyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
Um
five_two_prime_O_dimethyluridine
5,2'-O-dimethyluridine
5_2_prime_O_dimethyluridine is a modified uridine base feature.
RNAMOD:054
SO:0001346
five two prime O dimethyluridine
m5Um
sequence
5_2_prime_O_dimethyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
m5Um
one_methylpseudouridine
1-methylpseudouridine
1_methylpseudouridine is a modified uridine base feature.
RNAMOD:055
SO:0001347
m1Y
one methylpseudouridine
sequence
1_methylpseudouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
m1Y
two_prime_O_methylpseudouridine
2'-O-methylpseudouridine
2prime_O_methylpseudouridine is a modified uridine base feature.
RNAMOD:056
SO:0001348
Ym
sequence
two prime O methylpseudouridine
Ym
2prime_O_methylpseudouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
two_thiouridine
2-thiouridine
2_thiouridine is a modified uridine base feature.
RNAMOD:057
SO:0001349
s2U
sequence
two thiouridine
2_thiouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
s2U
four_thiouridine
4-thiouridine
4_thiouridine is a modified uridine base feature.
RNAMOD:058
SO:0001350
four thiouridine
s4U
sequence
s4U
4_thiouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_methyl_2_thiouridine
5-methyl-2-thiouridine
5_methyl_2_thiouridine is a modified uridine base feature.
RNAMOD:059
SO:0001351
five methyl 2 thiouridine
m5s2U
sequence
m5s2U
5_methyl_2_thiouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
two_thio_two_prime_O_methyluridine
2-thio-2'-O-methyluridine
2_thio_2prime_O_methyluridine is a modified uridine base feature.
RNAMOD:060
SO:0001352
s2Um
sequence
two thio two prime O methyluridine
s2Um
2_thio_2prime_O_methyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
three_three_amino_three_carboxypropyl_uridine
3-(3-amino-3-carboxypropyl)uridine
3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature.
RNAMOD:061
SO:0001353
acp3U
sequence
acp3U
3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_hydroxyuridine
5-hydroxyuridine
5_hydroxyuridine is a modified uridine base feature.
RNAMOD:060
SO:0001354
five hydroxyuridine
ho5U
sequence
ho5U
5_hydroxyuridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_methoxyuridine
5-methoxyuridine
5_methoxyuridine is a modified uridine base feature.
RNAMOD:063
SO:0001355
five methoxyuridine
mo5U
sequence
5_methoxyuridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
mo5U
uridine_five_oxyacetic_acid
RNAMOD:064
SO:0001356
Uridine_5_oxyacetic_acid is a modified uridine base feature.
cmo5U
sequence
uridine 5-oxyacetic acid
uridine five oxyacetic acid
cmo5U
Uridine_5_oxyacetic_acid is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
uridine_five_oxyacetic_acid_methyl_ester
RNAMOD:065
SO:0001357
Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature.
mcmo5U
sequence
uridine 5-oxyacetic acid methyl ester
uridine five oxyacetic acid methyl ester
mcmo5U
Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_carboxyhydroxymethyl_uridine
5-(carboxyhydroxymethyl)uridine
5_carboxyhydroxymethyl_uridine is a modified uridine base feature.
RNAMOD:066
SO:0001358
chm5U
five carboxyhydroxymethyl uridine
sequence
5_carboxyhydroxymethyl_uridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
chm5U
five_carboxyhydroxymethyl_uridine_methyl_ester
5-(carboxyhydroxymethyl)uridine methyl ester
5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature.
RNAMOD:067
SO:0001359
five carboxyhydroxymethyl uridine methyl ester
mchm5U
sequence
mchm5U
5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_methoxycarbonylmethyluridine
5-methoxycarbonylmethyluridine
Five_methoxycarbonylmethyluridine is a modified uridine base feature.
RNAMOD:068
SO:0001360
five methoxycarbonylmethyluridine
mcm5U
sequence
mcm5U
Five_methoxycarbonylmethyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_methoxycarbonylmethyl_two_prime_O_methyluridine
5-methoxycarbonylmethyl-2'-O-methyluridine
Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature.
RNAMOD:069
SO:0001361
five methoxycarbonylmethyl two prime O methyluridine
mcm5Um
sequence
Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
mcm5Um
five_methoxycarbonylmethyl_two_thiouridine
5-methoxycarbonylmethyl-2-thiouridine
5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature.
RNAMOD:070
SO:0001362
five methoxycarbonylmethyl two thiouridine
mcm5s2U
sequence
mcm5s2U
5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_aminomethyl_two_thiouridine
5-aminomethyl-2-thiouridine
5_aminomethyl_2_thiouridine is a modified uridine base feature.
RNAMOD:071
SO:0001363
five aminomethyl two thiouridine
nm5s2U
sequence
nm5s2U
5_aminomethyl_2_thiouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_methylaminomethyluridine
5-methylaminomethyluridine
5_methylaminomethyluridine is a modified uridine base feature.
RNAMOD:072
SO:0001364
five methylaminomethyluridine
mnm5U
sequence
5_methylaminomethyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
mnm5U
five_methylaminomethyl_two_thiouridine
5-methylaminomethyl-2-thiouridine
5_methylaminomethyl_2_thiouridine is a modified uridine base feature.
RNAMOD:073
SO:0001365
five methylaminomethyl two thiouridine
mnm5s2U
sequence
5_methylaminomethyl_2_thiouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
mnm5s2U
five_methylaminomethyl_two_selenouridine
5-methylaminomethyl-2-selenouridine
5_methylaminomethyl_2_selenouridine is a modified uridine base feature.
RNAMOD:074
SO:0001366
five methylaminomethyl two selenouridine
mnm5se2U
sequence
5_methylaminomethyl_2_selenouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
mnm5se2U
five_carbamoylmethyluridine
5-carbamoylmethyluridine
5_carbamoylmethyluridine is a modified uridine base feature.
RNAMOD:075
SO:0001367
five carbamoylmethyluridine
ncm5U
sequence
5_carbamoylmethyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
ncm5U
five_carbamoylmethyl_two_prime_O_methyluridine
5-carbamoylmethyl-2'-O-methyluridine
5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature.
RNAMOD:076
SO:0001368
five carbamoylmethyl two prime O methyluridine
ncm5Um
sequence
5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
ncm5Um
five_carboxymethylaminomethyluridine
5-carboxymethylaminomethyluridine
5_carboxymethylaminomethyluridine is a modified uridine base feature.
RNAMOD:077
SO:0001369
cmnm5U
five carboxymethylaminomethyluridine
sequence
cmnm5U
5_carboxymethylaminomethyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_carboxymethylaminomethyl_two_prime_O_methyluridine
5-carboxymethylaminomethyl- 2'-O-methyluridine
5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature.
RNAMOD:078
SO:0001370
cmnm5Um
five carboxymethylaminomethyl two prime O methyluridine
sequence
5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
cmnm5Um
five_carboxymethylaminomethyl_two_thiouridine
5-carboxymethylaminomethyl-2-thiouridine
5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature.
RNAMOD:079
SO:0001371
cmnm5s2U
five carboxymethylaminomethyl two thiouridine
sequence
cmnm5s2U
5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
three_methyluridine
3-methyluridine
3_methyluridine is a modified uridine base feature.
RNAMOD:085
SO:0001372
m3U
sequence
three methyluridine
m3U
3_methyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
one_methyl_three_three_amino_three_carboxypropyl_pseudouridine
1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine
1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature.
RNAMOD:086
SO:0001373
m1acp3Y
sequence
m1acp3Y
1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_carboxymethyluridine
5-carboxymethyluridine
5_carboxymethyluridine is a modified uridine base feature.
RNAMOD:087
SO:0001374
cm5U
five carboxymethyluridine
sequence
5_carboxymethyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
cm5U
three_two_prime_O_dimethyluridine
3,2'-O-dimethyluridine
3_2prime_O_dimethyluridine is a modified uridine base feature.
RNAMOD:092
SO:0001375
m3Um
sequence
three two prime O dimethyluridine
m3Um
3_2prime_O_dimethyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_methyldihydrouridine
5-methyldihydrouridine
5_methyldihydrouridine is a modified uridine base feature.
RNAMOD:093
SO:0001376
five methyldihydrouridine
m5D
sequence
5_methyldihydrouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
m5D
three_methylpseudouridine
3-methylpseudouridine
3_methylpseudouridine is a modified uridine base feature.
RNAMOD:094
SO:0001377
m3Y
sequence
three methylpseudouridine
m3Y
3_methylpseudouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_taurinomethyluridine
5-taurinomethyluridine
5_taurinomethyluridine is a modified uridine base feature.
RNAMOD:098
SO:0001378
five taurinomethyluridine
sequence
tm5U
5_taurinomethyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
tm5U
five_taurinomethyl_two_thiouridine
5-taurinomethyl-2-thiouridine
5_taurinomethyl_2_thiouridineis a modified uridine base feature.
RNAMOD:099
SO:0001379
five taurinomethyl two thiouridine
sequence
tm5s2U
tm5s2U
5_taurinomethyl_2_thiouridineis a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_isopentenylaminomethyl_uridine
5-(isopentenylaminomethyl)uridine
5_isopentenylaminomethyl_uridine is a modified uridine base feature.
RNAMOD:103
SO:0001380
five isopentenylaminomethyl uridine
inm5U
sequence
5_isopentenylaminomethyl_uridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
inm5U
five_isopentenylaminomethyl_two_thiouridine
5-(isopentenylaminomethyl)- 2-thiouridine
5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature.
RNAMOD:104
SO:0001381
five isopentenylaminomethyl two thiouridine
inm5s2U
sequence
inm5s2U
5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
five_isopentenylaminomethyl_two_prime_O_methyluridine
5-(isopentenylaminomethyl)- 2'-O-methyluridine
5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature.
RNAMOD:105
SO:0001382
five isopentenylaminomethyl two prime O methyluridine
inm5Um
sequence
inm5Um
5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature.
http://library.med.utah.edu/RNAmods/
histone_binding_site
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone.
SO:0001383
histone binding site
sequence
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone.
SO:ke
CDS_fragment
CDS fragment
SO:0001384
incomplete CDS
sequence
modified_amino_acid_feature
A post translationally modified amino acid feature.
SO:0001385
modified amino acid feature
sequence
A post translationally modified amino acid feature.
SO:ke
modified_glycine
A post translationally modified glycine amino acid feature.
MOD:00908
ModGly
SO:0001386
modified glycine
sequence
ModGly
A post translationally modified glycine amino acid feature.
SO:ke
modified_L_alanine
A post translationally modified alanine amino acid feature.
MOD:00901
ModAla
SO:0001387
modified L alanine
modified L-alanine
sequence
ModAla
A post translationally modified alanine amino acid feature.
SO:ke
modified_L_asparagine
A post translationally modified asparagine amino acid feature.
MOD:00903
ModAsn
SO:0001388
modified L asparagine
modified L-asparagine
sequence
ModAsn
A post translationally modified asparagine amino acid feature.
SO:ke
modified_L_aspartic_acid
A post translationally modified aspartic acid amino acid feature.
MOD:00904
ModAsp
SO:0001389
modified L aspartic acid
modified L-aspartic acid
sequence
ModAsp
A post translationally modified aspartic acid amino acid feature.
SO:ke
modified_L_cysteine
A post translationally modified cysteine amino acid feature.
MOD:00905
ModCys
SO:0001390
modified L cysteine
modified L-cysteine
sequence
A post translationally modified cysteine amino acid feature.
SO:ke
ModCys
modified_L_glutamic_acid
MOD:00906
ModGlu
SO:0001391
modified L glutamic acid
modified L-glutamic acid
sequence
ModGlu
modified_L_threonine
A post translationally modified threonine amino acid feature.
MOD:00917
ModThr
SO:0001392
modified L threonine
modified L-threonine
sequence
A post translationally modified threonine amino acid feature.
SO:ke
ModThr
modified_L_tryptophan
A post translationally modified tryptophan amino acid feature.
MOD:00918
ModTrp
SO:0001393
modified L tryptophan
modified L-tryptophan
sequence
A post translationally modified tryptophan amino acid feature.
SO:ke
ModTrp
modified_L_glutamine
A post translationally modified glutamine amino acid feature.
MOD:00907
ModGln
SO:0001394
modified L glutamine
modified L-glutamine
sequence
A post translationally modified glutamine amino acid feature.
SO:ke
modified_L_methionine
A post translationally modified methionine amino acid feature.
MOD:00913
ModMet
SO:0001395
modified L methionine
modified L-methionine
sequence
A post translationally modified methionine amino acid feature.
SO:ke
ModMet
modified_L_isoleucine
A post translationally modified isoleucine amino acid feature.
MOD:00910
ModIle
SO:0001396
modified L isoleucine
modified L-isoleucine
sequence
ModIle
A post translationally modified isoleucine amino acid feature.
SO:ke
modified_L_phenylalanine
A post translationally modified phenylalanine amino acid feature.
MOD:00914
ModPhe
SO:0001397
modified L phenylalanine
modified L-phenylalanine
sequence
ModPhe
A post translationally modified phenylalanine amino acid feature.
SO:ke
modified_L_histidine
A post translationally modified histidine amino acid feature.
MOD:00909
ModHis
SO:0001398
modified L histidine
modified L-histidine
sequence
A post translationally modified histidine amino acid feature.
SO:ke
modified_L_serine
A post translationally modified serine amino acid feature.
MOD:00916
MosSer
SO:0001399
modified L serine
modified L-serine
sequence
MosSer
A post translationally modified serine amino acid feature.
SO:ke
http://www.psidev.info/index.php?q=node/104
MOD:00916
modified_L_lysine
A post translationally modified lysine amino acid feature.
MOD:00912
ModLys
SO:0001400
modified L lysine
modified L-lysine
sequence
ModLys
A post translationally modified lysine amino acid feature.
SO:ke
modified_L_leucine
A post translationally modified leucine amino acid feature.
MOD:00911
ModLeu
SO:0001401
modified L leucine
modified L-leucine
sequence
A post translationally modified leucine amino acid feature.
SO:ke
ModLeu
modified_L_selenocysteine
A post translationally modified selenocysteine amino acid feature.
MOD:01158
SO:0001402
modified L selenocysteine
modified L-selenocysteine
sequence
A post translationally modified selenocysteine amino acid feature.
SO:ke
modified_L_valine
A post translationally modified valine amino acid feature.
MOD:00920
ModVal
SO:0001403
modified L valine
modified L-valine
sequence
ModVal
A post translationally modified valine amino acid feature.
SO:ke
modified_L_proline
A post translationally modified proline amino acid feature.
MOD:00915
ModPro
SO:0001404
modified L proline
modified L-proline
sequence
ModPro
A post translationally modified proline amino acid feature.
SO:ke
modified_L_tyrosine
A post translationally modified tyrosine amino acid feature.
MOD:00919
ModTry
SO:0001405
modified L tyrosine
modified L-tyrosine
sequence
A post translationally modified tyrosine amino acid feature.
SO:ke
ModTry
modified_L_arginine
A post translationally modified arginine amino acid feature.
MOD:00902
ModArg
SO:0001406
modified L arginine
modified L-arginine
sequence
A post translationally modified arginine amino acid feature.
SO:ke
ModArg
peptidyl
An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds.
SO:0001407
sequence
An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds.
SO:ke
cleaved_for_gpi_anchor_region
SO:0001408
The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor.
cleaved for gpi anchor region
sequence
EBI:rh
The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor.
biomaterial_region
A region which is intended for use in an experiment.
SO:0001409
biomaterial region
sequence
A region which is intended for use in an experiment.
SO:cb
experimental_feature
A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
SO:0001410
analysis feature
experimental output artefact
experimental_output_artefact
sequence
A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
SO:cb
biological_region
A region defined by its disposition to be involved in a biological process.
SO:0001411
biological region
sequence
A region defined by its disposition to be involved in a biological process.
SO:cb
topologically_defined_region
A region that is defined according to its relations with other regions within the same sequence.
SO:0001412
sequence
topologically defined region
A region that is defined according to its relations with other regions within the same sequence.
SO:cb
translocation_breakpoint
SO:0001413
The point within a chromosome where a translocation begins or ends.
sequence
translocation breakpoint
SO:cb
The point within a chromosome where a translocation begins or ends.
insertion_breakpoint
SO:0001414
The point within a chromosome where a insertion begins or ends.
insertion breakpoint
sequence
SO:cb
The point within a chromosome where a insertion begins or ends.
deletion_breakpoint
SO:0001415
The point within a chromosome where a deletion begins or ends.
deletion breakpoint
sequence
SO:cb
The point within a chromosome where a deletion begins or ends.
five_prime_flanking_region
5' flanking region
A flanking region located five prime of a specific region.
SO:0001416
five prime flanking region
sequence
A flanking region located five prime of a specific region.
SO:chado
three_prime_flanking_region
3' flanking region
A flanking region located three prime of a specific region.
SO:0001417
sequence
three prime flanking region
A flanking region located three prime of a specific region.
SO:chado
transcribed_fragment
An experimental region, defined by a tiling array experiment to be transcribed at some level.
SO:0001418
Term requested by the MODencode group.
sequence
transcribed fragment
transfrag
An experimental region, defined by a tiling array experiment to be transcribed at some level.
SO:ke
cis_splice_site
Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
SO:0001419
cis splice site
sequence
Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron.
SO:cjm
SO:ke
trans_splice_site
Primary transcript region bordering trans-splice junction.
SO:0001420
sequence
trans splice site
Primary transcript region bordering trans-splice junction.
SO:ke
splice_junction
SO:0001421
The boundary between an intron and an exon.
sequence
splice boundary
splice junction
SO:ke
The boundary between an intron and an exon.
conformational_switch
A region of a polypeptide, involved in the transition from one conformational state to another.
MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999.
SO:0001422
polypeptide conformational switch
sequence
A region of a polypeptide, involved in the transition from one conformational state to another.
SO:ke
dye_terminator_read
A read produced by the dye terminator method of sequencing.
SO:0001423
dye terminator read
sequence
A read produced by the dye terminator method of sequencing.
SO:ke
pyrosequenced_read
A read produced by pyrosequencing technology.
An example is a read produced by Roche 454 technology.
SO:0001424
pyorsequenced read
sequence
A read produced by pyrosequencing technology.
SO:ke
ligation_based_read
A read produced by ligation based sequencing technologies.
An example of this kind of read is one produced by ABI SOLiD.
SO:0001425
ligation based read
sequence
A read produced by ligation based sequencing technologies.
SO:ke
polymerase_synthesis_read
A read produced by the polymerase based sequence by synthesis method.
An example is a read produced by Illumina technology.
SO:0001426
polymerase synthesis read
sequence
A read produced by the polymerase based sequence by synthesis method.
SO:ke
cis_regulatory_frameshift_element
A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence.
SO:0001427
cis regulatory frameshift element
sequence
A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence.
RFAM:jd
expressed_sequence_assembly
A sequence assembly derived from expressed sequences.
From tracker [ 2372385 ] expressed_sequence_assembly.
SO:0001428
expressed sequence assembly
sequence
A sequence assembly derived from expressed sequences.
SO:ke
DNA_binding_site
A binding site that, in the molecule, interacts selectively and non-covalently with DNA.
DNA binding site
SO:0001429
sequence
A binding site that, in the molecule, interacts selectively and non-covalently with DNA.
SO:ke
cryptic_gene
A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.
SO:0001431
cryptic gene
sequence
A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.
SO:ke
sequence_variant_affecting_polyadenylation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001432
SO:0001545
mutation affecting polyadenylation
sequence
sequence variant affecting polyadenylation
true
three_prime_RACE_clone
3' RACE clone
A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host.
SO:0001433
sequence
A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host.
modENCODE:nlw
cassette_pseudogene
A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy.
Requested by the Trypanosome community.
SO:0001434
cassette pseudogene
cassette type psedogene
sequence
A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy.
SO:ke
alanine
A
A place holder for a cross product with chebi.
Ala
SO:0001435
sequence
A
Ala
valine
A place holder for a cross product with chebi.
SO:0001436
V
Val
sequence
V
Val
leucine
A place holder for a cross product with chebi.
L
Leu
SO:0001437
sequence
Leu
L
isoleucine
A place holder for a cross product with chebi.
I
Ile
SO:0001438
sequence
I
Ile
proline
A place holder for a cross product with chebi.
P
Pro
SO:0001439
sequence
P
Pro
tryptophan
A place holder for a cross product with chebi.
SO:0001440
Trp
W
sequence
W
Trp
phenylalanine
A place holder for a cross product with chebi.
F
Phe
SO:0001441
sequence
Phe
F
methionine
A place holder for a cross product with chebi.
M
Met
SO:0001442
sequence
Met
M
glycine
A place holder for a cross product with chebi.
G
Gly
SO:0001443
sequence
G
Gly
serine
A place holder for a cross product with chebi.
S
SO:0001444
Ser
sequence
Ser
S
threonine
A place holder for a cross product with chebi.
SO:0001445
T
Thr
sequence
Thr
T
tyrosine
A place holder for a cross product with chebi.
SO:0001446
Tyr
Y
sequence
Y
Tyr
cysteine
A place holder for a cross product with chebi.
C
Cys
SO:0001447
sequence
C
Cys
glutamine
A place holder for a cross product with chebi.
Gln
Q
SO:0001448
sequence
Gln
Q
asparagine
A place holder for a cross product with chebi.
Asn
N
SO:0001449
sequence
Asn
N
lysine
A place holder for a cross product with chebi.
K
Lys
SO:0001450
sequence
K
Lys
arginine
A place holder for a cross product with chebi.
Arg
R
SO:0001451
sequence
R
Arg
histidine
A place holder for a cross product with chebi.
H
His
SO:0001452
sequence
His
H
aspartic_acid
A place holder for a cross product with chebi.
Asp
D
SO:0001453
aspartic acid
sequence
Asp
D
glutamic_acid
A place holder for a cross product with chebi.
E
Glu
SO:0001454
glutamic acid
sequence
Glu
E
selenocysteine
A place holder for a cross product with chebi.
SO:0001455
Sec
U
sequence
Sec
U
pyrrolysine
A place holder for a cross product with chebi.
O
Pyl
SO:0001456
sequence
O
Pyl
transcribed_cluster
A region defined by a set of transcribed sequences from the same gene or expressed pseudogene.
SO:0001457
This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
sequence
transcribed cluster
unigene cluster
A region defined by a set of transcribed sequences from the same gene or expressed pseudogene.
SO:ke
unigene_cluster
A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene.
SO:0001458
This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
sequence
unigene cluster
A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene.
SO:ke
CRISPR
CRISPR element
Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences.
Clustered_Regularly_Interspaced_Short_Palindromic_Repeat
SO:0001459
http:en.wikipedia.org/wiki/CRISPR
sequence
Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences.
RFAM:jd
insulator_binding_site
A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
SO:0001460
See tracker ID 2060908.
insulator binding site
sequence
A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
SO:ke
enhancer_binding_site
A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
SO:0001461
enhancer binding site
sequence
A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
SO:ke
contig_collection
A collection of contigs.
SO:0001462
See tracker ID: 2138359.
contig collection
sequence
A collection of contigs.
SO:ke
lincRNA
A multiexonic non-coding RNA transcribed by RNA polymerase II.
SO:0001463
large intervening non-coding RNA
long intergenic non-coding RNA
sequence
A multiexonic non-coding RNA transcribed by RNA polymerase II.
PMID:19182780
SO:ke
UST
An EST spanning part or all of the untranslated regions of a protein-coding transcript.
SO:0001464
UTR sequence tag
sequence
An EST spanning part or all of the untranslated regions of a protein-coding transcript.
SO:nlw
three_prime_UST
3' UST
A UST located in the 3'UTR of a protein-coding transcript.
SO:0001465
sequence
A UST located in the 3'UTR of a protein-coding transcript.
SO:nlw
five_prime_UST
5' UST
An UST located in the 5'UTR of a protein-coding transcript.
SO:0001466
sequence
An UST located in the 5'UTR of a protein-coding transcript.
SO:nlw
RST
A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long.
RACE sequence tag
SO:0001467
sequence
A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long.
SO:nlw
three_prime_RST
3' RST
A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long.
SO:0001468
sequence
A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long.
SO:nlw
five_prime_RST
5' RST
A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long.
SO:0001469
sequence
A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long.
SO:nlw
UST_match
A match against an UST sequence.
SO:0001470
UST match
sequence
A match against an UST sequence.
SO:nlw
RST_match
A match against an RST sequence.
RST match
SO:0001471
sequence
A match against an RST sequence.
SO:nlw
primer_match
A nucleotide match to a primer sequence.
SO:0001472
primer match
sequence
A nucleotide match to a primer sequence.
SO:nlw
miRNA_antiguide
2009-05-27T03:35:43Z
A region of the pri miRNA that base pairs with the guide to form the hairpin.
SO:0001473
kareneilbeck
miRNA antiguide
miRNA passenger strand
miRNA star
sequence
A region of the pri miRNA that base pairs with the guide to form the hairpin.
SO:ke
trans_splice_junction
2009-07-13T04:50:49Z
SO:0001474
The boundary between the spliced leader and the first exon of the mRNA.
kareneilbeck
sequence
trans-splice junction
SO:ke
The boundary between the spliced leader and the first exon of the mRNA.
outron
2009-07-14T11:36:08Z
A region of a primary transcript, that is removed via trans splicing.
SO:0001475
kareneilbeck
sequence
A region of a primary transcript, that is removed via trans splicing.
PMID:16401417
SO:ke
natural_plasmid
2009-09-01T03:43:06Z
A plasmid that occurs naturally.
SO:0001476
kareneilbeck
natural plasmid
sequence
A plasmid that occurs naturally.
SO:xp
gene_trap_construct
2009-09-01T03:49:09Z
A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker.
SO:0001477
gene trap construct
kareneilbeck
sequence
A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker.
ZFIN:dh
promoter_trap_construct
2009-09-01T03:52:01Z
A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic.
SO:0001478
kareneilbeck
promoter trap construct
sequence
A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic.
ZFIN:dh
enhancer_trap_construct
2009-09-01T03:53:26Z
An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic.
SO:0001479
enhancer trap construct
kareneilbeck
sequence
An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic.
ZFIN:dh
PAC_end
2009-09-09T05:18:12Z
A region of sequence from the end of a PAC clone that may provide a highly specific marker.
PAC end
SO:0001480
kareneilbeck
sequence
A region of sequence from the end of a PAC clone that may provide a highly specific marker.
ZFIN:mh
RAPD
2009-09-09T05:26:10Z
RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers.
Random Amplification Polymorphic DNA
SO:0001481
kareneilbeck
sequence
RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers.
ZFIN:mh
shadow_enhancer
2009-09-09T05:29:29Z
SO:0001482
kareneilbeck
sequence
shadow enhancer
SNV
2009-10-08T11:37:49Z
SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
SO:0001483
kareneilbeck
sequence
single nucleotide variant
SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.
SO:bm
X_element_combinatorial_repeat
2009-11-10T11:03:37Z
An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element.
SO:0001484
X element combinatorial repeat
X element combinatorial repeats contain Tbf1p binding sites,
and possible functions include a role in telomerase-independent telomere
maintenance via recombination or as a barrier against transcriptional
silencing. These are usually present as a combination of one or more of
several types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
kareneilbeck
sequence
An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element.
http://www.yeastgenome.org/help/glossary.html
Y_prime_element
2009-11-10T12:08:57Z
A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies.
SO:0001485
This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
Y' element
kareneilbeck
sequence
A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies.
http:http://www.yeastgenome.org/help/glossary.html
standard_draft
2009-10-23T12:48:32Z
SO:0001486
The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete.
kareneilbeck
sequence
standard draft
DOI:10.1126
The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete.
high_quality_draft
2009-10-23T12:52:36Z
SO:0001487
The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome.
high quality draft
kareneilbeck
sequence
DOI:10.1126
The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome.
improved_high_quality_draft
2009-10-23T12:54:35Z
SO:0001488
The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution.
improved high quality draft
kareneilbeck
sequence
DOI:10.1126
The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution.
annotation_directed_improved_draft
2009-10-23T12:57:10Z
SO:0001489
The status of a whole genome sequence,where annotation, and verification of coding regions has occurred.
annotation directed improvement
kareneilbeck
sequence
DOI:10.1126
The status of a whole genome sequence,where annotation, and verification of coding regions has occurred.
noncontiguous_finished
2009-10-23T01:01:07Z
SO:0001490
The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions.
kareneilbeck
non contiguous finished
sequence
DOI:10.1126
The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions.
finished_genome
2009-10-23T01:04:43Z
SO:0001491
The status of a whole genome sequence, with less than 1 error per 100,000 base pairs.
finished
finished genome
kareneilbeck
sequence
DOI:10.1126
The status of a whole genome sequence, with less than 1 error per 100,000 base pairs.
intronic_regulatory_region
2009-11-08T02:48:02Z
A regulatory region that is part of an intron.
SO:0001492
intronic regulatory region
kareneilbeck
sequence
A regulatory region that is part of an intron.
SO:ke
centromere_DNA_Element_I
2009-11-09T05:47:23Z
A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p).
CDEI
Centromere DNA Element I
SO:0001493
This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
kareneilbeck
sequence
A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p).
PMID:11222754
centromere_DNA_Element_II
2009-11-09T05:51:26Z
A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length.
CDEII
SO:0001494
This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
centromere DNA Element II
kareneilbeck
sequence
A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length.
PMID:11222754
centromere_DNA_Element_III
2009-11-09T05:54:47Z
A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex.
CDEIII
SO:0001495
This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
centromere DNA Element III
kareneilbeck
sequence
A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex.
PMID:11222754
telomeric_repeat
2009-11-09T06:00:42Z
SO:0001496
The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739.
The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.
kareneilbeck
sequence
telomeric repeat
PMID:8720065
The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.
X_element
2009-11-10T10:56:54Z
Possible functions include roles in chromosomal segregation,
maintenance of chromosome stability, recombinational sequestering, or as a
barrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
From Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1.
SO:0001497
The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site.
X element
X element core sequence
kareneilbeck
sequence
PMID:7785338
PMID:8005434
The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site.
http://www.yeastgenome.org/help/glossary.html#xelemcoresequence
YAC_end
2009-11-19T11:07:18Z
A region of sequence from the end of a YAC clone that may provide a highly specific marker.
SO:0001498
YAC end
kareneilbeck
sequence
A region of sequence from the end of a YAC clone that may provide a highly specific marker.
SO:ke
whole_genome_sequence_status
2009-10-23T12:47:47Z
SO:0001499
The status of whole genome sequence.
This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms.
kareneilbeck
sequence
whole genome sequence status
DOI:10.1126
The status of whole genome sequence.
heritable_phenotypic_marker
2009-12-07T01:50:55Z
A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.
SO:0001500
heritable phenotypic marker
kareneilbeck
phenotypic marker
sequence
A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.
JAX:hdene
peptide_collection
2009-12-11T10:58:58Z
A collection of peptide sequences.
SO:0001501
Term requested via tracker ID: 2910829.
kareneilbeck
peptide collection
peptide set
sequence
A collection of peptide sequences.
BBOP:nlw
high_identity_region
2009-12-11T11:06:05Z
An experimental feature with high sequence identity to another sequence.
Requested by tracker ID: 2902685.
SO:0001502
high identity region
kareneilbeck
sequence
An experimental feature with high sequence identity to another sequence.
SO:ke
processed_transcript
2009-12-21T05:37:14Z
A transcript for which no open reading frame has been identified and for which no other function has been determined.
Ensembl and Vega also use this term name. Requested by Howard Deen of MGI.
SO:0001503
kareneilbeck
processed transcript
sequence
A transcript for which no open reading frame has been identified and for which no other function has been determined.
MGI:hdeen
assortment_derived_variation
2010-03-02T05:03:18Z
A chromosome variation derived from an event during meiosis.
SO:0001504
assortment derived variation
kareneilbeck
sequence
A chromosome variation derived from an event during meiosis.
SO:ke
reference_genome
2010-03-03T02:10:03Z
A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly.
SO:0001505
kareneilbeck
reference genome
sequence
A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly.
SO:ke
variant_genome
2010-03-03T02:11:25Z
A collection of sequences (often chromosomes) of an individual.
SO:0001506
kareneilbeck
sequence
variant genome
A collection of sequences (often chromosomes) of an individual.
SO:ke
variant_collection
2010-03-03T02:13:28Z
A collection of one or more sequences of an individual.
SO:0001507
kareneilbeck
sequence
variant collection
A collection of one or more sequences of an individual.
SO:ke
alteration_attribute
2010-03-04T02:53:23Z
SO:0001508
alteration attribute
kareneilbeck
sequence
chromosomal_variation_attribute
2010-03-04T02:54:30Z
SO:0001509
chromosomal variation attribute
kareneilbeck
sequence
intrachromosomal
2010-03-04T02:55:25Z
SO:0001510
kareneilbeck
sequence
interchromosomal
2010-03-04T02:55:43Z
SO:0001511
kareneilbeck
sequence
insertion_attribute
2010-03-04T02:55:56Z
A quality of a chromosomal insertion,.
SO:0001512
insertion attribute
kareneilbeck
sequence
A quality of a chromosomal insertion,.
SO:ke
tandem
2010-03-04T02:56:37Z
SO:0001513
kareneilbeck
sequence
direct
2010-03-04T02:56:49Z
A quality of an insertion where the insert is not in a cytologically inverted orientation.
SO:0001514
kareneilbeck
sequence
A quality of an insertion where the insert is not in a cytologically inverted orientation.
SO:ke
inverted
2010-03-04T02:57:40Z
A quality of an insertion where the insert is in a cytologically inverted orientation.
SO:0001515
kareneilbeck
sequence
A quality of an insertion where the insert is in a cytologically inverted orientation.
SO:ke
free
2010-03-04T02:57:51Z
SO:0001516
The quality of a duplication where the new region exists independently of the original.
kareneilbeck
sequence
SO:ke
The quality of a duplication where the new region exists independently of the original.
inversion_attribute
2010-03-04T02:58:10Z
SO:0001517
inversion attribute
kareneilbeck
sequence
pericentric
2010-03-04T02:58:24Z
SO:0001518
kareneilbeck
sequence
paracentric
2010-03-04T02:58:35Z
SO:0001519
kareneilbeck
sequence
translocaton_attribute
2010-03-04T02:58:47Z
SO:0001520
kareneilbeck
sequence
translocation attribute
reciprocal
2010-03-04T02:59:34Z
SO:0001521
kareneilbeck
sequence
insertional
2010-03-04T02:59:51Z
SO:0001522
kareneilbeck
sequence
duplication_attribute
2010-03-05T01:56:33Z
SO:0001523
duplication attribute
kareneilbeck
sequence
chromosomally_aberrant_genome
2010-03-05T02:21:00Z
SO:0001524
chromosomally aberrant genome
kareneilbeck
sequence
assembly_error_correction
2010-03-09T02:16:31Z
A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake.
SO:0001525
assembly error correction
kareneilbeck
sequence
A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake.
SO:ke
base_call_error_correction
2010-03-09T02:18:07Z
A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake.
SO:0001526
base call error correction
kareneilbeck
sequence
A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake.
SO:ke
peptide_localization_signal
2010-03-11T02:15:05Z
A region of peptide sequence used to target the polypeptide molecule to a specific organelle.
SO:0001527
kareneilbeck
localization signal
peptide localization signal
sequence
A region of peptide sequence used to target the polypeptide molecule to a specific organelle.
SO:ke
nuclear_localization_signal
2010-03-11T02:16:38Z
A polypeptide region that targets a polypeptide to the nucleus.
NLS
SO:0001528
http://en.wikipedia.org/wiki/Nuclear_localization_signal
kareneilbeck
sequence
wikipedia
http://en.wikipedia.org/wiki/Nuclear_localization_signal
A polypeptide region that targets a polypeptide to the nucleus.
SO:ke
endosomal_localization_signal
2010-03-11T02:20:58Z
A polypeptide region that targets a polypeptide to the endosome.
SO:0001529
endosomal localization signal
kareneilbeck
sequence
A polypeptide region that targets a polypeptide to the endosome.
SO:ke
lysosomal_localization_signal
2010-03-11T02:24:10Z
A polypeptide region that targets a polypeptide to the lysosome.
SO:0001530
kareneilbeck
lysosomal localization signal
sequence
A polypeptide region that targets a polypeptide to the lysosome.
SO:ke
nuclear_export_signal
2010-03-11T02:25:25Z
A polypeptide region that targets a polypeptide to he cytoplasm.
NES
SO:0001531
http://en.wikipedia.org/wiki/Nuclear_export_signal
kareneilbeck
nuclear export signal
sequence
A polypeptide region that targets a polypeptide to he cytoplasm.
SO:ke
recombination_signal_sequence
2010-03-11T03:16:47Z
A region recognized by a recombinase.
SO:0001532
http://en.wikipedia.org/wiki/Recombination_Signal_Sequences
kareneilbeck
recombination signal sequence
sequence
A region recognized by a recombinase.
SO:ke
wikipedia
http://en.wikipedia.org/wiki/Recombination_Signal_Sequences
cryptic_splice_site
2010-03-11T03:25:06Z
A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error.
SO:0001533
cryptic splice signal
cryptic splice site
kareneilbeck
sequence
A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error.
SO:ke
nuclear_rim_localization_signal
2010-03-11T03:31:30Z
A polypeptide region that targets a polypeptide to the nuclear rim.
PMID:16027110
SO:0001534
kareneilbeck
nuclear rim localization signal
sequence
A polypeptide region that targets a polypeptide to the nuclear rim.
SO:ke
p_element
2010-03-12T03:40:33Z
A P_element is a DNA transposon responsible for hybrid dysgenesis.
P element
SO:0001535
kareneilbeck
sequence
A P_element is a DNA transposon responsible for hybrid dysgenesis.
SO:ke
functional_variant
2010-03-22T11:30:25Z
A sequence variant in which the function of a gene product is altered with respect to a reference.
SO:0001536
functional variant
kareneilbeck
sequence
A sequence variant in which the function of a gene product is altered with respect to a reference.
SO:ke
structural_variant
2010-03-22T11:31:01Z
A sequence variant that changes one or more sequence features.
SO:0001537
kareneilbeck
sequence
structural variant
A sequence variant that changes one or more sequence features.
SO:ke
transcript_function_variant
2010-03-22T11:32:58Z
A sequence variant which alters the functioning of a transcript with respect to a reference sequence.
SO:0001538
kareneilbeck
sequence
transcript function variant
A sequence variant which alters the functioning of a transcript with respect to a reference sequence.
SO:ke
translational_product_function_variant
2010-03-22T11:46:15Z
A sequence variant that affects the functioning of a translational product with respect to a reference sequence.
SO:0001539
kareneilbeck
sequence
translational product variant
A sequence variant that affects the functioning of a translational product with respect to a reference sequence.
SO:ke
level_of_transcript_variant
2010-03-22T11:47:07Z
A sequence variant which alters the level of a transcript.
SO:0001540
kareneilbeck
level of transcript variant
sequence
A sequence variant which alters the level of a transcript.
SO:ke
decreased_transcript_level_variant
2010-03-22T11:47:47Z
A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.
SO:0001541
decreased transcript level
kareneilbeck
sequence
A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.
SO:ke
increased_transcript_level_variant
2010-03-22T11:48:17Z
A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.
SO:0001542
increased transcript level variant
kareneilbeck
sequence
A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.
SO:ke
transcript_processing_variant
2010-03-22T11:48:48Z
A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence.
SO:0001543
kareneilbeck
sequence
transcript processing variant
A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence.
SO:ke
editing_variant
2010-03-22T11:49:25Z
A transcript processing variant whereby the process of editing is disrupted with respect to the reference.
SO:0001544
editing variant
kareneilbeck
sequence
A transcript processing variant whereby the process of editing is disrupted with respect to the reference.
SO:ke
polyadenylation_variant
2010-03-22T11:49:40Z
A sequence variant that changes polyadenylation with respect to a reference sequence.
SO:0001545
kareneilbeck
polyadenylation variant
sequence
A sequence variant that changes polyadenylation with respect to a reference sequence.
SO:ke
transcript_stability_variant
2010-03-22T11:50:01Z
A variant that changes the stability of a transcript with respect to a reference sequence.
SO:0001546
kareneilbeck
sequence
transcript stability variant
A variant that changes the stability of a transcript with respect to a reference sequence.
SO:ke
decreased_transcript_stability_variant
2010-03-22T11:50:23Z
A sequence variant that decreases transcript stability with respect to a reference sequence.
SO:0001547
decrease transcript stability variant
kareneilbeck
sequence
A sequence variant that decreases transcript stability with respect to a reference sequence.
SO:ke
increased_transcript_stability_variant
2010-03-22T11:50:39Z
A sequence variant that increases transcript stability with respect to a reference sequence.
SO:0001548
increased transcript stability variant
kareneilbeck
sequence
A sequence variant that increases transcript stability with respect to a reference sequence.
SO:ke
transcription_variant
2010-03-22T11:51:26Z
A variant that changes alters the transcription of a transcript with respect to a reference sequence.
SO:0001549
kareneilbeck
sequence
transcription variant
A variant that changes alters the transcription of a transcript with respect to a reference sequence.
SO:ke
rate_of_transcription_variant
2010-03-22T11:51:50Z
A sequence variant that changes the rate of transcription with respect to a reference sequence.
SO:0001550
kareneilbeck
rate of transcription variant
sequence
A sequence variant that changes the rate of transcription with respect to a reference sequence.
SO:ke
increased_transcription_rate_variant
2010-03-22T11:52:17Z
A sequence variant that increases the rate of transcription with respect to a reference sequence.
SO:0001551
increased transcription rate variant
kareneilbeck
sequence
A sequence variant that increases the rate of transcription with respect to a reference sequence.
SO:ke
decreased_transcription_rate_variant
2010-03-22T11:52:43Z
A sequence variant that decreases the rate of transcription with respect to a reference sequence.
SO:0001552
decreased transcription rate variant
kareneilbeck
sequence
A sequence variant that decreases the rate of transcription with respect to a reference sequence.
SO:ke
translational_product_level_variant
2010-03-22T11:53:32Z
A functional variant that changes the translational product level with respect to a reference sequence.
SO:0001553
kareneilbeck
sequence
translational product level variant
A functional variant that changes the translational product level with respect to a reference sequence.
SO:ke
polypeptide_function_variant
2010-03-22T11:53:54Z
A sequence variant which changes polypeptide functioning with respect to a reference sequence.
SO:0001554
kareneilbeck
polypeptide function variant
sequence
A sequence variant which changes polypeptide functioning with respect to a reference sequence.
SO:ke
decreased_translational_product_level
2010-03-22T11:54:25Z
A sequence variant which decreases the translational product level with respect to a reference sequence.
SO:0001555
decrease translational product level
kareneilbeck
sequence
A sequence variant which decreases the translational product level with respect to a reference sequence.
SO:ke
increased_translational_product_level
2010-03-22T11:55:25Z
A sequence variant which increases the translational product level with respect to a reference sequence.
SO:0001556
increase translational product level
kareneilbeck
sequence
A sequence variant which increases the translational product level with respect to a reference sequence.
SO:ke
polypeptide_gain_of_function_variant
2010-03-22T11:56:12Z
A sequence variant which causes gain of polypeptide function with respect to a reference sequence.
SO:0001557
kareneilbeck
polypeptide gain of function variant
sequence
A sequence variant which causes gain of polypeptide function with respect to a reference sequence.
SO:ke
polypeptide_localization_variant
2010-03-22T11:56:37Z
A sequence variant which changes the localization of a polypeptide with respect to a reference sequence.
SO:0001558
kareneilbeck
polypeptide localization variant
sequence
A sequence variant which changes the localization of a polypeptide with respect to a reference sequence.
SO:ke
polypeptide_loss_of_function_variant
2010-03-22T11:56:58Z
A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence.
SO:0001559
kareneilbeck
polypeptide loss of function variant
sequence
A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence.
SO:ke
inactive_ligand_binding_site
2010-03-22T11:58:00Z
A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence.
SO:0001560
inactive ligand binding site
kareneilbeck
sequence
A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence.
SO:ke
polypeptide_partial_loss_of_function
2010-03-22T11:58:32Z
A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence.
SO:0001561
kareneilbeck
polypeptide partial loss of function
sequence
A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence.
SO:ke
polypeptide_post_translational_processing_variant
2010-03-22T11:59:06Z
A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence.
SO:0001562
kareneilbeck
polypeptide post translational processing variant
sequence
A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence.
SO:ke
copy_number_change
2010-03-22T02:27:33Z
A sequence variant where copies of a feature (CNV) are either increased or decreased.
SO:0001563
copy number change
kareneilbeck
sequence
A sequence variant where copies of a feature (CNV) are either increased or decreased.
SO:ke
gene_variant
2010-03-22T02:28:01Z
A sequence variant where the structure of the gene is changed.
SO:0001564
VAAST:gene_variant
gene structure variant
kareneilbeck
sequence
snpEff:GENE
A sequence variant where the structure of the gene is changed.
SO:ke
snpEff:GENE
VAAST:gene_variant
gene_fusion
2010-03-22T02:28:28Z
A sequence variant whereby a two genes have become joined.
SO:0001565
gene fusion
kareneilbeck
sequence
A sequence variant whereby a two genes have become joined.
SO:ke
regulatory_region_variant
2010-03-22T02:28:48Z
A sequence variant located within a regulatory region.
EBI term: Regulatory region variations - In regulatory region annotated by Ensembl.
SO:0001566
kareneilbeck
regulatory region variant
regulatory_region_
sequence
http://ensembl.org/info/docs/variation/index.html
regulatory_region_
A sequence variant located within a regulatory region.
SO:ke
stop_retained_variant
2010-04-19T05:02:30Z
A sequence variant where at least one base in the terminator codon is changed, but the terminator remains.
SO:0001567
VAAST:stop_retained
kareneilbeck
sequence
snpEff:SYNONYMOUS_STOP
stop retained variant
A sequence variant where at least one base in the terminator codon is changed, but the terminator remains.
SO:ke
snpEff:SYNONYMOUS_STOP
VAAST:stop_retained
splicing_variant
2010-03-22T02:29:22Z
A sequence variant that changes the process of splicing.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001568
kareneilbeck
sequence
splicing variant
A sequence variant that changes the process of splicing.
SO:ke
cryptic_splice_site_variant
2010-03-22T02:29:41Z
A sequence variant causing a new (functional) splice site.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001569
cryptic splice site activation
kareneilbeck
sequence
A sequence variant causing a new (functional) splice site.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
cryptic_splice_acceptor
2010-03-22T02:30:11Z
A sequence variant whereby a new splice site is created due to the activation of a new acceptor.
SO:0001570
cryptic splice acceptor
kareneilbeck
sequence
A sequence variant whereby a new splice site is created due to the activation of a new acceptor.
SO:ke
cryptic_splice_donor
2010-03-22T02:30:35Z
A sequence variant whereby a new splice site is created due to the activation of a new donor.
SO:0001571
cryptic splice donor
kareneilbeck
sequence
A sequence variant whereby a new splice site is created due to the activation of a new donor.
SO:ke
exon_loss_variant
2010-03-22T02:31:09Z
A sequence variant whereby an exon is lost from the transcript.
SO:0001572
exon loss
kareneilbeck
sequence
snpEff:EXON_DELETED
snpEff:EXON_DELETED
A sequence variant whereby an exon is lost from the transcript.
SO:ke
intron_gain_variant
2010-03-22T02:31:25Z
A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001573
intron gain
intron gain variant
kareneilbeck
sequence
A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
splice_acceptor_variant
2010-03-22T02:31:52Z
A splice variant that changes the 2 base region at the 3' end of an intron.
SO:0001574
VAAST:splice_acceptor_variant
kareneilbeck
sequence
snpEff:SPLICE_SITE_ACCEPTOR
splice acceptor variant
VAAST:splice_acceptor_variant
snpEff:SPLICE_SITE_ACCEPTOR
A splice variant that changes the 2 base region at the 3' end of an intron.
SO:ke
splice_donor_variant
2010-03-22T02:32:10Z
A splice variant that changes the 2 base pair region at the 5' end of an intron.
SO:0001575
VAAST:splice_donor_variant
kareneilbeck
sequence
snpEff:SPLICE_SITE_DONOR
splice donor variant
snpEff:SPLICE_SITE_DONOR
VAAST:splice_donor_variant
A splice variant that changes the 2 base pair region at the 5' end of an intron.
SO:ke
transcript_variant
2010-03-22T02:32:41Z
A sequence variant that changes the structure of the transcript.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001576
VAAST:transcript_variant
kareneilbeck
sequence
snpEff:TRANSCRIPT
transcript variant
VAAST:transcript_variant
A sequence variant that changes the structure of the transcript.
SO:ke
snpEff:TRANSCRIPT
complex_transcript_variant
2010-03-22T02:33:03Z
A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
SO:0001577
complex transcript variant
complex_indel
complext change in transcript
kareneilbeck
sequence
complex_indel
http://ensembl.org/info/docs/variation/index.html
A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
http://ensembl.org/info/docs/variation/index.html
stop_lost
2010-03-23T03:46:42Z
A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript.
ANNOVAR:stoploss
EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.
SO:0001578
VAAST:stop_lost
kareneilbeck
sequence
snpEff:STOP_LOST
stop codon lost
stop lost
snpEff:STOP_LOST
http://ensembl.org/info/docs/variation/index.html
stop lost
VAAST:stop_lost
A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript.
SO:ke
ANNOVAR:stoploss
http://www.openbioinformatics.org/annovar/annovar_download.html
transcript_sequence_variant
SO:0001579
sequence
transcript sequence variant
true
coding_sequence_variant
2010-03-22T02:34:36Z
A sequence variant that changes the coding sequence.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001580
SO:0001581
VAAST:coding_sequence_variant
coding sequence variant
coding variant
codon variant
codon_variant
kareneilbeck
sequence
snpEff:CDS
snpEff:CODON_CHANGE
snpEff:CODON_CHANGE
A sequence variant that changes the coding sequence.
SO:ke
snpEff:CDS
VAAST:coding_sequence_variant
initiator_codon_variant
2010-03-22T02:35:18Z
A codon variant that changes at least one base of the first codon of a transcript.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001582
This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called.
initiatior codon variant
initiator codon change
kareneilbeck
loinc:LA6695-6
sequence
A codon variant that changes at least one base of the first codon of a transcript.
SO:ke
Initiating Methionine
loinc:LA6695-6
missense_variant
2010-03-22T02:35:49Z
A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.
ANNOVAR:nonsynonymous SNV
EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001583
SO:0001584
SO:0001783
VAAST:non_synonymous_codon
http://en.wikipedia.org/wiki/Missense_mutation
kareneilbeck
loinc:LA6698-0
missense
missense codon
sequence
snpEff:NON_SYSNONYMOUS_CODING
snpEff:NON_SYSNONYMOUS_CODING
A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.
EBI:fc
EBI:gr
SO:ke
VAAST:non_synonymous_codon
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
missense
ANNOVAR:nonsynonymous SNV
http://www.openbioinformatics.org/annovar/annovar_download.html
Missense
loinc:LA6698-0
conservative_missense_variant
2010-03-22T02:36:40Z
A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001585
conservative missense codon
conservative missense variant
kareneilbeck
neutral missense codon
quiet missense codon
sequence
A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious.
SO:ke
non_conservative_missense_variant
2010-03-22T02:37:16Z
A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001586
kareneilbeck
non conservative missense codon
non conservative missense variant
sequence
A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties.
SO:ke
stop_gained
2010-03-22T02:37:52Z
A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript.
ANNOVAR:stopgain
EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).
SO:0001587
VAAST:stop_gained
kareneilbeck
loinc:LA6699-8
nonsense
nonsense codon
sequence
snpEFF:STOP_GAINED
stop codon gained
stop gained
http://ensembl.org/info/docs/variation/index.html
stop gained
A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript.
SO:ke
Nonsense
loinc:LA6699-8
VAAST:stop_gained
ANNOVAR:stopgain
http://www.openbioinformatics.org/annovar/annovar_download.html
snpEFF:STOP_GAINED
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
nonsense
frameshift_variant
2010-03-22T02:40:19Z
A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.
ANNOVAR:frameshift block substitution
EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.
SO:0001589
VAAST:frameshift_variant
frameshift variant
frameshift_
frameshift_coding
kareneilbeck
loinc:LA6694-9
sequence
snpEff:FRAME_SHIFT
snpEff:FRAME_SHIFT
Frameshift
loinc:LA6694-9
VAAST:frameshift_variant
frameshift_
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
ANNOVAR:frameshift block substitution
http://www.openbioinformatics.org/annovar/annovar_download.html
A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.
SO:ke
frameshift_coding
http://ensembl.org/info/docs/variation/index.html
terminator_codon_variant
2010-03-22T02:40:37Z
A sequence variant whereby at least one of the bases in the terminator codon is changed.
SO:0001590
SO:0001625
The terminal codon may be the terminator, or in an incomplete transcript the last available codon.
kareneilbeck
loinc:LA6700-2
sequence
terminal codon variant
terminal_codon_variant
terminator codon variant
A sequence variant whereby at least one of the bases in the terminator codon is changed.
SO:ke
Stop Codon Mutation
loinc:LA6700-2
frame_restoring_variant
2010-03-22T02:41:09Z
A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame.
SO:0001591
frame restoring variant
kareneilbeck
sequence
A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame.
SO:ke
minus_1_frameshift_variant
-1 frameshift variant
2010-03-22T02:41:30Z
A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead.
SO:0001592
kareneilbeck
minus 1 frameshift variant
sequence
A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead.
http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535
minus_2_frameshift_variant
-2 frameshift variant
2010-03-22T02:41:52Z
SO:0001593
kareneilbeck
minus 2 frameshift variant
sequence
plus_1_frameshift_variant
+1 frameshift variant
2010-03-22T02:42:06Z
A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward.
SO:0001594
kareneilbeck
plus 1 frameshift variant
sequence
A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward.
http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535
plus_2_frameshift_variant
+2 frameshift variant
2010-03-22T02:42:23Z
SO:0001595
kareneilbeck
plus 2 frameshift variant
sequence
transcript_secondary_structure_variant
2010-03-22T02:43:18Z
A sequence variant within a transcript that changes the secondary structure of the RNA product.
SO:0001596
kareneilbeck
sequence
transcript secondary structure variant
A sequence variant within a transcript that changes the secondary structure of the RNA product.
SO:ke
compensatory_transcript_secondary_structure_variant
2010-03-22T02:43:54Z
A secondary structure variant that compensate for the change made by a previous variant.
SO:0001597
compensatory transcript secondary structure variant
kareneilbeck
sequence
A secondary structure variant that compensate for the change made by a previous variant.
SO:ke
translational_product_structure_variant
2010-03-22T02:44:17Z
A sequence variant within the transcript that changes the structure of the translational product.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001598
kareneilbeck
sequence
translational product structure variant
A sequence variant within the transcript that changes the structure of the translational product.
SO:ke
3D_polypeptide_structure_variant
2010-03-22T02:44:46Z
3D polypeptide structure variant
A sequence variant that changes the resulting polypeptide structure.
SO:0001599
kareneilbeck
sequence
A sequence variant that changes the resulting polypeptide structure.
SO:ke
complex_3D_structural_variant
2010-03-22T02:45:13Z
A sequence variant that changes the resulting polypeptide structure.
SO:0001600
complex 3D structural variant
kareneilbeck
sequence
A sequence variant that changes the resulting polypeptide structure.
SO:ke
conformational_change_variant
2010-03-22T02:45:48Z
A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence.
SO:0001601
conformational change variant
kareneilbeck
sequence
A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence.
SO:ke
complex_change_of_translational_product_variant
2010-03-22T02:46:54Z
SO:0001602
complex change of translational product variant
kareneilbeck
sequence
polypeptide_sequence_variant
2010-03-22T02:47:13Z
A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence.
SO:0001603
kareneilbeck
polypeptide sequence variant
sequence
A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence.
SO:ke
amino_acid_deletion
2010-03-22T02:47:36Z
A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001604
amino acid deletion
kareneilbeck
sequence
A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide.
SO:ke
amino_acid_insertion
2010-03-22T02:47:56Z
A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001605
amino acid insertion
kareneilbeck
sequence
A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide.
SO:ke
amino_acid_substitution
2010-03-22T02:48:17Z
A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001606
VAAST:amino_acid_substitution
amino acid substitution
kareneilbeck
sequence
A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide.
SO:ke
VAAST:amino_acid_substitution
conservative_amino_acid_substitution
2010-03-22T02:48:57Z
A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide.
SO:0001607
conservative amino acid substitution
kareneilbeck
sequence
A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide.
SO:ke
non_conservative_amino_acid_substitution
2010-03-22T02:49:23Z
A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide.
SO:0001608
kareneilbeck
non conservative amino acid substitution
sequence
A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide.
SO:ke
elongated_polypeptide
2010-03-22T02:49:52Z
A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001609
elongated polypeptide
kareneilbeck
sequence
A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence.
SO:ke
elongated_polypeptide_C_terminal
2010-03-22T02:50:20Z
A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus.
SO:0001610
elongated polypeptide C terminal
kareneilbeck
sequence
A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus.
SO:ke
elongated_polypeptide_N_terminal
2010-03-22T02:50:31Z
A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus.
SO:0001611
elongated polypeptide N terminal
kareneilbeck
sequence
A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus.
SO:ke
elongated_in_frame_polypeptide_C_terminal
2010-03-22T02:51:05Z
A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus.
SO:0001612
elongated in frame polypeptide C terminal
kareneilbeck
sequence
A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus.
SO:ke
elongated_out_of_frame_polypeptide_C_terminal
2010-03-22T02:51:20Z
A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus.
SO:0001613
elongated polypeptide out of frame C terminal
kareneilbeck
sequence
A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus.
SO:ke
elongated_in_frame_polypeptide_N_terminal_elongation
2010-03-22T02:51:49Z
A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus.
SO:0001614
elongated in frame polypeptide N terminal
kareneilbeck
sequence
A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus.
SO:ke
elongated_out_of_frame_polypeptide_N_terminal
2010-03-22T02:52:05Z
A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus.
SO:0001615
elongated out of frame N terminal
kareneilbeck
sequence
A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus.
SO:ke
polypeptide_fusion
2010-03-22T02:52:43Z
A sequence variant that causes a fusion of two polypeptide sequences.
SO:0001616
kareneilbeck
polypeptide fusion
sequence
A sequence variant that causes a fusion of two polypeptide sequences.
SO:ke
polypeptide_truncation
2010-03-22T02:53:07Z
A sequence variant of the CD that causes a truncation of the resulting polypeptide.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001617
kareneilbeck
polypeptide truncation
sequence
A sequence variant of the CD that causes a truncation of the resulting polypeptide.
SO:ke
inactive_catalytic_site
2010-03-22T03:06:14Z
A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence.
SO:0001618
inactive catalytic site
kareneilbeck
sequence
A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence.
SO:ke
non_coding_transcript_variant
2010-03-23T11:16:23Z
A transcript variant of a non coding RNA gene.
ANNOVAR:ncRNA
SO:0001619
Within non-coding gene - Located within a gene that does not code for a protein.
kareneilbeck
nc transcript variant
non coding transcript variant
sequence
within_non_coding_gene
ANNOVAR:ncRNA
http:http://www.openbioinformatics.org/annovar/annovar_download.html
http://ensembl.org/info/docs/variation/index.html
within_non_coding_gene
A transcript variant of a non coding RNA gene.
SO:ke
mature_miRNA_variant
2010-03-23T11:16:58Z
A transcript variant located with the sequence of the mature miRNA.
EBI term: Within mature miRNA - Located within a microRNA.
SO:0001620
kareneilbeck
mature miRNA variant
sequence
within_mature_miRNA
A transcript variant located with the sequence of the mature miRNA.
SO:ke
http://ensembl.org/info/docs/variation/index.html
within_mature_miRNA
NMD_transcript_variant
2010-03-23T11:20:40Z
A variant in a transcript that is the target of NMD.
NMD transcript variant
NMD_transcript
SO:0001621
kareneilbeck
sequence
NMD_transcript
http://ensembl.org/info/docs/variation/index.html
A variant in a transcript that is the target of NMD.
SO:ke
UTR_variant
2010-03-23T11:22:58Z
A transcript variant that is located within the UTR.
SO:0001622
UTR variant
UTR_
kareneilbeck
sequence
UTR_
http://ensembl.org/info/docs/variation/index.html
A transcript variant that is located within the UTR.
SO:ke
5_prime_UTR_variant
2010-03-23T11:23:29Z
5'UTR variant
5PRIME_UTR
A UTR variant of the 5' UTR.
ANNOVAR:UTR5
EBI term: 5prime UTR variations - In 5prime UTR (untranslated region).
SO:0001623
VAAST:five_prime_UTR_variant
five prime UTR variant
kareneilbeck
sequence
snpEff:UTR_5_PRIME
untranslated-5
VAAST:five_prime_UTR_variant
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
untranslated-5
snpEff:UTR_5_PRIME
ANNOVAR:UTR5
http://www.openbioinformatics.org/annovar/annovar_download.html
5PRIME_UTR
http://ensembl.org/info/docs/variation/index.html
A UTR variant of the 5' UTR.
SO:ke
3_prime_UTR_variant
2010-03-23T11:23:54Z
3'UTR variant
3PRIME_UTR
A UTR variant of the 3' UTR.
ANNOVAR:UTR3
EBI term 3prime UTR variations - In 3prime UTR.
SO:0001624
VAAST:three_prime_UTR_variant
kareneilbeck
sequence
snpEff:UTR_3_PRIME
three prime UTR variant
untranslated-3
ANNOVAR:UTR3
http://www.openbioinformatics.org/annovar/annovar_download.html
VAAST:three_prime_UTR_variant
A UTR variant of the 3' UTR.
SO:ke
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
untranslated-3
3PRIME_UTR
http://ensembl.org/info/docs/variation/index.html
snpEff:UTR_3_PRIME
incomplete_terminal_codon_variant
2010-03-23T03:51:15Z
A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed.
EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown.
SO:0001626
incomplete terminal codon variant
kareneilbeck
partial_codon
sequence
A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed.
SO:ke
http://ensembl.org/info/docs/variation/index.html
partial_codon
intron_variant
2010-03-23T03:52:38Z
A transcript variant occurring within an intron.
ANNOVAR:intronic
EBI term: Intronic variations - In intron.
SO:0001627
VAAST:intron_variant
intron variant
intron_
intronic
kareneilbeck
sequence
snpEff:INTRON
snpEff:INTRON
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
intron_
A transcript variant occurring within an intron.
SO:ke
http://ensembl.org/info/docs/variation/index.html
intronic
ANNOVAR:intronic
http://www.openbioinformatics.org/annovar/annovar_download.html
VAAST:intron_variant
intergenic_variant
2010-03-23T05:07:37Z
A sequence variant located in the intergenic region, between genes.
ANNOVAR:intergenic
EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript.
SO:0001628
intergenic
intergenic variant
kareneilbeck
sequence
snpEff:INTERGENIC
A sequence variant located in the intergenic region, between genes.
SO:ke
http://ensembl.org/info/docs/variation/index.html
intergenic
ANNOVAR:intergenic
http://www.openbioinformatics.org/annovar/annovar_download.html
snpEff:INTERGENIC
splice_site_variant
2010-03-24T09:42:00Z
A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript.
EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger.
SO:0001629
essential_splice_site
kareneilbeck
sequence
splice site variant
A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript.
http://ensembl.org/info/docs/variation/index.html
essential_splice_site
http://ensembl.org/info/docs/variation/index.html
splice_region_variant
2010-03-24T09:46:02Z
A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
ANNOVAR:splicing
EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron.
SO:0001630
VAAST:splice_region_variant
kareneilbeck
sequence
splice region variant
VAAST:splice_region_variant
http://ensembl.org/info/docs/variation/index.html
splice region variant
ANNOVAR:splicing
http://www.openbioinformatics.org/annovar/annovar_download.html
A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
http://ensembl.org/info/docs/variation/index.html
upstream_gene_variant
2010-03-24T09:49:13Z
A sequence variant located 5' of a gene.
ANNOVAR:upstream
Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
SO:0001631
kareneilbeck
sequence
snpEff:UPSTREAM
upstream gene variant
A sequence variant located 5' of a gene.
SO:ke
snpEff:UPSTREAM
ANNOVAR:upstream
http://www.openbioinformatics.org/annovar/annovar_download.html
downstream_gene_variant
2010-03-24T09:49:38Z
A sequence variant located 3' of a gene.
ANNOVAR:downstream
Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
SO:0001632
downstream gene variant
kareneilbeck
sequence
snpEff:DOWNSTREAM
snpEff:DOWNSTREAM
ANNOVAR:downstream
http://www.openbioinformatics.org/annovar/annovar_download.html
A sequence variant located 3' of a gene.
SO:ke
5KB_downstream_variant
2010-03-24T09:50:16Z
5KB downstream variant
A sequence variant located within 5 KB of the end of a gene.
EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.
SO:0001633
downstream
kareneilbeck
sequence
within 5KB downstream
A sequence variant located within 5 KB of the end of a gene.
SO:ke
downstream
http://ensembl.org/info/docs/variation/index.html
500B_downstream_variant
2010-03-24T09:50:42Z
500B downstream variant
A sequence variant located within a half KB of the end of a gene.
SO:0001634
kareneilbeck
near-gene-3
sequence
A sequence variant located within a half KB of the end of a gene.
SO:ke
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
near-gene-3
5KB_upstream_variant
2010-03-24T09:51:06Z
5kb upstream variant
A sequence variant located within 5KB 5' of a gene.
EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.
SO:0001635
kareneilbeck
sequence
upstream
http://ensembl.org/info/docs/variation/index.html
upstream
A sequence variant located within 5KB 5' of a gene.
SO:ke
2KB_upstream_variant
2010-03-24T09:51:22Z
2KB upstream variant
A sequence variant located within 2KB 5' of a gene.
SO:0001636
kareneilbeck
near-gene-5
sequence
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
near-gene-5
A sequence variant located within 2KB 5' of a gene.
SO:ke
rRNA_gene
2010-04-21T10:10:32Z
A gene that encodes for ribosomal RNA.
SO:0001637
kareneilbeck
rDNA
rRNA gene
sequence
A gene that encodes for ribosomal RNA.
SO:ke
piRNA_gene
2010-04-21T10:11:36Z
A gene that encodes for an piwi associated RNA.
SO:0001638
kareneilbeck
piRNA gene
sequence
A gene that encodes for an piwi associated RNA.
SO:ke
RNase_P_RNA_gene
2010-04-21T10:13:23Z
A gene that encodes an RNase P RNA.
RNase P RNA gene
SO:0001639
kareneilbeck
sequence
A gene that encodes an RNase P RNA.
SO:ke
RNase_MRP_RNA_gene
2010-04-21T10:13:58Z
A gene that encodes a RNase_MRP_RNA.
RNase MRP RNA gene
SO:0001640
kareneilbeck
sequence
A gene that encodes a RNase_MRP_RNA.
SO:ke
lincRNA_gene
2010-04-21T10:14:24Z
A gene that encodes large intervening non-coding RNA.
SO:0001641
kareneilbeck
lincRNA gene
sequence
A gene that encodes large intervening non-coding RNA.
SO:ke
mathematically_defined_repeat
2010-05-03T11:50:14Z
A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness.
Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.).
SO:0001642
kareneilbeck
mathematically defined repeat
sequence
A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness.
SO:jestill
telomerase_RNA_gene
2010-05-18T05:26:38Z
A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.
SO:0001643
TERC
Telomerase RNA component
http:http://en.wikipedia.org/wiki/Telomerase_RNA_component
kareneilbeck
sequence
telomerase RNA gene
A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.
SO:ke
wikipedia
http:http://en.wikipedia.org/wiki/Telomerase_RNA_component
targeting_vector
2010-05-28T02:05:25Z
An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications.
SO:0001644
kareneilbeck
sequence
targeting vector
An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications.
MGD:tm
PMID:10354467
genetic_marker
2010-05-28T02:33:07Z
A measurable sequence feature that varies within a population.
SO:0001645
genetic marker
kareneilbeck
sequence
A measurable sequence feature that varies within a population.
SO:db
DArT_marker
2010-05-28T02:34:43Z
A genetic marker, discovered using Diversity Arrays Technology (DArT) technology.
DArT marker
SO:0001646
kareneilbeck
sequence
A genetic marker, discovered using Diversity Arrays Technology (DArT) technology.
SO:ke
kozak_sequence
2010-06-07T03:12:20Z
A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
SO:0001647
http://en.wikipedia.org/wiki/Kozak_consensus_sequence
kareneilbeck
kozak consensus
kozak consensus sequence
kozak sequence
sequence
wikipedia
http://en.wikipedia.org/wiki/Kozak_consensus_sequence
A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.
SO:ke
nested_transposon
2010-06-23T03:22:57Z
A transposon that is disrupted by the insertion of another element.
SO:0001648
kareneilbeck
nested transposon
sequence
A transposon that is disrupted by the insertion of another element.
SO:ke
nested_repeat
2010-06-23T03:24:55Z
A repeat that is disrupted by the insertion of another element.
SO:0001649
kareneilbeck
nested repeat
sequence
A repeat that is disrupted by the insertion of another element.
SO:ke
inframe_variant
2010-07-19T01:24:44Z
A sequence variant which does not cause a disruption of the translational reading frame.
ANNOVAR:nonframeshift block substitution
SO:0001650
VAAST:inframe_variant
cds-indel
inframe variant
kareneilbeck
sequence
A sequence variant which does not cause a disruption of the translational reading frame.
SO:ke
cds-indel
VAAST:inframe_variant
ANNOVAR:nonframeshift block substitution
http://www.openbioinformatics.org/annovar/annovar_download.html
retinoic_acid_responsive_element
2010-08-03T10:46:12Z
A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.
RARE
SO:0001653
kareneilbeck
retinoic acid responsive element
sequence
A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.
PMID:11327309
PMID:19917671
nucleotide_to_protein_binding_site
2010-08-03T12:26:05Z
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
SO:0001654
kareneilbeck
nucleotide to protein binding site
sequence
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
SO:ke
nucleotide_binding_site
2010-08-03T12:30:04Z
A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.
SO:0001655
See GO:0000166 : nucleotide binding.
kareneilbeck
np_bind
nucleotide binding site
sequence
np_bind
uniprot:feature
A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.
SO:cb
metal_binding_site
2010-08-03T12:31:42Z
A binding site that, in the molecule, interacts selectively and non-covalently with metal ions.
SO:0001656
See GO:0046872 : metal ion binding.
kareneilbeck
metal binding site
sequence
A binding site that, in the molecule, interacts selectively and non-covalently with metal ions.
SO:cb
ligand_binding_site
2010-08-03T12:32:58Z
A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone.
SO:0001657
kareneilbeck
ligand binding site
sequence
A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone.
SO:ke
nested_tandem_repeat
2010-08-26T09:36:16Z
An NTR is a nested repeat of two distinct tandem motifs interspersed with each other.
NTR
SO:0001658
Tracker ID: 3052459.
kareneilbeck
nested tandem repeat
sequence
An NTR is a nested repeat of two distinct tandem motifs interspersed with each other.
SO:AF
promoter_element
2010-10-01T11:48:32Z
SO:0001659
kareneilbeck
promoter element
sequence
core_promoter_element
2010-10-01T11:49:03Z
SO:0001660
core promoter element
general transcription factor binding site
kareneilbeck
sequence
RNA_polymerase_II_TATA_box
2010-10-01T02:42:12Z
A TATA box core promoter of a gene transcribed by RNA polymerase II.
RNA polymerase II TATA box
SO:0001661
kareneilbeck
sequence
A TATA box core promoter of a gene transcribed by RNA polymerase II.
PMID:16858867
RNA_polymerase_III_TATA_box
2010-10-01T02:43:16Z
A TATA box core promoter of a gene transcribed by RNA polymerase III.
RNA polymerase III TATA box
SO:0001662
kareneilbeck
sequence
A TATA box core promoter of a gene transcribed by RNA polymerase III.
SO:ke
BREd_motif
2010-10-01T02:49:55Z
A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G).
BREd
BREd motif
SO:0001663
kareneilbeck
sequence
A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G).
PMID:16858867
DCE
2010-10-01T02:56:41Z
A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII.
SO:0001664
downstream core element
kareneilbeck
sequence
A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII.
PMID:16858867
DCE_SI
2010-10-01T03:00:10Z
A sub element of the DCE core promoter element, with consensus sequence CTTC.
DCE SI
SO:0001665
kareneilbeck
sequence
A sub element of the DCE core promoter element, with consensus sequence CTTC.
PMID:16858867
SO:ke
DCE_SII
2010-10-01T03:00:30Z
A sub element of the DCE core promoter element with consensus sequence CTGT.
DCE SII
SO:0001666
kareneilbeck
sequence
A sub element of the DCE core promoter element with consensus sequence CTGT.
PMID:16858867
SO:ke
DCE_SIII
2010-10-01T03:00:44Z
A sub element of the DCE core promoter element with consensus sequence AGC.
DCE SIII
SO:0001667
kareneilbeck
sequence
A sub element of the DCE core promoter element with consensus sequence AGC.
PMID:16858867
SO:ke
proximal_promoter_element
2010-10-01T03:10:23Z
DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor).
SO:0001668
kareneilbeck
proximal promoter element
sequence
specific transcription factor binding site
DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor).
PMID:12515390
PMID:9679020
SO:ml
RNApol_II_core_promoter
2010-10-01T03:13:41Z
RNApol II core promoter
SO:0001669
The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.
kareneilbeck
sequence
PMID:16858867
The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.
distal_promoter_element
2010-10-01T03:21:08Z
SO:0001670
distal promoter element
kareneilbeck
sequence
bacterial_RNApol_promoter_sigma_70
2010-10-06T01:41:34Z
SO:0001671
bacterial RNA polymerase promoter sigma 70
kareneilbeck
sequence
bacterial_RNApol_promoter_sigma54
2010-10-06T01:42:37Z
SO:0001672
bacterial RNA polymerase promoter sigma54
kareneilbeck
sequence
minus_12_signal
2010-10-06T01:44:57Z
A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.
SO:0001673
kareneilbeck
minus 12 signal
sequence
A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.
PMID:18331472
minus_24_signal
2010-10-06T01:45:24Z
A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.
SO:0001674
kareneilbeck
minus 24 signal
sequence
A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.
PMID:18331472
A_box_type_1
2010-10-06T05:43:43Z
A box type 1
An A box within an RNA polymerase III type 1 promoter.
SO:0001675
The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
kareneilbeck
sequence
An A box within an RNA polymerase III type 1 promoter.
SO:ke
A_box_type_2
2010-10-06T05:44:18Z
A box type 2
An A box within an RNA polymerase III type 2 promoter.
SO:0001676
The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
kareneilbeck
sequence
An A box within an RNA polymerase III type 2 promoter.
SO:ke
intermediate_element
2010-10-06T05:52:03Z
A core promoter region of RNA polymerase III type 1 promoters.
IE
SO:0001677
intermediate element
kareneilbeck
sequence
A core promoter region of RNA polymerase III type 1 promoters.
PMID:12381659
regulatory_promoter_element
2010-10-07T04:39:48Z
A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region.
SO:0001678
kareneilbeck
regulatory promoter element
sequence
A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region.
PMID:12381659
transcription_regulatory_region
2010-10-12T03:49:35Z
A regulatory region that is involved in the control of the process of transcription.
SO:0001679
kareneilbeck
sequence
transcription regulatory region
A regulatory region that is involved in the control of the process of transcription.
SO:ke
translation_regulatory_region
2010-10-12T03:52:45Z
A regulatory region that is involved in the control of the process of translation.
SO:0001680
kareneilbeck
sequence
translation regulatory region
A regulatory region that is involved in the control of the process of translation.
SO:ke
recombination_regulatory_region
2010-10-12T03:53:35Z
A regulatory region that is involved in the control of the process of recombination.
SO:0001681
kareneilbeck
recombination regulatory region
sequence
A regulatory region that is involved in the control of the process of recombination.
SO:ke
replication_regulatory_region
2010-10-12T03:54:09Z
A regulatory region that is involved in the control of the process of nucleotide replication.
SO:0001682
kareneilbeck
replication regulatory region
sequence
A regulatory region that is involved in the control of the process of nucleotide replication.
SO:ke
sequence_motif
2010-10-14T04:13:22Z
A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
SO:0001683
http://en.wikipedia.org/wiki/Sequence_motif
kareneilbeck
sequence
sequence motif
wikipedia
http://en.wikipedia.org/wiki/Sequence_motif
A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
http://en.wikipedia.org/wiki/Sequence_motif
experimental_feature_attribute
2010-10-28T02:22:23Z
An attribute of an experimentally derived feature.
SO:0001684
experimental feature attribute
kareneilbeck
sequence
An attribute of an experimentally derived feature.
SO:ke
score
2010-10-28T02:23:16Z
SO:0001685
The score of an experimentally derived feature such as a p-value.
kareneilbeck
sequence
SO:ke
The score of an experimentally derived feature such as a p-value.
quality_value
2010-10-28T02:24:11Z
An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score.
SO:0001686
kareneilbeck
quality value
sequence
An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score.
SO:ke
restriction_enzyme_recognition_site
2010-10-29T12:29:57Z
SO:0001687
The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.
kareneilbeck
restriction endonuclease recognition site
restriction enzyme recognition site
sequence
SO:ke
The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.
restriction_enzyme_cleavage_junction
2010-10-29T12:35:02Z
SO:0001688
The boundary at which a restriction enzyme breaks the nucleotide sequence.
kareneilbeck
restriction enzyme cleavage junction
sequence
SO:ke
The boundary at which a restriction enzyme breaks the nucleotide sequence.
five_prime_restriction_enzyme_junction
2010-10-29T12:36:24Z
5' restriction enzyme junction
SO:0001689
The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence.
kareneilbeck
sequence
SO:ke
The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence.
three_prime_restriction_enzyme_junction
2010-10-29T12:37:52Z
3' restriction enzyme junction
SO:0001690
kareneilbeck
sequence
blunt_end_restriction_enzyme_cleavage_site
2010-10-29T12:39:53Z
SO:0001691
blunt end restriction enzyme cleavage site
kareneilbeck
sequence
sticky_end_restriction_enzyme_cleavage_site
2010-10-29T12:40:50Z
SO:0001692
kareneilbeck
sequence
sticky end restriction enzyme cleavage site
blunt_end_restriction_enzyme_cleavage_junction
2010-10-29T12:43:14Z
A restriction enzyme cleavage site where both strands are cut at the same position.
SO:0001693
blunt end restriction enzyme cleavage site
kareneilbeck
sequence
A restriction enzyme cleavage site where both strands are cut at the same position.
SO:ke
single_strand_restriction_enzyme_cleavage_site
2010-10-29T12:44:48Z
A restriction enzyme cleavage site whereby only one strand is cut.
SO:0001694
kareneilbeck
sequence
single strand restriction enzyme cleavage site
A restriction enzyme cleavage site whereby only one strand is cut.
SO:ke
restriction_enzyme_single_strand_overhang
2010-10-29T12:48:35Z
A terminal region of DNA sequence where the end of the region is not blunt ended.
SO:0001695
kareneilbeck
sequence
single strand overhang
sticky end
A terminal region of DNA sequence where the end of the region is not blunt ended.
SO:ke
experimentally_defined_binding_region
2010-11-02T11:39:59Z
A region that has been implicated in binding although the exact coordinates of binding may be unknown.
SO:0001696
experimentally defined binding region
kareneilbeck
sequence
A region that has been implicated in binding although the exact coordinates of binding may be unknown.
SO:ke
ChIP_seq_region
2010-11-02T11:43:07Z
A region of sequence identified by CHiP seq technology to contain a protein binding site.
ChIP seq region
SO:0001697
kareneilbeck
sequence
A region of sequence identified by CHiP seq technology to contain a protein binding site.
SO:ke
ASPE_primer
"A primer containing an SNV at the 3' end for accurate genotyping.
2010-11-11T03:25:21Z
ASPE primer
SO:0001698
allele specific primer extension primer
kareneilbeck
sequence
"A primer containing an SNV at the 3' end for accurate genotyping.
http://www.ncbi.nlm.nih.gov/pubmed/11252801
dCAPS_primer
2010-11-11T03:27:09Z
A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site.
SO:0001699
dCAPS primer
derived cleaved amplified polymorphic primer
kareneilbeck
sequence
A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site.
http://www.ncbi.nlm.nih.gov/pubmed/9628033
histone_modification
2010-03-31T10:22:08Z
Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation.
SO:0001700
histone modification
histone modification site
kareneilbeck
sequence
Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation.
http:en.wikipedia.org/wiki/Histone
histone_methylation_site
2010-03-31T10:23:02Z
A histone modification site where the modification is the methylation of the residue.
SO:0001701
histone methylation
histone methylation site
kareneilbeck
sequence
A histone modification site where the modification is the methylation of the residue.
SO:ke
histone_acetylation_site
2010-03-31T10:23:27Z
A histone modification where the modification is the acylation of the residue.
SO:0001702
histone acetylation
histone acetylation site
kareneilbeck
sequence
A histone modification where the modification is the acylation of the residue.
SO:ke
H3K9_acetylation_site
2010-03-31T10:25:05Z
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated.
H3K9 acetylation site
H3K9Ac
SO:0001703
kareneilbeck
sequence
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated.
http://en.wikipedia.org/wiki/Histone
H3K14_acetylation_site
2010-03-31T10:25:53Z
A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated.
H3K14 acetylation site
H3K14Ac
SO:0001704
kareneilbeck
sequence
A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated.
http://en.wikipedia.org/wiki/Histone
H3K4_monomethylation_site
2010-03-31T10:28:14Z
A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated.
H3K4 mono-methylation site
H3K4me1
SO:0001705
kareneilbeck
sequence
A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated.
http://en.wikipedia.org/wiki/Histone
H3K4_trimethylation
2010-03-31T10:29:12Z
A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated.
H3K4 tri-methylation
H3K4me3
SO:0001706
kareneilbeck
sequence
A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated.
http://en.wikipedia.org/wiki/Histone
H3K9_trimethylation_site
2010-03-31T10:30:34Z
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
H3K9 tri-methylation site
H3K9Me3
SO:0001707
kareneilbeck
sequence
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
http://en.wikipedia.org/wiki/Histone
H3K27_monomethylation_site
2010-03-31T10:31:54Z
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
H2K27 mono-methylation site
H2K27Me1
SO:0001708
kareneilbeck
sequence
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
http://en.wikipedia.org/wiki/Histone
H3K27_trimethylation_site
2010-03-31T10:32:41Z
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
H3K27 tri-methylation site
H3K27Me3
SO:0001709
kareneilbeck
sequence
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
http://en.wikipedia.org/wiki/Histone
H3K79_monomethylation_site
2010-03-31T10:33:42Z
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated.
H3K79 mono-methylation site
H3K79me1
SO:0001710
kareneilbeck
sequence
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated.
http://en.wikipedia.org/wiki/Histone
H3K79_dimethylation_site
2010-03-31T10:34:39Z
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated.
H3K79 di-methylation site
H3K79Me2
SO:0001711
kareneilbeck
sequence
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated.
http://en.wikipedia.org/wiki/Histone
H3K79_trimethylation_site
2010-03-31T10:35:30Z
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
H3K79 tri-methylation site
H3K79Me3
SO:0001712
kareneilbeck
sequence
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
http://en.wikipedia.org/wiki/Histone
H4K20_monomethylation_site
2010-03-31T10:36:43Z
A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated.
H4K20 mono-methylation site
H4K20Me1
SO:0001713
kareneilbeck
sequence
A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated.
http://en.wikipedia.org/wiki/Histone
H2BK5_monomethylation_site
2010-03-31T10:38:12Z
A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated.
H2BK5 mono-methylation site
SO:0001714
kareneilbeck
sequence
A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated.
http://en.wikipedia.org/wiki/Histone
ISRE
2010-04-05T11:15:08Z
An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.
SO:0001715
Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term.
interferon stimulated response element
kareneilbeck
sequence
An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.
http://genesdev.cshlp.org/content/2/4/383.abstrac
histone_ubiqitination_site
2010-04-13T10:12:18Z
A histone modification site where ubiquitin may be added.
SO:0001716
histone ubiquitination site
kareneilbeck
sequence
A histone modification site where ubiquitin may be added.
SO:ke
H2B_ubiquitination_site
2010-04-13T10:13:28Z
A histone modification site on H2B where ubiquitin may be added.
H2BUbiq
SO:0001717
kareneilbeck
sequence
A histone modification site on H2B where ubiquitin may be added.
SO:ke
H3K18_acetylation_site
2010-04-13T10:39:35Z
A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated.
H3K18 acetylation site
H3K18Ac
SO:0001718
kareneilbeck
sequence
A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated.
SO:ke
H3K23_acylation_site
2010-04-13T10:42:45Z
A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated.
H3K23 acylation site
H3K23Ac
SO:0001719
kareneilbeck
sequence
A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated.
SO:ke
epigenetically_modified_region
2010-03-27T12:02:29Z
A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence.
SO:0001720
epigenetically modified region
kareneilbeck
sequence
A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence.
SO:ke
http://en.wikipedia.org/wiki/Epigenetics
H3K27_acylation_site
2010-04-13T10:44:09Z
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated.
H3K27 acylation site
H3K27Ac
SO:0001721
kareneilbeck
sequence
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated.
SO:ke
H3K36_monomethylation_site
2010-04-13T10:46:32Z
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
H3K36 mono-methylation site
H3K36<Me1
SO:0001722
kareneilbeck
sequence
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
SO:ke
H3K36_dimethylation_site
2010-04-13T10:59:35Z
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated.
H3K36 di-methylation site
H3K36Me2
SO:0001723
kareneilbeck
sequence
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated.
SO:ke
H3K36_trimethylation_site
2010-04-13T11:01:58Z
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
H3K36 tri-methylation site
H3K36Me3
SO:0001724
kareneilbeck
sequence
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated.
SO:ke
H3K4_dimethylation_site
2010-04-13T11:03:15Z
A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated.
H3K4 di-methylation site
H3K4Me2
SO:0001725
kareneilbeck
sequence
A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated.
SO:ke
H3K27_dimethylation_site
2010-04-13T01:45:41Z
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated.
H3K27 di-methylation site
H3K27Me2
SO:0001726
kareneilbeck
sequence
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated.
SO:ke
H3K9_monomethylation_site
2010-04-13T11:06:17Z
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
H3K9 mono-methylation site
H3K9Me1
SO:0001727
kareneilbeck
sequence
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated.
SO:ke
H3K9_dimethylation_site
2010-04-13T11:08:19Z
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated.
H3K9 di-methylation site
H3K9Me2
SO:0001728
kareneilbeck
sequence
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated.
SO:ke
H4K16_acylation_site
2010-04-13T11:09:41Z
A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated.
H4K16 acylation_site
H4K16Ac
SO:0001729
kareneilbeck
sequence
A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated.
SO:ke
H4K5_acylation_site
2010-04-13T11:13:00Z
A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated.
H4K5 acylation site
H4K5Ac
SO:0001730
kareneilbeck
sequence
A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated.
SO:ke
H4K8_acylation_site
2010-04-13T11:14:24Z
A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated.
H4K8 acylation site
H4K8Ac
SO:0001731
kareneilbeck
sequence
A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated.
SO:KE
H3K27_methylation_site
2010-04-13T11:26:22Z
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated.
H3K27 methylation site
SO:0001732
kareneilbeck
sequence
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated.
SO:ke
H3K36_methylation_site
2010-04-13T11:27:28Z
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated.
H3K36 methylation site
SO:0001733
kareneilbeck
sequence
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated.
SO:ke
H3K4_methylation_site
2010-04-13T11:28:14Z
A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated.
H3K4 methylation site
SO:0001734
kareneilbeck
sequence
A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated.
SO:ke
H3K79_methylation_site
2010-04-13T11:29:16Z
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated.
H3K79 methylation site
SO:0001735
kareneilbeck
sequence
A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated.
SO:ke
H3K9_methylation_site
2010-04-13T11:31:37Z
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated.
H3K9 methylation site
SO:0001736
kareneilbeck
sequence
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated.
SO:ke
histone_acylation_region
2010-04-13T01:58:21Z
A histone modification, whereby the histone protein is acylated at multiple sites in a region.
SO:0001737
histone acylation region
kareneilbeck
sequence
A histone modification, whereby the histone protein is acylated at multiple sites in a region.
SO:ke
H4K_acylation_region
2010-04-13T02:00:06Z
A region of the H4 histone whereby multiple lysines are acylated.
H4K acylation region
H4KAc
SO:0001738
kareneilbeck
sequence
A region of the H4 histone whereby multiple lysines are acylated.
SO:ke
gene_with_non_canonical_start_codon
2011-01-10T01:30:31Z
A gene with a start codon other than AUG.
Requested by flybase, Dec 2010.
SO:0001739
gene with non canonical start codon
kareneilbeck
sequence
A gene with a start codon other than AUG.
SO:xp
gene_with_start_codon_CUG
2011-01-10T01:32:35Z
A gene with a translational start codon of CUG.
Requested by flybase, Dec 2010.
SO:0001740
gene with start codon CUG
kareneilbeck
sequence
A gene with a translational start codon of CUG.
SO:mc
pseudogenic_gene_segment
2011-02-15T05:07:52Z
A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product.
SO:0001741
batchelorc
pseudogenic gene segment
sequence
A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product.
SO:hd
copy_number_gain
2011-02-28T01:54:09Z
A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.
SO:0001742
copy number gain
gain
kareneilbeck
sequence
gain
http://www.ncbi.nlm.nih.gov/dbvar/
A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.
SO:ke
copy_number_loss
2011-02-28T01:55:02Z
A sequence alteration whereby the copy number of a given region is less than the reference sequence.
SO:0001743
copy number loss
kareneilbeck
loss
sequence
http://www.ncbi.nlm.nih.gov/dbvar/
loss
A sequence alteration whereby the copy number of a given region is less than the reference sequence.
SO:ke
UPD
2011-02-28T02:01:05Z
SO:0001744
UPD
Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent.
http:http://en.wikipedia.org/wiki/Uniparental_disomy
kareneilbeck
sequence
uniparental disomy
SO:BM
Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent.
UPD
http://www.ncbi.nlm.nih.gov/dbvar/
wikipedia
http:http://en.wikipedia.org/wiki/Uniparental_disomy
maternal_uniparental_disomy
2011-02-28T02:03:01Z
SO:0001745
Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father.
kareneilbeck
maternal uniparental disomy
sequence
SO:bm
Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father.
paternal_uniparental_disomy
2011-02-28T02:03:30Z
SO:0001746
Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother.
kareneilbeck
paternal uniparental disomy
sequence
SO:bm
Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother.
open_chromatin_region
2011-02-28T02:21:52Z
A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA.
Requested by John Calley 3125900.
SO:0001747
kareneilbeck
open chromatin region
sequence
A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA.
SO:cb
SL3_acceptor_site
2011-02-28T02:58:40Z
A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SL3 acceptor site
SO:0001748
kareneilbeck
sequence
A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
SL4_acceptor_site
2011-02-28T03:08:47Z
A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SL4 acceptor site
SO:0001749
kareneilbeck
sequence
A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
SL5_acceptor_site
2011-02-28T03:09:36Z
A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SL5 acceptor site
SO:0001750
kareneilbeck
sequence
A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
SL6_acceptor_site
2011-02-28T03:10:14Z
A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SL6 acceptor site
SO:0001751
kareneilbeck
sequence
A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
SL7_acceptor_site
2011-02-28T03:13:20Z
A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SL37 acceptor site
SO:0001752
kareneilbeck
sequence
A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
SL8_acceptor_site
2011-02-28T03:15:26Z
A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SL8 acceptor site
SO:0001753
kareneilbeck
sequence
A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
SL9_acceptor_site
2011-02-28T03:15:57Z
A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SL9 acceptor site
SO:0001754
kareneilbeck
sequence
A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
SL10_acceptor_site
2011-02-28T03:16:31Z
A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SL10 acceptor site
SO:0001755
kareneilbeck
sequence
A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
SL11_acceptor_site
2011-02-28T03:16:54Z
A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SL11 acceptor site
SO:0001756
kareneilbeck
sequence
A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
SL12_acceptor_site
2011-02-28T03:17:23Z
A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SL12 acceptor site
SO:0001757
kareneilbeck
sequence
A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts.
SO:nlw
duplicated_pseudogene
2011-03-09T09:58:04Z
A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence.
SO:0001758
duplicated pseudogene
kareneilbeck
sequence
A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence.
http://en.wikipedia.org/wiki/Pseudogene
unitary_pseudogene
2011-03-09T10:04:04Z
A pseudogene, deactivated from original state by mutation, fixed in a population.
SO:0001759
This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates.
disabled gene
kareneilbeck
sequence
unitary pseudogene
A pseudogene, deactivated from original state by mutation, fixed in a population.
SO:ke
http://en.wikipedia.org/wiki/Pseudogene
non_processed_pseudogene
2011-03-09T10:54:47Z
A pseudogene that arose from a means other than retrotransposition.
SO:0001760
kareneilbeck
non processed pseudogene
sequence
A pseudogene that arose from a means other than retrotransposition.
SO:ke
variant_quality
2011-03-15T03:40:35Z
A dependent entity that inheres in a bearer, a sequence variant.
SO:0001761
kareneilbeck
sequence
variant quality
A dependent entity that inheres in a bearer, a sequence variant.
PMID:17597783
SO:ke
variant_origin
2011-03-15T03:42:13Z
A quality inhering in a variant by virtue of its origin.
SO:0001762
kareneilbeck
sequence
variant origin
A quality inhering in a variant by virtue of its origin.
PMID:17597783
SO:ke
variant_frequency
2011-03-15T03:44:39Z
A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.
SO:0001763
kareneilbeck
sequence
variant frequency
A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.
PMID:17597783
SO:ke
unique_variant
2011-03-15T03:47:20Z
A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.
SO:0001764
kareneilbeck
sequence
unique variant
A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.
SO:ke
rare_variant
2011-03-15T03:48:29Z
SO:0001765
kareneilbeck
rare variant
sequence
polymorphic_variant
2011-03-15T03:48:51Z
SO:0001766
kareneilbeck
polymorphic variant
sequence
common_variant
2011-03-15T03:50:36Z
SO:0001767
common variant
kareneilbeck
sequence
fixed_variant
2011-03-15T03:50:53Z
SO:0001768
fixed variant
kareneilbeck
sequence
variant_phenotype
2011-03-15T03:53:15Z
A quality inhering in a variant by virtue of its phenotype.
SO:0001769
kareneilbeck
sequence
variant phenotype
A quality inhering in a variant by virtue of its phenotype.
PMID:17597783
SO:ke
benign_variant
2011-03-15T03:55:40Z
SO:0001770
benign variant
kareneilbeck
sequence
disease_associated_variant
2011-03-15T04:05:16Z
SO:0001771
disease associated variant
kareneilbeck
sequence
disease_causing_variant
2011-03-15T04:05:46Z
SO:0001772
disease causing variant
kareneilbeck
sequence
lethal_variant
2011-03-15T04:06:22Z
SO:0001773
kareneilbeck
lethal variant
sequence
quantitative_variant
2011-03-15T04:28:13Z
SO:0001774
kareneilbeck
quantitative variant
sequence
maternal_variant
2011-03-15T04:30:23Z
SO:0001775
kareneilbeck
maternal variant
sequence
paternal_variant
2011-03-15T04:30:47Z
SO:0001776
kareneilbeck
paternal variant
sequence
somatic_variant
2011-03-15T04:31:12Z
SO:0001777
kareneilbeck
sequence
somatic variant
germline_variant
2011-03-15T04:31:46Z
SO:0001778
germline variant
kareneilbeck
sequence
pedigree_specific_variant
2011-03-15T04:32:18Z
SO:0001779
kareneilbeck
pedigree specific variant
sequence
population_specific_variant
2011-03-15T04:33:05Z
SO:0001780
kareneilbeck
population specific variant
sequence
de_novo_variant
2011-03-15T04:33:34Z
SO:0001781
de novo variant
kareneilbeck
sequence
TF_binding_site_variant
2011-03-17T10:59:20Z
A sequence variant located within a transcription factor binding site.
SO:0001782
TF binding site variant
kareneilbeck
sequence
A sequence variant located within a transcription factor binding site.
EBI:fc
complex_structural_alteration
2011-03-23T03:21:19Z
A structural sequence alteration or rearrangement encompassing one or more genome fragments.
SO:0001784
complex
kareneilbeck
sequence
A structural sequence alteration or rearrangement encompassing one or more genome fragments.
NCBI:th
SO:ke
complex
http://www.ncbi.nlm.nih.gov/dbvar/
structural_alteration
2011-03-25T02:27:41Z
SO:0001785
kareneilbeck
sequence
structural alteration
loss_of_heterozygosity
2011-03-25T02:32:58Z
A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene.
LOH
SO:0001786
kareneilbeck
loss of heterozygosity
sequence
A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene.
SO:ke
splice_donor_5th_base_variant
2011-04-05T04:16:28Z
A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript.
SO:0001787
kareneilbeck
sequence
splice donor 5th base variant
A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript.
EBI:gr
U_box
2011-04-08T10:39:14Z
An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription.
SO:0001788
U-box
kareneilbeck
sequence
An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription.
PMID:10556309
PMID:11577982
PMID:9649446
mating_type_region
2011-04-08T11:14:07Z
A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type.
SO:0001789
http://en.wikipedia.org/wiki/Mating-type_region
kareneilbeck
mating type region
sequence
A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type.
SO:ke
paired_end_fragment
2011-04-14T01:48:20Z
An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair).
SO:0001790
kareneilbeck
paired end fragment
sequence
An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair).
SO:ke
exon_variant
2011-05-06T01:51:17Z
A sequence variant that changes exon sequence.
ANNOVAR:exonic
SO:0001791
VAAST:exon_variant
exon variant
kareneilbeck
sequence
snpEff:EXON
ANNOVAR:exonic
http://www.openbioinformatics.org/annovar/annovar_download.html
snpEff:EXON
VAAST:exon_variant
A sequence variant that changes exon sequence.
SO:ke
non_coding_transcript_exon_variant
2011-05-06T01:51:59Z
A sequence variant that changes non-coding exon sequence in a non-coding transcript.
SO:0001792
kareneilbeck
non coding transcript exon variant
sequence
A sequence variant that changes non-coding exon sequence in a non-coding transcript.
EBI:fc
SO:ke
clone_end
2011-05-13T11:32:27Z
A read from an end of the clone sequence.
SO:0001793
clone end
kareneilbeck
sequence
A read from an end of the clone sequence.
SO:ke
point_centromere
2011-05-31T12:42:35Z
A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae.
SO:0001794
kareneilbeck
point centromere
sequence
A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae.
PMID:7502067
SO:vw
regional_centromere
2011-05-31T12:43:07Z
A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions.
SO:0001795
kareneilbeck
regional centromere
sequence
A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions.
PMID:7502067
SO:vw
regional_centromere_central_core
2011-05-31T12:56:30Z
A conserved region within the central region of a modular centromere, where the kinetochore is formed.
SO:0001796
kareneilbeck
regional centromere central core
sequence
A conserved region within the central region of a modular centromere, where the kinetochore is formed.
SO:vw
centromeric_repeat
2011-05-31T12:59:27Z
A repeat region found within the modular centromere.
SO:0001797
centromeric repeat
kareneilbeck
sequence
A repeat region found within the modular centromere.
SO:ke
regional_centromere_inner_repeat_region
2011-05-31T01:01:08Z
SO:0001798
The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm.
kareneilbeck
lmr repeat
lmr1L
lmr1R
regional centromere inner repeat region
sequence
SO:vw
The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm.
regional_centromere_outer_repeat_region
2011-05-31T01:03:23Z
SO:0001799
The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms.
kareneilbeck
regional centromere outer repeat region
sequence
SO:vw
The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms.
tasiRNA
2011-05-31T03:24:06Z
SO:0001800
The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene.
kareneilbeck
sequence
trans acting small interfering RNA
PMID:16145017
The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene.
tasiRNA_primary_transcript
2011-05-31T03:27:35Z
A primary transcript encoding a tasiRNA.
SO:0001801
kareneilbeck
sequence
tasiRNA primary transcript
A primary transcript encoding a tasiRNA.
PMID:16145017
increased_polyadenylation_variant
2011-06-01T10:53:12Z
A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference.
SO:0001802
Term requested by M. Dumontier, June 1 2011.
increased polyadenylation variant
kareneilbeck
sequence
A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference.
SO:ke
decreased_polyadenylation_variant
2011-06-01T10:53:40Z
A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference.
SO:0001803
Term requested by M. Dumontier, June 1 2011.
decreased polyadenylation variant
kareneilbeck
sequence
A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference.
SO:ke
DDB_box
2011-06-17T12:10:44Z
A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases.
DDB box
DDB-box
Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence.
SO:0001804
kareneilbeck
sequence
A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases.
PMID:18794354
PMID:19818632
destruction_box
2011-06-17T12:16:02Z
A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN.
D-box
SO:0001805
destruction box
kareneilbeck
sequence
A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN.
PMID:12208841
PMID:1842691
ER_retention_signal
2011-06-17T12:19:49Z
A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL.
ER retention signal
SO:0001806
endoplasmic reticulum retention signal
kareneilbeck
sequence
A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL.
PMID:2077689
doi:10.1093/jxb/50.331.157
KEN_box
2011-06-17T12:24:14Z
A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN.
KEN box
SO:0001807
kareneilbeck
sequence
A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN.
PMID:10733526
PMID:1220884
PMID:18426916
mitochondrial_targeting_signal
2011-06-17T12:26:35Z
A polypeptide region that targets a polypeptide to the mitochondrion.
MTS
SO:0001808
kareneilbeck
mitochondrial signal sequence
mitochondrial targeting signal
sequence
A polypeptide region that targets a polypeptide to the mitochondrion.
PomBase:mah
signal_anchor
2011-06-17T12:28:53Z
A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane.
SO:0001809
kareneilbeck
sequence
signal anchor
uncleaved signal peptide
A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane.
http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php
PIP_box
2011-06-17T12:33:25Z
A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains.
PIP box
SO:0001810
kareneilbeck
sequence
A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains.
PMID:9631646
phosphorylation_site
2011-06-17T12:36:20Z
A post-translationally modified region in which residues of the protein are modified by phosphorylation.
SO:0001811
kareneilbeck
phosphorylation site
sequence
A post-translationally modified region in which residues of the protein are modified by phosphorylation.
PomBase:mah
transmembrane_helix
2011-06-17T12:39:46Z
A region that traverses the lipid bilayer and adopts a helical secondary structure.
SO:0001812
kareneilbeck
sequence
transmembrane helix
A region that traverses the lipid bilayer and adopts a helical secondary structure.
PomBase:mah
vacuolar_sorting_signal
2011-06-17T12:42:48Z
A polypeptide region that targets a polypeptide to the vacuole.
SO:0001813
kareneilbeck
sequence
vacuolar sorting signal
A polypeptide region that targets a polypeptide to the vacuole.
PomBase:mah
coding_variant_quality
2011-06-24T03:32:25Z
SO:0001814
coding variant quality
kareneilbeck
sequence
synonymous
2011-06-24T03:33:16Z
SO:0001815
kareneilbeck
sequence
non_synonymous
2011-06-24T03:33:36Z
SO:0001816
kareneilbeck
non synonymous
sequence
inframe
2011-06-24T03:34:03Z
An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3.
SO:0001817
kareneilbeck
sequence
An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3.
SO:ke
protein_altering_variant
2011-06-24T03:38:02Z
A sequence_variant which is predicted to change the protein encoded in the coding sequence.
SO:0001818
kareneilbeck
protein altering variant
sequence
A sequence_variant which is predicted to change the protein encoded in the coding sequence.
EBI:gr
synonymous_variant
2011-06-24T03:38:30Z
A sequence variant where there is no resulting change to the encoded amino acid.
ANNOVAR:synonymous SNV
EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).
This term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
SO:0001588
SO:0001819
VAAST:synonymous_codon
coding-synon
http://en.wikipedia.org/wiki/Silent_mutation
http://en.wikipedia.org/wiki/Synonymous_mutation
kareneilbeck
sequence
silent mutation
silent substitution
silent_mutation
snpEff:SYNONYMOUS_CODING
synonymous codon
synonymous_coding
synonymous_codon
coding-synon
ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd
A sequence variant where there is no resulting change to the encoded amino acid.
SO:ke
wiki
http://en.wikipedia.org/wiki/Silent_mutation
snpEff:SYNONYMOUS_CODING
VAAST:synonymous_codon
ANNOVAR:synonymous SNV
http://www.openbioinformatics.org/annovar/annovar_download.html
inframe_indel
2011-06-27T11:25:33Z
A coding sequence variant where the change does not alter the frame of the transcript.
SO:0001820
inframe change in CDS length
inframe indel
kareneilbeck
sequence
A coding sequence variant where the change does not alter the frame of the transcript.
SO:ke
inframe_insertion
2011-06-27T11:26:22Z
ANNOVAR:nonframeshift insertion
An inframe non synonymous variant that inserts bases into in the coding sequence.
SO:0001651
SO:0001821
inframe codon gain
inframe increase in CDS length
inframe insertion
inframe_codon_gain
kareneilbeck
sequence
snpEFF:CODON_INSERTION
snpEFF:CODON_INSERTION
ANNOVAR:nonframeshift insertion
http://www.openbioinformatics.org/annovar/annovar_download.html
An inframe non synonymous variant that inserts bases into in the coding sequence.
EBI:gr
inframe_deletion
2011-06-27T11:27:10Z
ANNOVAR:nonframeshift deletion
An inframe non synonymous variant that deletes bases from the coding sequence.
SO:0001652
SO:0001822
inframe codon loss
inframe decrease in CDS length
inframe deletion
inframe_codon_loss
kareneilbeck
sequence
snpEff:CODON_DELETION
ANNOVAR:nonframeshift deletion
http://www.openbioinformatics.org/annovar/annovar_download.html
snpEff:CODON_DELETION
An inframe non synonymous variant that deletes bases from the coding sequence.
EBI:gr
conservative_inframe_insertion
2011-06-27T11:28:02Z
An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons.
SO:0001823
conservative increase in CDS length
conservative inframe insertion
kareneilbeck
sequence
An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons.
EBI:gr
disruptive_inframe_insertion
2011-06-27T11:28:37Z
An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon.
SO:0001824
disruptive increase in CDS length
disruptive inframe insertion
kareneilbeck
sequence
snpEff:CODON_CHANGE_PLUS_CODON_INSERTION
An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon.
EBI:gr
snpEff:CODON_CHANGE_PLUS_CODON_INSERTION
conservative_inframe_deletion
2011-06-27T11:30:43Z
An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons.
SO:0001825
conservative decrease in CDS length
conservative inframe deletion
kareneilbeck
sequence
An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons.
EBI:gr
disruptive_inframe_deletion
2011-06-27T11:31:31Z
An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon.
SO:0001826
disruptive decrease in CDS length
disruptive inframe deletion
kareneilbeck
sequence
snpEff:CODON_CHANGE_PLUS_CODON_DELETION
snpEff:CODON_CHANGE_PLUS_CODON_DELETION
An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon.
EBI:gr
mRNA_read
2011-06-28T04:04:32Z
A sequencer read of an mRNA substrate.
Requested by Bayer Cropscience June, 2011.
SO:0001827
kareneilbeck
mRNA read
sequence
A sequencer read of an mRNA substrate.
SO:ke
genomic_DNA_read
2011-06-28T04:06:10Z
A sequencer read of a genomic DNA substrate.
SO:0001828
genomic DNA read
kareneilbeck
sequence
A sequencer read of a genomic DNA substrate.
SO:ke
mRNA_contig
2011-06-28T04:07:09Z
A contig composed of mRNA_reads.
Requested by Bayer Cropscience June, 2011.
SO:0001829
kareneilbeck
mRNA contig
sequence
A contig composed of mRNA_reads.
SO:ke
AFLP_fragment
2011-07-14T12:12:35Z
A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments.
AFLP
AFLP fragment
AFLP-PCR
Requested by Bayer Cropscience June, 2011.
SO:0001830
amplified fragment length polymorphism
amplified fragment length polymorphism PCR
http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism
kareneilbeck
sequence
wiki
http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism
A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments.
GMOD:ea
protein_hmm_match
2011-08-11T03:20:27Z
A match to a protein HMM such as pfam.
SO:0001831
kareneilbeck
protein hmm match
sequence
A match to a protein HMM such as pfam.
SO:ke
immunoglobulin_region
2011-09-01T03:27:20Z
A region of immunoglobulin sequence, either constant or variable.
SO:0001832
immunoglobulin region
kareneilbeck
sequence
A region of immunoglobulin sequence, either constant or variable.
SO:ke
V_region
2011-09-01T03:28:40Z
SO:0001833
The variable region of an immunoglobulin polypeptide sequence.
V region
kareneilbeck
sequence
SO:ke
The variable region of an immunoglobulin polypeptide sequence.
C_region
2011-09-01T03:29:41Z
C region
SO:0001834
The constant region of an immunoglobulin polypeptide sequence.
kareneilbeck
sequence
SO:ke
The constant region of an immunoglobulin polypeptide sequence.
N_region
2011-09-01T03:50:16Z
Extra nucleotides inserted between rearranged immunoglobulin segments.
N-region
SO:0001835
kareneilbeck
sequence
Extra nucleotides inserted between rearranged immunoglobulin segments.
SO:ke
S_region
2011-09-01T03:52:05Z
S region
SO:0001836
The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell.
kareneilbeck
sequence
SO:ke
The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell.
mobile_element_insertion
2011-10-04T12:36:52Z
A kind of insertion where the inserted sequence is a mobile element.
Requested by the EBI.
SO:0001837
kareneilbeck
mobile element insertion
sequence
A kind of insertion where the inserted sequence is a mobile element.
EBI:dvga
novel_sequence_insertion
2011-10-04T01:14:50Z
An insertion the sequence of which cannot be mapped to the reference genome.
Requested by the NCBI.
SO:0001838
kareneilbeck
novel sequence insertion
sequence
An insertion the sequence of which cannot be mapped to the reference genome.
NCBI:th
CSL_response_element
2011-10-07T03:37:43Z
A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors.
CSL response element
SO:0001839
kareneilbeck
sequence
A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors.
PMID:19101542
GATA_box
2011-10-07T03:42:05Z
A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G).
GATA box
GATA element
SO:0001840
kareneilbeck
sequence
A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G).
PMID:8321208
polymorphic_pseudogene
2011-10-07T03:46:57Z
Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.
SO:0001841
This terms is used by Ensembl and Vega.
kareneilbeck
polymorphic psuedogene
sequence
JAX:hd
Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.
AP_1_binding_site
2011-10-07T03:54:52Z
A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors.
AP-1 binding site
SO:0001842
kareneilbeck
sequence
A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors.
PMID:1899230
PMID:3034432
PMID:3125983
CRE
2011-10-07T03:58:48Z
A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors.
ATF/CRE site
SO:0001843
cyclic AMP response element
kareneilbeck
sequence
A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors.
PMID:11483355
PMID:11483993
ATF/CRE site
PMID:11483993
CuRE
2011-10-07T04:02:51Z
A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast).
SO:0001844
copper-response element
kareneilbeck
sequence
A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast).
PMID:10593913
PMID:9188496
PMID:9211922
DRE
2011-10-07T04:17:25Z
A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis.
DNA damage response element
SO:0001845
kareneilbeck
sequence
A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis.
PMID:11073995
PMID:8668127
FLEX_element
2011-10-07T04:20:01Z
A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain.
FLEX element
SO:0001846
kareneilbeck
sequence
A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain.
PMID:10747048
PMID:14871934
forkhead_motif
2011-10-07T04:22:06Z
A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain.
SO:0001847
forkhead motif
kareneilbeck
sequence
A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain.
PMID:15195092
homol_D_box
2011-10-07T04:24:14Z
A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence.
SO:0001848
homol D box
kareneilbeck
sequence
A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence.
PMID:7501449
PMID:8458332
homol_E_box
2011-10-07T04:26:09Z
A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence.
SO:0001849
homol E box
kareneilbeck
sequence
A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence.
PMID:7501449
HSE
2011-10-07T04:29:10Z
A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF.
SO:0001850
heat shock element
kareneilbeck
sequence
A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF.
PMID:17347150
PMID:8689565
iron_repressed_GATA_element
2011-10-07T04:32:42Z
A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron.
IDP (GATA)
SO:0001851
The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes.
iron repressed GATA element
kareneilbeck
sequence
A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron.
PMID:11956219
PMID:17211681
mating_type_M_box
2011-10-07T04:39:43Z
A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc.
Note that this should not be confused with the M-box that has consensus sequence CATGTG and is bound by bHLH transcription factors such as MITF.
SO:0001852
kareneilbeck
mating type M-box
sequence
A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc.
PMID:9233811
androgen_response_element
2011-10-10T04:52:44Z
A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen.
ARE
SO:0001853
androgen response element
kareneilbeck
sequence
A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen.
PMID:21796522
smFISH_probe
2011-10-10T05:00:30Z
A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment.
SO:0001854
kareneilbeck
sequence
single molecule fish probe
smFISH probe
A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment.
PMID:18806792
MCB
2011-10-10T05:09:45Z
A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle.
MluI cell cycle box
SO:0001855
kareneilbeck
sequence
A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle.
PMID:16285853
CCAAT_motif
2011-10-10T05:13:54Z
A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels.
CCAAT motif
SO:0001856
kareneilbeck
sequence
A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels.
PMID:16963626
Ace2_UAS
2011-10-10T05:19:10Z
A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2.
Ace2 upstream activating sequence
SO:0001857
kareneilbeck
sequence
A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2.
PMID:16678171
TR_box
2011-10-10T05:22:13Z
A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis.
SO:0001858
TR box
kareneilbeck
sequence
A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis.
PMID:1657709
STREP_motif
2011-10-14T10:25:02Z
A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2.
SO:0001859
STREP motif
kareneilbeck
sequence
stress-starvation response element of Schizosaccharomyces pombe
A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2.
PMID:11739717
rDNA_intergenic_spacer_element
2011-10-19T11:23:09Z
A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1).
SO:0001860
kareneilbeck
rDIS
sequence
A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1).
PMID:9016645
sterol_regulatory_element
2011-10-19T03:02:05Z
A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs.
SO:0001861
SRE
kareneilbeck
sequence
A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs.
GO:mah
PMID:11111080
PMID:16537923
GO:mah
SRE
GT_dinucleotide_repeat
2011-10-19T03:54:37Z
A dinucleotide repeat region composed of GT repeating elements.
SO:0001862
d(GT)n
kareneilbeck
paper:PMID:16043634.
sequence
A dinucleotide repeat region composed of GT repeating elements.
SO:ke
GTT_trinucleotide_repeat
2011-10-19T03:56:54Z
A trinucleotide repeat region composed of GTT repeating elements.
SO:0001863
d(GTT)
kareneilbeck
sequence
A trinucleotide repeat region composed of GTT repeating elements.
SO:ke
Sap1_recognition_motif
2011-10-19T04:24:16Z
A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats.
SO:0001864
Sap1 recognitions site
kareneilbeck
sequence
A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats.
PMID:16166653
PMID:7651412
CDRE_motif
2011-10-20T10:12:19Z
An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA.
CDRE motif
SO:0001865
calcineurin-dependent response element
kareneilbeck
sequence
An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA.
PMID:16928959
PMID:16928959
calcineurin-dependent response element
BAC_read_contig
2012-01-17T02:45:04Z
A contig of BAC reads.
BAC read contig
Requested by Bayer Cropscience December, 2011.
SO:0001866
kareneilbeck
sequence
A contig of BAC reads.
GMOD:ea
candidate_gene
2012-01-17T02:53:03Z
A gene suspected of being involved in the expression of a trait.
Requested by Bayer Cropscience December, 2011.
SO:0001867
candidate gene
kareneilbeck
sequence
target gene
A gene suspected of being involved in the expression of a trait.
GMOD:ea
positional_candidate_gene
2012-01-17T02:54:42Z
A candidate gene whose association with a trait is based on the gene's location on a chromosome.
Requested by Bayer Cropscience December, 2011.
SO:0001868
kareneilbeck
positional candidate gene
positional target gene
sequence
A candidate gene whose association with a trait is based on the gene's location on a chromosome.
GMOD:ea
functional_candidate_gene
2012-01-17T02:57:30Z
A candidate gene whose function has something in common biologically with the trait under investigation.
Requested by Bayer Cropscience December, 2011.
SO:0001869
functional candidate gene
functional target gene
kareneilbeck
sequence
A candidate gene whose function has something in common biologically with the trait under investigation.
GMOD:ea
enhancerRNA
2012-01-17T03:09:35Z
A short ncRNA that is transcribed from an enhancer. May have a regulatory function.
SO:0001870
eRNA
kareneilbeck
sequence
A short ncRNA that is transcribed from an enhancer. May have a regulatory function.
SO:cjm
doi:10.1038/465173a
PCB
2012-01-17T03:14:02Z
A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle.
SO:0001871
kareneilbeck
sequence
A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle.
GO:mah
PMID:12411492
rearrangement_breakpoint
2012-02-03T04:38:35Z
A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome.
NCBI definition: An orphan rearrangement between chromosomal location observed in isolation.
SO:0001872
kareneilbeck
rearrangement breakpoint
sequence
A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome.
NCBI:th
PMID:18564416
interchromosomal_breakpoint
2012-02-03T04:43:45Z
A rearrangement breakpoint between two different chromosomes.
SO:0001873
interchromosomal breakpoint
kareneilbeck
sequence
A rearrangement breakpoint between two different chromosomes.
NCBI:th
intrachromosomal_breakpoint
2012-02-03T04:44:53Z
A rearrangement breakpoint within the same chromosome.
SO:0001874
intrachromosomal breakpoint
kareneilbeck
sequence
A rearrangement breakpoint within the same chromosome.
NCBI:th
unassigned_supercontig
2012-02-14T05:02:20Z
A supercontig that is not been assigned to any ultracontig during a genome assembly project.
Requested by Bayer Cropscience January, 2012.
SO:0001875
kareneilbeck
sequence
unassigned scaffold
unassigned supercontig
A supercontig that is not been assigned to any ultracontig during a genome assembly project.
GMOD:ea
partial_genomic_sequence_assembly
2012-02-14T05:05:32Z
A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's.
Requested by Bayer Cropscience January, 2012.
SO:0001876
kareneilbeck
partial genomic sequence assembly
pseudomolecule
sequence
sequence assembly with N-gaps
A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's.
GMOD:ea
lnc_RNA
2012-02-14T05:18:01Z
A non-coding RNA over 200nucleotides in length.
SO:0001877
kareneilbeck
long non-coding RNA
sequence
A non-coding RNA over 200nucleotides in length.
HGNC:mw
feature_variant
2012-04-03T11:27:27Z
A sequence variant that falls entirely or partially within a genomic feature.
Created in conjunction with the EBI.
SO:0001878
feature alteration
kareneilbeck
sequence
A sequence variant that falls entirely or partially within a genomic feature.
EBI:fc
SO:ke
feature_ablation
2012-04-03T11:36:48Z
A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features.
Created in conjunction with the EBI.
SO:0001879
feature ablation
kareneilbeck
sequence
A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features.
SO:ke
feature_amplification
2012-04-03T11:37:48Z
A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features.
Created in conjunction with the EBI.
SO:0001880
feature amplification
kareneilbeck
sequence
A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features.
SO:ke
feature_translocation
2012-04-03T11:38:52Z
A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features.
Created in conjunction with the EBI.
SO:0001881
feature translocation
kareneilbeck
sequence
A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features.
SO:ke
feature_fusion
2012-04-03T11:39:20Z
A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features.
Created in conjunction with the EBI.
SO:0001882
feature fusion
kareneilbeck
sequence
A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features.
SO:ke
transcript_translocation
2012-04-03T12:29:52Z
A feature translocation where the region contains a transcript.
Created in conjunction with the EBI.
SO:0001883
kareneilbeck
sequence
transcript translocation
A feature translocation where the region contains a transcript.
SO:ke
regulatory_region_translocation
2012-04-03T12:31:04Z
A feature translocation where the region contains a regulatory region.
Created in conjunction with the EBI.
SO:0001884
kareneilbeck
regulatory region translocation
sequence
A feature translocation where the region contains a regulatory region.
SO:ke
TFBS_translocation
2012-04-03T12:31:15Z
A feature translocation where the region contains a transcription factor binding site.
Created in conjunction with the EBI.
SO:0001885
TFBS binding site translocation
kareneilbeck
sequence
transcription factor binding site translocation
A feature translocation where the region contains a transcription factor binding site.
SO:ke
transcript_fusion
2012-04-03T12:34:56Z
A feature fusion where the deletion brings together transcript regions.
Created in conjunction with the EBI.
SO:0001886
kareneilbeck
sequence
transcript fusion
A feature fusion where the deletion brings together transcript regions.
SO:ke
regulatory_region_fusion
2012-04-03T12:35:58Z
A feature fusion where the deletion brings together regulatory regions.
Created in conjunction with the EBI.
SO:0001887
kareneilbeck
regulatory region fusion
sequence
A feature fusion where the deletion brings together regulatory regions.
SO:ke
TFBS_fusion
2012-04-03T12:36:42Z
A fusion where the deletion brings together transcription factor binding sites.
Created in conjunction with the EBI.
SO:0001888
TFBS fusion
kareneilbeck
sequence
transcription factor binding site fusion
A fusion where the deletion brings together transcription factor binding sites.
SO:ke
transcript_amplification
2012-04-03T12:39:23Z
A feature amplification of a region containing a transcript.
Created in conjunction with the EBI.
SO:0001889
kareneilbeck
sequence
transcript amplification
A feature amplification of a region containing a transcript.
SO:ke
transcript_regulatory_region_fusion
2012-04-03T12:40:17Z
A feature fusion where the deletion brings together a regulatory region and a transcript region.
Created in conjunction with the EBI.
SO:0001890
kareneilbeck
sequence
transcript regulatory region fusion
A feature fusion where the deletion brings together a regulatory region and a transcript region.
SO:ke
regulatory_region_amplification
2012-04-03T12:41:28Z
A feature amplification of a region containing a regulatory region.
Created in conjunction with the EBI.
SO:0001891
kareneilbeck
regulatory region amplification
sequence
A feature amplification of a region containing a regulatory region.
SO:ke
TFBS_amplification
2012-04-03T12:42:48Z
A feature amplification of a region containing a transcription factor binding site.
Created in conjunction with the EBI.
SO:0001892
TFBS amplification
kareneilbeck
sequence
transcription factor binding site amplification
A feature amplification of a region containing a transcription factor binding site.
SO:ke
transcript_ablation
2012-04-03T12:44:19Z
A feature ablation whereby the deleted region includes a transcript feature.
Created in conjunction with the EBI.
SO:0001893
kareneilbeck
sequence
transcript ablation
A feature ablation whereby the deleted region includes a transcript feature.
SO:ke
regulatory_region_ablation
2012-04-03T12:45:13Z
A feature ablation whereby the deleted region includes a regulatory region.
Created in conjunction with the EBI.
SO:0001894
kareneilbeck
regulatory region ablation
sequence
A feature ablation whereby the deleted region includes a regulatory region.
SO:ke
TFBS_ablation
2012-04-03T12:45:56Z
A feature ablation whereby the deleted region includes a transcription factor binding site.
Created in conjunction with the EBI.
SO:0001895
TFBS ablation
kareneilbeck
sequence
transcription factor binding site ablation
A feature ablation whereby the deleted region includes a transcription factor binding site.
SO:ke
transposable_element_CDS
2012-04-05T01:57:04Z
A CDS that is part of a transposable element.
SO:0001896
kareneilbeck
sequence
transposable element CDS
A CDS that is part of a transposable element.
SO:ke
transposable_element_pseudogene
2012-04-05T04:09:45Z
A pseudogene contained within a transposable element.
SO:0001897
kareneilbeck
sequence
transposable element pseudogene
A pseudogene contained within a transposable element.
SO:ke
dg_repeat
2012-04-06T11:48:48Z
A repeat region which is part of the regional centromere outer repeat region.
For the S. pombe project - requested by Val Wood.
SO:0001898
dg repeat
kareneilbeck
sequence
A repeat region which is part of the regional centromere outer repeat region.
PMID:16407326
SO:vw
dh_repeat
2012-04-06T11:50:07Z
A repeat region which is part of the regional centromere outer repeat region.
For the S. pombe project - requested by Val Wood.
SO:0001899
dh repeat
kareneilbeck
sequence
A repeat region which is part of the regional centromere outer repeat region.
PMID:16407326
SO:vw
M26_binding_site
2012-04-06T12:02:10Z
A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components.
SO:0001900
kareneilbeck
m26 site
sequence
A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components.
PMID:15448137
AACCCT_box
2012-04-06T12:05:24Z
A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site.
AACCCT box
SO:0001901
kareneilbeck
sequence
A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site.
PMID:17452352
PMID:4092687
splice_region
2012-04-06T12:23:32Z
A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
SO:0001902
kareneilbeck
sequence
splice region
A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
SO:bm
intronic_lncRNA
2012-04-06T04:34:17Z
A lnc_RNA totally contained within an intron.
SO:0001903
intronic lncRNA
kareneilbeck
sequence
A lnc_RNA totally contained within an intron.
PMID:19071207
SO:ke
antisense_lncRNA
2012-04-06T04:36:44Z
Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA.
SO:0001904
antisense lncRNA
kareneilbeck
natural antisense transcript
sequence
Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA.
PMID:19638999
regional_centromere_outer_repeat_transcript
2012-04-11T04:54:22Z
A transcript that is transcribed from the outer repeat region of a regional centromere.
SO:0001905
centromere outer repeat transcript
kareneilbeck
regional centromere outer repeat region transcript
regional_centromere_outer_repeat_region_transcript
sequence
A transcript that is transcribed from the outer repeat region of a regional centromere.
PomBase:mah
feature_truncation
2012-04-12T05:05:28Z
A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence.
SO:0001906
feature truncation
kareneilbeck
sequence
A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence.
SO:ke
feature_elongation
2012-04-12T05:05:56Z
A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence.
SO:0001907
feature elongation
kareneilbeck
sequence
A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence.
SO:ke
internal_feature_elongation
2012-04-12T05:06:20Z
A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence.
SO:0001908
internal feature elongation
kareneilbeck
sequence
A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence.
SO:ke
frameshift_elongation
2012-04-12T05:10:05Z
A frameshift variant that causes the translational reading frame to be extended relative to the reference feature.
ANNOVAR:frameshift insertion
SO:0001909
frameshift elongation
kareneilbeck
sequence
A frameshift variant that causes the translational reading frame to be extended relative to the reference feature.
SO:ke
ANNOVAR:frameshift insertion
http://www.openbioinformatics.org/annovar/annovar_download.html
frameshift_truncation
2012-04-12T05:10:45Z
A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature.
ANNOVAR:frameshit deletion
SO:0001910
frameshft truncation
kareneilbeck
sequence
A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature.
SO:ke
ANNOVAR:frameshit deletion
http://www.openbioinformatics.org/annovar/annovar_download.html
copy_number_increase
2012-04-13T11:26:32Z
A sequence variant where copies of a feature are increased relative to the reference.
SO:0001911
copy number increase
kareneilbeck
sequence
A sequence variant where copies of a feature are increased relative to the reference.
SO:ke
copy_number_decrease
2012-04-13T11:27:52Z
A sequence variant where copies of a feature are decreased relative to the reference.
SO:0001912
kareneilbeck
sequence
A sequence variant where copies of a feature are decreased relative to the reference.
SO:ke
bacterial_RNApol_promoter_sigma_ecf
2012-06-11T02:41:33Z
A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation.
Requested by Kevin Clancy - invitrogen -May 2012.
SO:0001913
bacterial RNApol promoter sigma ecf
kareneilbeck
sequence
A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation.
Invitrogen:kc
rDNA_replication_fork_barrier
2012-06-11T02:55:02Z
A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.
DNA spacer replication fork barrier
RFB
RTS1 barrier
RTS1 element
Requested by Midori - June 2012.
SO:0001914
kareneilbeck
rDNA replication fork barrier
sequence
A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.
PMID:14645529
transcription_start_cluster
2012-10-17T12:09:50Z
A region defined by a cluster of experimentally determined transcription starting sites.
SO:0001915
TSC
TSS cluster
kareneilbeck
sequence
transcriptional initiation cluster
transcriptional start site cluster
A region defined by a cluster of experimentally determined transcription starting sites.
PMID:19624849
PMID:21372179
SO:andrewgibson
CAGE_tag
2012-10-17T12:36:58Z
A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites.
CAGE tag
SO:0001916
kareneilbeck
sequence
A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites.
SO:andrewgibson
CAGE_cluster
2012-10-17T12:42:03Z
A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region.
CAGE cluster
CAGE peak
CAGE_peak
SO:0001917
kareneilbeck
sequence
A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region.
PMID:16645617
SO:andrewgibson
5_methylcytosine
2012-10-17T12:46:10Z
5 methylcytosine
5-mC
A cytosine methylated at the 5 carbon.
SO:0001918
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
kareneilbeck
m-5C
m5c
sequence
A cytosine methylated at the 5 carbon.
SO:rtapella
4_methylcytosine
2012-10-17T12:50:40Z
4-mC
4-methylcytosine
A cytosine methylated at the 4 nitrogen.
N4 methylcytosine
N4-methylcytosine
N4_methylcytosine
SO:0001919
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
kareneilbeck
m-4C
m4c
sequence
A cytosine methylated at the 4 nitrogen.
SO:rtapella
N6_methyladenine
2012-10-17T12:54:23Z
6-mA
6-methyladenine
6mA
An adenine methylated at the 6 nitrogen.
N6-methyladenine
SO:0001920
http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
kareneilbeck
m-6A
m6a
sequence
An adenine methylated at the 6 nitrogen.
SO:rtapella
mitochondrial_contig
2012-10-31T12:34:38Z
A contig of mitochondria derived sequences.
Requested by Bayer Cropscience, October, 2012.
SO:0001921
kareneilbeck
mitochondrial contig
sequence
A contig of mitochondria derived sequences.
GMOD:ea
mitochondrial_supercontig
2012-10-31T12:42:45Z
A scaffold composed of mitochondrial contigs.
SO:0001922
kareneilbeck
mitochondrial scaffold
mitochondrial supercontig
mitochondrial_scaffold
sequence
A scaffold composed of mitochondrial contigs.
GMOD:ea
TERRA
2012-10-31T01:06:40Z
A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long.
SO:0001923
Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
kareneilbeck
sequence
telomeric repeat containing RNA
A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long.
PMID:22139915
ARRET
2012-10-31T01:11:49Z
A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats.
SO:0001924
Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
kareneilbeck
sequence
A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats.
PMID:2139915
ARIA
2012-10-31T01:24:37Z
A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats.
SO:0001925
Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
kareneilbeck
sequence
A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats.
PMID:22139915
anti_ARRET
2012-10-31T01:40:22Z
A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts.
SO:0001926
Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
anti-ARRET
kareneilbeck
sequence
A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts.
PMID:22139915
telomeric_transcript
2012-10-31T01:42:15Z
A non-coding transcript derived from the transcript of the telomere.
SO:0001927
kareneilbeck
sequence
telomeric transcript
A non-coding transcript derived from the transcript of the telomere.
PMID:22139915
distal_duplication
2012-10-31T01:56:44Z
A duplication of the distal region of a chromosome.
SO:0001928
This term is used by Complete Genomics in the structural variant analysis files.
distal duplication
kareneilbeck
sequence
A duplication of the distal region of a chromosome.
SO:bm
mitochondrial_DNA_read
2012-11-14T04:39:56Z
A sequencer read of a mitochondrial DNA sample.
Requested by Bayer Cropscience, October, 2012.
SO:0001929
kareneilbeck
mitochondrial DNA read
sequence
A sequencer read of a mitochondrial DNA sample.
GMOD:ea
chloroplast_DNA_read
2012-11-14T04:43:45Z
A sequencer read of a chloroplast DNA sample.
Requested by Bayer Cropscience, October, 2012.
SO:0001930
chloroplast DNA read
kareneilbeck
sequence
A sequencer read of a chloroplast DNA sample.
GMOD:ea
consensus_gDNA
2012-11-28T12:53:14Z
Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input.
Requested by Bayer Cropscience November, 2012.
SO:0001931
consensus gDNA
consensus genomic DNA
kareneilbeck
sequence
GMOD:ea
Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input.
restriction_enzyme_five_prime_single_strand_overhang
2013-03-06T09:50:44Z
A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end.
SO:0001932
kareneilbeck
restriction enzyme five prime single strand overhang
sequence
A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end.
SO:ke
restriction_enzyme_three_prime_single_strand_overhang
2013-03-06T09:52:14Z
A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end.
SO:0001933
kareneilbeck
restriction enzyme three prime single strand overhang
sequence
A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end.
SO:ke
monomeric_repeat
2013-03-06T09:59:15Z
A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem.
SO:0001934
kareneilbeck
monomeric repeat
sequence
A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem.
SO:ke
H3K20_trimethylation_site
2013-03-06T10:13:48Z
A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated.
H3K20 trimethylation site
SO:0001935
kareneilbeck
sequence
A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated.
EBI:nj
H3K36_acetylation_site
2013-03-06T10:16:55Z
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated.
H3K36 acetylation site
H3K36ac
SO:0001936
kareneilbeck
sequence
A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated.
EBI:nj
H2BK12_acetylation_site
2013-03-06T10:19:13Z
A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated.
H2BK12 acetylation site
H2BK12ac
SO:0001937
kareneilbeck
sequence
A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated.
EBI:nj
H2AK5_acetylation_site
2013-03-06T10:20:57Z
A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated.
H2AK5 acetylation site
H2AK5ac
SO:0001938
kareneilbeck
sequence
A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated.
EBI:nj
H4K12_acetylation_site
2013-03-06T10:26:15Z
A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated.
H4K12 acetylation site
H4K12ac
SO:0001939
kareneilbeck
sequence
A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated.
EBI:nj
H2BK120_acetylation_site
2013-03-06T10:28:38Z
A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated.
H2BK120 acetylation site
H2BK120ac
SO:0001940
kareneilbeck
sequence
A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated.
EBI:nj
H4K91_acetylation_site
2013-03-06T10:41:04Z
A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated.
H4K91 acetylation site
SO:0001941
kareneilbeck
sequence
A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated.
EBI:nj
H2BK20_acetylation_site
2013-03-06T10:44:31Z
A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated.
H2BK20 acetylation site
H2BK20ac
SO:0001942
kareneilbeck
sequence
A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated.
EBI:nj
H3K4ac_acetylation_site
2013-03-06T10:46:32Z
A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated.
H3K4ac
H3K4ac acetylation site
SO:0001943
kareneilbeck
sequence
A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated.
EBI:nj
H2AK9_acetylation_site
2013-03-06T10:48:11Z
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated.
H2AK9 acetylation site
H2AK9ac
SO:0001944
kareneilbeck
sequence
A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated.
EBI:nj
H3K56_acetylation_site
2013-03-06T10:51:14Z
A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated.
H3K56 acetylation site
H3K56ac
SO:0001945
kareneilbeck
sequence
A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated.
EBI:nj
H2BK15_acetylation_site
2013-03-06T10:53:23Z
A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated.
H2BK15 acetylation site
H2BK15ac
SO:0001946
kareneilbeck
sequence
A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated.
EBI:nj
H3R2_monomethylation_site
H3R2me1
2013-03-06T10:57:13Z
A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated.
H3R2 monomethylation site
SO:0001947
kareneilbeck
sequence
A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated.
EBI:nj
H3R2_dimethylation_site
2013-03-06T10:59:17Z
A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated.
H3R2 dimethylation site
H3R2me2
SO:0001948
kareneilbeck
sequence
A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated.
EBI:nj
H4R3_dimethylation_site
2013-03-06T11:01:27Z
A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated.
H4R3 dimethylation site
H4R3me2
SO:0001949
kareneilbeck
sequence
A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated.
EBI:nj
H4K4_trimethylation_site
H4K4me3
2013-03-06T11:03:29Z
A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated.
H4K4 trimethylation site
SO:0001950
kareneilbeck
sequence
A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated.
EBI:nj
H3K23_dimethylation_site
2013-03-06T11:05:33Z
A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated.
H3K23 dimethylation site
H3K23me2
SO:0001951
kareneilbeck
sequence
A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated.
EBI:nj
promoter_flanking_region
2013-03-06T11:36:25Z
A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites.
SO:0001952
kareneilbeck
promoter flanking region
sequence
A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites.
EBI:nj
restriction_enzyme_assembly_scar
2013-03-06T03:18:11Z
A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends.
SO:0001953
kareneilbeck
sequence
A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends.
SO:ke
restriction_enzyme_region
2013-03-06T03:23:34Z
A region related to restriction enzyme function.
Not a great term for annotation, but used to classify the various regions related to restriction enzymes.
SO:0001954
kareneilbeck
restriction enzyme region
sequence
A region related to restriction enzyme function.
SO:ke
protein_stability_element
2013-03-06T03:32:47Z
A polypeptide region that proves structure in a protein that affects the stability of the protein.
SO:0001955
kareneilbeck
protein stability element
sequence
A polypeptide region that proves structure in a protein that affects the stability of the protein.
SO:ke
protease_site
2013-03-06T03:36:28Z
A polypeptide_region that codes for a protease cleavage site.
SO:0001956
kareneilbeck
protease site
sequence
A polypeptide_region that codes for a protease cleavage site.
SO:ke
RNA_stability_element
2013-03-06T03:38:35Z
RNA secondary structure that affects the stability of an RNA molecule.
SO:0001957
kareneilbeck
rna stability element
sequence
true
RNA secondary structure that affects the stability of an RNA molecule.
SO:ke
lariat_intron
2013-03-07T10:58:40Z
A kind of intron whereby the excision is driven by lariat formation.
Requested by PomBase 3604508.
SO:0001958
kareneilbeck
lariat intron
sequence
A kind of intron whereby the excision is driven by lariat formation.
SO:ke
TCT_motif
2013-05-17T04:38:48Z
A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator.
SO:0001959
TCT element
kareneilbeck
polypyrimidine initiator
sequence
A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator.
PMID:20801935
SO:myl
5_hydroxymethylcytosine
2013-05-17T05:05:31Z
5-hmC
5-hydroxymethylcytosine
A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon.
SO:0001960
http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
kareneilbeck
sequence
A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon.
SO:ke
5_formylcytosine
2013-05-17T05:06:13Z
5-fC
5-formylcytosine
A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon.
SO:0001961
http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
kareneilbeck
sequence
A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon.
SO:ke
modified_adenine
2013-05-20T01:22:30Z
A modified adenine DNA base feature.
SO:0001962
kareneilbeck
sequence
A modified adenine DNA base feature.
SO:ke
modified_cytosine
2013-05-20T01:23:47Z
A modified cytosine DNA base feature.
SO:0001963
kareneilbeck
sequence
A modified cytosine DNA base feature.
SO:ke
modified_guanine
2013-05-20T01:25:31Z
A modified guanine DNA base feature.
SO:0001964
kareneilbeck
sequence
A modified guanine DNA base feature.
SO:ke
8_oxoguanine
2013-05-20T01:27:51Z
8-oxoG
8-oxoguanine
A modified DNA guanine base,at the 8 carbon, often the product of DNA damage.
SO:0001965
http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
kareneilbeck
sequence
A modified DNA guanine base,at the 8 carbon, often the product of DNA damage.
SO:ke
5_carboxylcytosine
2013-05-20T01:30:01Z
5-caC
5-carboxycytosine
A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon.
SO:0001966
http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
kareneilbeck
sequence
A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon.
SO:ke
8_oxoadenine
2013-05-20T01:31:05Z
8-oxoA
8-oxoadenine
A modified DNA adenine base,at the 8 carbon, often the product of DNA damage.
SO:0001967
http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
kareneilbeck
sequence
A modified DNA adenine base,at the 8 carbon, often the product of DNA damage.
SO:ke
coding_transcript_variant
2013-05-22T04:34:49Z
A transcript variant of a protein coding gene.
SO:0001968
coding transcript variant
kareneilbeck
sequence
A transcript variant of a protein coding gene.
SO:ke
coding_transcript_intron_variant
2013-05-23T10:54:17Z
A transcript variant occurring within an intron of a coding transcript.
SO:0001969
coding sequence intron variant
kareneilbeck
sequence
A transcript variant occurring within an intron of a coding transcript.
SO:ke
non_coding_transcript_intron_variant
2013-05-23T10:55:03Z
A transcript variant occurring within an intron of a non coding transcript.
SO:0001970
kareneilbeck
non coding transcript intron variant
sequence
A transcript variant occurring within an intron of a non coding transcript.
SO:ke
zinc_finger_binding_site
2013-07-29T04:41:53Z
SO:0001971
kareneilbeck
sequence
zinc finger binding site
zinc_fing
unirot:features
zinc_fing
histone_4_acylation_site
2013-07-30T10:43:04Z
A histone 4 modification where the modification is the acylation of the residue.
H4ac
SO:0001972
kareneilbeck
sequence
A histone 4 modification where the modification is the acylation of the residue.
EBI:nj
SO:ke
histone_3_acetylation_site
2013-07-30T10:46:42Z
A histone 3 modification where the modification is the acylation of the residue.
H3ac
SO:0001973
kareneilbeck
sequence
A histone 3 modification where the modification is the acylation of the residue.
EBI:nj
SO:ke
CTCF_binding_site
2013-07-30T10:59:11Z
A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor.
CCCTF binding site
CTCF binding site
SO:0001974
kareneilbeck
sequence
A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor.
EBI:nj
five_prime_sticky_end_restriction_enzyme_cleavage_site
2013-07-30T11:32:16Z
A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs.
Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
SO:0001975
five prime sticky end restriction enzyme cleavage site
kareneilbeck
sequence
A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs.
SO:ke
three_prime_sticky_end_restriction_enzyme_cleavage_site
2013-07-30T11:37:19Z
A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs.
Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
SO:0001976
kareneilbeck
sequence
three prime sticky end restriction enzyme cleavage site
A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs.
SO:ke
ribonuclease_site
2013-07-30T11:41:06Z
A region of a transcript encoding the cleavage site for a ribonuclease enzyme.
SO:0001977
kareneilbeck
ribonuclease site
sequence
A region of a transcript encoding the cleavage site for a ribonuclease enzyme.
SO:ke
signature
2013-07-30T11:49:22Z
A region of sequence where developer information is encoded.
DNA signature
Requested by Jackie Quinn for use in synthetic biology.
SO:0001978
kareneilbeck
sequence
A region of sequence where developer information is encoded.
SO:ke
RNA_stability_element
2013-07-30T03:33:53Z
A motif that affects the stability of RNA.
RNA stability element
SO:0001979
kareneilbeck
sequence
A motif that affects the stability of RNA.
PMID:22495308
SO:ke
G_box
2013-07-30T04:00:50Z
A plant specific region.
A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a.
G-box
GBF binding sequence
SO:0001980
kareneilbeck
sequence
A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a.
PMID:19249238
PMID:8571452
SO:ml
L_box
2013-07-30T04:12:19Z
An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants.
L-box
L-box promoter element
SO:0001981
kareneilbeck
sequence
An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants.
PMID:17381552
PMID:2902624
SO:ml
I-box
2013-07-30T04:17:55Z
A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core).
I-box promoter motif
SO:0001982
kareneilbeck
sequence
A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core).
PMID:2347304
PMID:2902624
SO:ml
5_prime_UTR_premature_start_codon_variant
2013-07-30T04:36:25Z
5' UTR premature start codon variant
A 5' UTR variant where a premature start codon is introduced, moved or lost.
Requested by Andy Menzies at the Sanger. This isn't necessarily a protein coding change. A premature start codon can effect the production of a mature protein product by providing a competing translation start point. Some genes balance their expression this way, eg THPO requires the presence of a premature start to limit expression, its loss leads to Familial thrombocythemia.
SO:0001983
kareneilbeck
sequence
snpEff:START_GAINED
A 5' UTR variant where a premature start codon is introduced, moved or lost.
SANGER:am
snpEff:START_GAINED
silent_mating_type_cassette_array
2013-07-31T02:40:38Z
A gene cassette array that corresponds to a silenced version of a mating type region.
SO:0001984
kareneilbeck
sequence
silent mating-type cassette
A gene cassette array that corresponds to a silenced version of a mating type region.
PomBase:mah
Okazaki_fragment
2013-07-31T02:57:55Z
Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication.
Okazaki fragment
Requested by Midori Harris, 2013.
SO:0001985
kareneilbeck
sequence
Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication.
ISBN:0805350152
upstream_transcript_variant
2013-07-31T03:46:14Z
A feature variant, where the alteration occurs upstream of the transcript TSS.
Requested by Graham Ritchie, EBI/Sanger.
SO:0001986
kareneilbeck
sequence
upstream transcript variant
A feature variant, where the alteration occurs upstream of the transcript TSS.
EBI:gr
downstream_transcript_variant
2013-07-31T03:47:51Z
Requested by Graham Ritchie, EBI/Sanger.
SO:0001987
downstream transcript variant
kareneilbeck
sequence
5_prime_UTR_premature_start_codon_gain_variant
2013-07-31T03:53:06Z
5 prime UTR premature start codon gain variant
A 5' UTR variant where a premature start codon is gained.
SO:0001988
kareneilbeck
sequence
A 5' UTR variant where a premature start codon is gained.
Sanger:am
5_prime_UTR_premature_start_codon_loss_variant
2013-07-31T03:56:48Z
A 5' UTR variant where a premature start codon is lost.
SO:0001989
kareneilbeck
sequence
A 5' UTR variant where a premature start codon is lost.
SANGER:am
five_prime_UTR_premature_start_codon_location_variant
2013-07-31T03:57:47Z
A 5' UTR variant where a premature start codon is moved.
SO:0001990
kareneilbeck
sequence
A 5' UTR variant where a premature start codon is moved.
SANGER:am
consensus_AFLP_fragment
2013-09-24T10:43:41Z
A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input.
Requested by Bayer Cropscience September, 2013.
SO:0001991
consensus AFLP fragment
consensus amplified fragment length polymorphism fragment
kareneilbeck
sequence
A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input.
GMOD:ea
nonsynonymous_variant
2013-10-16T11:47:51Z
A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change.
SO:0001992
kareneilbeck
non_synonymous_coding
nonsynonymous variant
sequence
http://ensembl.org/info/docs/variation/index.html
non_synonymous_coding
A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change.
SO:ke
extended_cis_splice_site
2014-01-04T06:20:00Z
Added by Andy Menzies (Sanger).
Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after.
SO:0001993
extended cis splice site
kareneilbeck
sequence
Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after.
SANGER:am
intron_base_5
2014-01-04T06:26:02Z
Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron.
SO:0001994
intron base 5
kareneilbeck
sequence
Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron.
SANGER:am
extended_intronic_splice_region_variant
2014-01-04T06:37:27Z
A sequence variant occurring in the intron, within 10 bases of exon.
Added by Andy Menzies (Sanger).
SO:0001995
extended intronic splice region variant
kareneilbeck
sequence
A sequence variant occurring in the intron, within 10 bases of exon.
sanger:am
extended_intronic_splice_region
2014-01-04T06:41:23Z
Region of intronic sequence within 10 bases of an exon.
SO:0001996
extended intronic splice region
kareneilbeck
sequence
Region of intronic sequence within 10 bases of an exon.
SANGER:am
subtelomere
2014-01-05T07:02:01Z
A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed.
SO:0001997
kareneilbeck
sequence
A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed.
POMBE:al
sgRNA
2014-01-05T07:25:08Z
A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method.
SO:0001998
gRNA
guide RNA
kareneilbeck
sequence
small guide RNA
A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method.
PMID:23934893
mating_type_region_motif
2014-01-05T07:30:17Z
DNA motif that is a component of a mating type region.
SO:0001999
kareneilbeck
mating type region motif
sequence
DNA motif that is a component of a mating type region.
SO:ke
Y_region
2014-01-05T07:33:30Z
A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha).
Requested by Janos Demeter, SGD.
SO:0002001
Y-region
kareneilbeck
sequence
A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha).
SGD:jd
Z1_region
2014-01-05T07:34:59Z
A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR).
Requested by Janos Demeter, SGD.
SO:0002002
Z1-region
kareneilbeck
sequence
A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR).
SGD:jd
Z2_region
2014-01-05T07:36:45Z
A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR).
Requested by Janos Demeter, SGD.
SO:0002003
Z2-segment
kareneilbeck
sequence
A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR).
SGD:jd
ARS_consensus_sequence
2014-01-05T07:47:48Z
ACS
ARS consensus sequence
SO:0002004
The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS.
kareneilbeck
sequence
SGD:jd
The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS.
DSR_motif
2014-01-05T07:51:27Z
DSR motif
Requested by Antonia Locke, (Pombe).
SO:0002005
The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome.
kareneilbeck
sequence
PMID:22645662
The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome.
zinc_repressed_element
2014-01-05T09:23:27Z
A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc.
SO:0002006
This element is bound by Loz1 in S. pombe. The paper does not name the element. This term was requested by Midoris Harris, for Pombe.
kareneilbeck
sequence
zinc repressed element
A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc.
PMID:24003116
POMBE:mh
MNV
2014-01-13T03:48:40Z
An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence.
SO:0002007
kareneilbeck
multiple nucleotide substitution
multiple nucleotide variant
sequence
An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence.
NCBI:th
rare_amino_acid_variant
2014-03-24T02:24:01Z
A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid.
Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
SO:0002008
kareneilbeck
rare amino acid variant
sequence
A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid.
SO:ke
selenocysteine_loss
2014-03-24T02:29:44Z
A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid.
Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
SO:0002009
kareneilbeck
selenocysteine loss
sequence
A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid.
SO:ke
pyrrolysine_loss
2014-03-24T02:30:16Z
A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid.
Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
SO:0002010
kareneilbeck
pyrrolysine loss
sequence
A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid.
SO:ke
intragenic_variant
2014-03-24T02:33:13Z
A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence.
Requested by Pablo Cingolani, for use in SnpEff.
SO:0002011
intragenic variant
kareneilbeck
sequence
snpEff:INTRAGENIC
snpEff:INTRAGENIC
A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence.
SO:ke
start_lost
2014-03-24T02:41:28Z
A codon variant that changes at least one base of the canonical start codon.
Request from Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts.
SO:0002012
kareneilbeck
sequence
snpEff:START_LOST
A codon variant that changes at least one base of the canonical start codon.
SO:ke
snpEff:START_LOST
5_prime_UTR_truncation
2014-03-25T10:46:42Z
5 prime UTR truncation
A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence.
SO:0002013
kareneilbeck
sequence
snpEff:UTR_5_DELETED
snpEff:UTR_5_DELETED
A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence.
SO:ke
5_prime_UTR_elongation
2014-03-25T10:48:26Z
5 prime UTR elongation
A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence.
SO:0002014
kareneilbeck
sequence
A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence.
SO:ke
3_prime_UTR_truncation
2014-03-25T10:54:50Z
3 prime UTR truncation
A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence.
SO:0002015
kareneilbeck
sequence
snpEff:UTR_3_DELETED
A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence.
SO:ke
snpEff:UTR_3_DELETED
3_prime_UTR_elongation
2014-03-25T10:55:33Z
3 prime UTR elongation
A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence.
SO:0002016
kareneilbeck
sequence
A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence.
SO:ke
conserved_intergenic_variant
2014-03-25T02:54:39Z
A sequence variant located in a conserved intergenic region, between genes.
Requested by Uma Paila (UVA) for snpEff.
SO:0002017
conserved intergenic variant
kareneilbeck
sequence
snpEff:INTERGENIC_CONSERVED
A sequence variant located in a conserved intergenic region, between genes.
SO:ke
snpEff:INTERGENIC_CONSERVED
conserved_intron_variant
2014-03-25T02:58:41Z
A transcript variant occurring within a conserved region of an intron.
Requested by Uma Paila (UVA) for snpEff.
SO:0002018
conserved intron variant
kareneilbeck
sequence
snpEff:INTRON_CONSERVED
A transcript variant occurring within a conserved region of an intron.
SO:ke
snpEff:INTRON_CONSERVED
start_retained_variant
2014-03-28T10:08:41Z
A sequence variant where at least one base in the start codon is changed, but the start remains.
Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation.
SO:0002019
kareneilbeck
sequence
A sequence variant where at least one base in the start codon is changed, but the start remains.
SO:ke
boundary_element
2014-05-30T14:45:37Z
Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions.
Requested by Antonia Lock.
SO:0002020
boundary element
kareneilbeck
sequence
Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions.
PMID:24013502
mating_type_region_replication_fork_barrier
2014-05-30T14:57:26Z
A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.
Requested by Midori Harris.
SO:0002021
kareneilbeck
mating type region replication fork barrier
sequence
A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.
PMID:17614787
priRNA
2014-05-30T15:01:24Z
A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts.
SO:0002022
kareneilbeck
primal small RNA
sequence
A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts.
PMID:20178743
PMID:24095277
PomBase:al
multiplexing_sequence_identifier
2014-05-30T15:13:16Z
A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library.
SO:0002023
kareneilbeck
multiplexing sequence identifier
sequence
A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library.
OBO:prs
PMID:22574170
W_region
2014-07-11T13:20:08Z
MERGED COMMENT:
TARGET COMMENT: Requested by Janos Demeter, SGD.
--------------------
SOURCE COMMENT: Requested by Janos Demeter, SGD.
SO:0002000
SO:0002024
The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR.
W-region
kareneilbeck
sequence
SGD:jd
The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR.
cis_acting_homologous_chromosome_pairing_region
2014-07-14T11:40:34Z
A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I.
SO:0002025
cis-acting homologous chromosome pairing region
comment: An example of this is the Sme2 locus in fission yeast S. pombe, where is coincident with an ribonuclear complex termed the "Mei2 dot". This term was Requested by Val Wood, PomBase.
kareneilbeck
sequence
A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I.
PMID:22582262
PMID:23117617
PMID:24173580
PomBase:vw
intein_encoding_region
2014-07-14T11:53:21Z
Requested by Janos Demeter 2014.
SO:0002026
The nucleotide sequence which encodes the intein portion of the precursor gene.
kareneilbeck
sequence
PMID:8165123
The nucleotide sequence which encodes the intein portion of the precursor gene.
uORF
2014-07-14T11:59:23Z
A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation.
SO:0002027
kareneilbeck
sequence
upstream ORF
A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation.
PMID:12890013
PMID:16153175
POMBASE:mah
sORF
2014-07-14T12:02:33Z
An open reading frame that encodes a peptide of less than 100 amino acids.
SO:0002028
kareneilbeck
sequence
smORF
small ORF
An open reading frame that encodes a peptide of less than 100 amino acids.
PMID:23970561
PMID:24705786
POMBASE:mah
tnaORF
2014-07-14T12:04:32Z
A translated ORF encoded entirely within the antisense strand of a known protein coding gene.
SO:0002029
kareneilbeck
sequence
translated nested antisense gene
A translated ORF encoded entirely within the antisense strand of a known protein coding gene.
POMBASE:vw
X_region
2014-07-14T18:43:21Z
One of two segments of homology found at all three mating loci (HML, MAT and HMR).
SO:0002030
kareneilbeck
sequence
x-region
One of two segments of homology found at all three mating loci (HML, MAT and HMR).
SGD:jd
shRNA
2014-10-23T09:16:29Z
A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference.
SO:0002031
http:http:en.wikipedia.org/wiki/Small_hairpin_RNA
kareneilbeck
sequence
short hairpin RNA
small hairpin RNA
wikipedia
http:http:en.wikipedia.org/wiki/Small_hairpin_RNA
A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference.
PMID:6699500
SO:ke
moR
2015-01-09T13:57:43Z
A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA.
MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.
Requested by Thomas Desvignes, Jan 2015.
SO:0002032
kareneilbeck
microRNA-offset RNA
sequence
A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA.
SO:ke
loR
2015-01-09T14:02:02Z
A short, non coding transcript of loop-derived sequences encoded in precursor miRNA.
MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.
Requested by Thomas Desvignes, Jan 2015.
SO:0002033
kareneilbeck
loop-origin miRs
sequence
A short, non coding transcript of loop-derived sequences encoded in precursor miRNA.
SO:ke
miR_encoding_snoRNA_primary_transcript
2015-01-09T15:02:13Z
A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:0002034
kareneilbeck
miR encoding snoRNA primary transcript
sequence
A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:ke
lncRNA_primary_transcript
2015-01-09T15:23:03Z
A primary transcript encoding a lncRNA.
SO:0002035
kareneilbeck
lncRNA primary transcript
sequence
A primary transcript encoding a lncRNA.
SO:ke
miR_encoding_lncRNA_primary_transcript
2015-01-09T15:23:48Z
A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:0002036
kareneilbeck
miR encoding lncRNA primary transcript
sequence
A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:ke
miR_encoding_tRNA_primary_transcript
2015-01-09T15:28:23Z
A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:0002037
kareneilbeck
miR encoding tRNA primary transcript
sequence
A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:ke
shRNA_primary_transcript
2015-01-09T15:30:43Z
A primary transcript encoding an shRNA.
SO:0002038
kareneilbeck
sequence
shRNA primary transcript
A primary transcript encoding an shRNA.
SO:ke
miR_encoding_shRNA_primary_transcript
2015-01-09T15:32:00Z
A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:0002039
kareneilbeck
miR encoding shRNA primary transcript
sequence
A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:ke
vaultRNA_primary_transcript
2015-01-09T15:33:33Z
A primary transcript encoding a vaultRNA.
SO:0002040
kareneilbeck
sequence
vaultRNA primary transcript
A primary transcript encoding a vaultRNA.
SO:ke
miR_encoding_vaultRNA_primary_transcript
2015-01-09T15:34:32Z
A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:0002041
kareneilbeck
miR encoding vaultRNA primary transcript
sequence
A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:ke
Y_RNA_primary_transcript
2015-01-09T15:36:51Z
A primary transcript encoding a Y-RNA.
SO:0002042
Y-RNA primary transcript
kareneilbeck
sequence
A primary transcript encoding a Y-RNA.
SO:ke
miR_encoding_Y_RNA_primary_transcript
2015-01-09T15:37:46Z
A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:0002043
kareneilbeck
miR encoding Y-RNA primary transcript
sequence
A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.
SO:ke
TCS_element
2015-02-09T15:02:53Z
A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT.
Requested by Rama - SGD.
SO:0002044
TCS element
TEA Consensus Sequence
kareneilbeck
sequence
A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT.
PMID:1489142
PMID:20118212
SO:ke
pheromone_response_element
2015-02-09T15:05:43Z
A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)].
PRE
Requested by Rama, SGD.
SO:0002045
kareneilbeck
pheromone response element
sequence
A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)].
PMID:1489142
SO:ke
FRE
2015-02-09T15:09:47Z
A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae.
Requested by Rama, SGD.
SO:0002046
filamentation and invasion response element
kareneilbeck
sequence
A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae.
PMID:1489142
SO:ke
transcription_pause_site
2015-02-09T15:32:52Z
SO:0002047
Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli.
kareneilbeck
sequence
transcription pause site
PMID:24789973
SO:ke
Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli.
disabled_reading_frame
2015-02-09T16:15:46Z
A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons).
SO:0002048
dORF
disabled ORF
disabled_reading frame
kareneilbeck
sequence
A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons).
SGD:se
H3K27_acetylation_site
2015-05-14T10:17:11Z
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated.
H3K27 acetylation site
Requested by: Sagar Jain, Richard Scheuermann.
SO:0002049
kareneilbeck
sequence
A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated.
SO:rs
constitutive_promoter
2015-05-14T10:39:09Z
SO:0002050
constitutive promoter
kareneilbeck
sequence
inducible_promoter
2015-05-14T10:39:56Z
A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors.
SO:0002051
inducible promoter
kareneilbeck
sequence
A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors.
SO:ke
dominant_negative_variant
2015-05-14T11:16:28Z
A variant where the mutated gene product adversely affects the other (wild type) gene product.
Requested by Deanna Church.
SO:0002052
dominant negative
dominant negative variant
kareneilbeck
sequence
A variant where the mutated gene product adversely affects the other (wild type) gene product.
SO:ke
gain_of_function_variant
2015-05-14T11:20:47Z
A sequence variant whereby new or enhanced function is conferred on the gene product.
SO:0002053
gain of function variant
kareneilbeck
sequence
A sequence variant whereby new or enhanced function is conferred on the gene product.
SO:ke
loss_of_function_variant
2015-05-14T11:21:29Z
A sequence variant whereby the gene product has diminished or abolished function.
SO:0002054
kareneilbeck
loss of function variant
sequence
A sequence variant whereby the gene product has diminished or abolished function.
SO:ke
null_mutation
2015-05-14T11:21:57Z
A variant whereby the gene product is not functional or the gene product is not produced.
SO:0002055
kareneilbeck
null mutation
sequence
A variant whereby the gene product is not functional or the gene product is not produced.
SO:ke
intronic_splicing_silencer
2015-05-14T12:24:10Z
An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.
ISS
Requested by Javier Diez Perez.
SO:0002056
intronic splicing silencer
kareneilbeck
sequence
An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.
PMID:23241926
SO:ke
intronic_splicing_enhancer
2015-05-14T12:28:31Z
ISE
SO:0002057
kareneilbeck
sequence
true
exonic_splicing_silencer
2015-05-14T12:42:12Z
An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.
ESS
Requested by Javier Diez Perez.
SO:0002058
exonic splicing silencer
kareneilbeck
sequence
An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.
PMID:23241926
SO:ke
recombination_enhancer
2015-05-14T13:08:58Z
A regulatory_region that promotes or induces the process of recombination.
SO:0002059
kareneilbeck
recombination enhancer
sequence
A regulatory_region that promotes or induces the process of recombination.
PMID:8861911
SGD:se
regulatory_region
A region of sequence that is involved in the control of a biological process.
SO:0005836
http://en.wikipedia.org/wiki/Regulatory_region
regulatory region
sequence
wiki
http://en.wikipedia.org/wiki/Regulatory_region
A region of sequence that is involved in the control of a biological process.
SO:ke
U14_snoRNA_primary_transcript
4.5S snRNA primary transcript
SO:0005837
The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
U14 snoRNA primary transcript
sequence
PMID:2251119
The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
methylation_guide_snoRNA
A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.
Has RNA 2'-O-ribose methylation guide activity (GO:0030561).
SO:0005841
methylation guide snoRNA
sequence
A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.
GOC:mah
PMID:12457565
rRNA_cleavage_RNA
An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.
SO:0005843
rRNA cleavage RNA
sequence
An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.
GOC:kgc
exon_of_single_exon_gene
An exon that is the only exon in a gene.
SO:0005845
exon of single exon gene
sequence
single_exon
singleton exon
An exon that is the only exon in a gene.
RSC:cb
cassette_array_member
SO:0005847
cassette array member
sequence
gene_cassette_member
SO:0005848
gene cassette member
sequence
gene_subarray_member
SO:0005849
gene subarray member
sequence
primer_binding_site
Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.
SO:0005850
http://en.wikipedia.org/wiki/Primer_binding_site
primer binding site
sequence
wiki
http://en.wikipedia.org/wiki/Primer_binding_site
Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
gene_array
An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so.
SO:0005851
This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.
gene array
sequence
An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so.
SO:ma
gene_subarray
A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function.
SO:0005852
This would include, for example, a cluster of genes encoding different histones.
gene subarray
sequence
A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function.
SO:ma
gene_cassette
A gene that can be substituted for a related gene at a different site in the genome.
SO:0005853
This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid.
gene cassette
http://en.wikipedia.org/wiki/Gene_cassette
sequence
wiki
http://en.wikipedia.org/wiki/Gene_cassette
A gene that can be substituted for a related gene at a different site in the genome.
SGD:se
gene_cassette_array
An array of non-functional genes whose members, when captured by recombination form functional genes.
SO:0005854
This would include, for example, the arrays of non-functional VSG genes of Trypanosomes.
gene cassette array
sequence
An array of non-functional genes whose members, when captured by recombination form functional genes.
SO:ma
gene_group
A collection of related genes.
SO:0005855
gene group
sequence
A collection of related genes.
SO:ma
selenocysteine_tRNA_primary_transcript
A primary transcript encoding seryl tRNA (SO:000269).
SO:0005856
selenocysteine tRNA primary transcript
sequence
A primary transcript encoding seryl tRNA (SO:000269).
SO:ke
selenocysteinyl_tRNA
A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.
SO:0005857
selenocysteinyl tRNA
selenocysteinyl-transfer RNA
selenocysteinyl-transfer ribonucleic acid
sequence
A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.
SO:ke
syntenic_region
A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species.
SO:0005858
sequence
syntenic region
A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species.
http://www.informatics.jax.org/silverbook/glossary.shtml
biochemical_region_of_peptide
A region of a peptide that is involved in a biochemical function.
Range.
SO:0100001
biochemical motif
biochemical region of peptide
biochemical_region
sequence
A region of a peptide that is involved in a biochemical function.
EBIBS:GAR
molecular_contact_region
A region that is involved a contact with another molecule.
Range.
SO:0100002
molecular contact region
sequence
A region that is involved a contact with another molecule.
EBIBS:GAR
intrinsically_unstructured_polypeptide_region
A region of polypeptide chain with high conformational flexibility.
SO:0100003
disordered region
intrinsically unstructured polypeptide region
sequence
disordered region
A region of polypeptide chain with high conformational flexibility.
EBIBS:GAR
catmat_left_handed_three
A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.
SO:0100004
catmat-3l
sequence
A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
catmat_left_handed_four
A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.
SO:0100005
catmat-4l
sequence
A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
catmat_right_handed_three
A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.
SO:0100006
catmat-3r
sequence
A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
catmat_right_handed_four
A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.
SO:0100007
catmat-4r
sequence
A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
alpha_beta_motif
A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative.
SO:0100008
alpha beta motif
sequence
A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative.
EBIBS:GAR
http://www.ebi.ac.uk/msd-srv/msdmotif/
lipoprotein_signal_peptide
A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes.
SO:0100009
lipoprotein signal peptide
prokaryotic membrane lipoprotein lipid attachment site
sequence
A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes.
EBIBS:GAR
no_output
An experimental region wherean analysis has been run and not produced any annotation.
SO:0100010
no output
sequence
An experimental region wherean analysis has been run and not produced any annotation.
EBIBS:GAR
no output
cleaved_peptide_region
Range.
SO:0100011
The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation.
cleaved peptide region
sequence
EBIBS:GAR
The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation.
peptide_coil
Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds).
SO:0100012
coil
peptide coil
random coil
sequence
coil
EBIBS:GAR
Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds).
random coil
hydrophobic_region_of_peptide
Hydrophobic regions are regions with a low affinity for water.
Range.
SO:0100013
hydropathic
hydrophobic region of peptide
hydrophobic_region
hydrophobicity
sequence
EBIBS:GAR
Hydrophobic regions are regions with a low affinity for water.
n_terminal_region
N-region
SO:0100014
The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa).
sequence
EBIBS:GAR
The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa).
c_terminal_region
C-region
SO:0100015
The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa).
sequence
EBIBS:GAR
The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa).
central_hydrophobic_region_of_signal_peptide
H-region
SO:0100016
The central, hydrophobic region of the signal peptide (approx 7-15 aa).
central hydrophobic region of signal peptide
central_hydrophobic_region
sequence
EBIBS:GAR
The central, hydrophobic region of the signal peptide (approx 7-15 aa).
polypeptide_conserved_motif
A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.
SO:0100017
motif
sequence
A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.
EBIBS:GAR
polypeptide_binding_motif
A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand.
SO:0100018
binding
polypeptide binding motif
sequence
A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand.
EBIBS:GAR
binding
uniprot:feature_type
polypeptide_catalytic_motif
A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues.
SO:0100019
catalytic_motif
polypeptide catalytic motif
sequence
A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues.
EBIBS:GAR
polypeptide_DNA_contact
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA.
DNA_bind
SO:0100020
polypeptide DNA contact
sequence
DNA_bind
uniprot:feature
A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA.
EBIBS:GAR
SO:ke
polypeptide_conserved_region
A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.
SO:0100021
polypeptide conserved region
sequence
A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.
EBIBS:GAR
substitution
A sequence alteration where the length of the change in the variant is the same as that of the reference.
SO:1000002
loinc:LA6690-7
sequence
Substitution
loinc:LA6690-7
A sequence alteration where the length of the change in the variant is the same as that of the reference.
SO:ke
complex_substitution
SO:1000005
When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change.
complex substitution
sequence
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change.
point_mutation
A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.
SO:1000008
http://en.wikipedia.org/wiki/Point_mutation
point mutation
sequence
A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.
SO:immuno_workshop
wiki
http://en.wikipedia.org/wiki/Point_mutation
transition
Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.
SO:1000009
sequence
Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
pyrimidine_transition
A substitution of a pyrimidine, C or T, for another pyrimidine.
SO:1000010
pyrimidine transition
sequence
A substitution of a pyrimidine, C or T, for another pyrimidine.
SO:ke
C_to_T_transition
A transition of a cytidine to a thymine.
C to T transition
SO:1000011
sequence
A transition of a cytidine to a thymine.
SO:ke
C_to_T_transition_at_pCpG_site
C to T transition at pCpG site
SO:1000012
The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.
sequence
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.
T_to_C_transition
SO:1000013
T to C transition
sequence
purine_transition
A substitution of a purine, A or G, for another purine.
SO:1000014
purine transition
sequence
A substitution of a purine, A or G, for another purine.
SO:ke
A_to_G_transition
A to G transition
A transition of an adenine to a guanine.
SO:1000015
sequence
A transition of an adenine to a guanine.
SO:ke
G_to_A_transition
A transition of a guanine to an adenine.
G to A transition
SO:1000016
sequence
A transition of a guanine to an adenine.
SO:ke
transversion
Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.
SO:1000017
http://en.wikipedia.org/wiki/Transversion
sequence
wiki
http://en.wikipedia.org/wiki/Transversion
Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
pyrimidine_to_purine_transversion
Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.
SO:1000018
pyrimidine to purine transversion
sequence
Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.
SO:ke
C_to_A_transversion
A transversion from cytidine to adenine.
C to A transversion
SO:1000019
sequence
A transversion from cytidine to adenine.
SO:ke
C_to_G_transversion
C to G transversion
SO:1000020
sequence
T_to_A_transversion
A transversion from T to A.
SO:1000021
T to A transversion
sequence
A transversion from T to A.
SO:ke
T_to_G_transversion
A transversion from T to G.
SO:1000022
T to G transversion
sequence
A transversion from T to G.
SO:ke
purine_to_pyrimidine_transversion
Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.
SO:1000023
purine to pyrimidine transversion
sequence
Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.
SO:ke
A_to_C_transversion
A to C transversion
A transversion from adenine to cytidine.
SO:1000024
sequence
A transversion from adenine to cytidine.
SO:ke
A_to_T_transversion
A to T transversion
A transversion from adenine to thymine.
SO:1000025
sequence
A transversion from adenine to thymine.
SO:ke
G_to_C_transversion
A transversion from guanine to cytidine.
G to C transversion
SO:1000026
sequence
A transversion from guanine to cytidine.
SO:ke
G_to_T_transversion
A transversion from guanine to thymine.
G to T transversion
SO:1000027
sequence
A transversion from guanine to thymine.
SO:ke
intrachromosomal_mutation
A chromosomal structure variation within a single chromosome.
SO:1000028
intrachromosomal mutation
sequence
A chromosomal structure variation within a single chromosome.
SO:ke
chromosomal_deletion
(Drosophila)Df
(bacteria)&Dgr;
(fungi)D
An incomplete chromosome.
SO:1000029
chromosomal deletion
deficiency
http://en.wikipedia.org/wiki/Chromosomal_deletion
sequence
wiki
http://en.wikipedia.org/wiki/Chromosomal_deletion
An incomplete chromosome.
SO:ke
chromosomal_inversion
(Drosophila)In
(bacteria)IN
(fungi)In
An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type.
SO:1000030
chromosomal inversion
http://en.wikipedia.org/wiki/Chromosomal_inversion
sequence
An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type.
SO:ke
wiki
http://en.wikipedia.org/wiki/Chromosomal_inversion
interchromosomal_mutation
A chromosomal structure variation whereby more than one chromosome is involved.
SO:1000031
interchromosomal mutation
sequence
A chromosomal structure variation whereby more than one chromosome is involved.
SO:ke
indel
A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.
Indels can have a different number of bases than the corresponding reference sequence.
SO:1000032
http://en.wikipedia.org/wiki/Indel
loinc:LA9659-9
sequence
Insertion and Deletion
loinc:LA9659-9
A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http:http://www.hgvs.org/mutnomen/recs-DNA.html#indel
wiki
http://en.wikipedia.org/wiki/Indel
duplication
An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome.
SO:1000035
loinc:LA6686-5
nucleotide duplication
nucleotide_duplication
sequence
An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
NCBI:th
Duplication
loinc:LA6686-5
inversion
A continuous nucleotide sequence is inverted in the same position.
SO:1000036
inversion
loinc:LA6689-9
sequence
Inversion
loinc:LA6689-9
A continuous nucleotide sequence is inverted in the same position.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
http://www.ncbi.nlm.nih.gov/dbvar/
inversion
chromosomal_duplication
(Drosophila)Dp
(fungi)Dp
An extra chromosome.
SO:1000037
chromosomal duplication
http://en.wikipedia.org/wiki/Chromosomal_duplication
sequence
An extra chromosome.
SO:ke
wiki
http://en.wikipedia.org/wiki/Chromosomal_duplication
intrachromosomal_duplication
A duplication that occurred within a chromosome.
SO:1000038
intrachromosomal duplication
sequence
A duplication that occurred within a chromosome.
SO:ke
direct_tandem_duplication
A tandem duplication where the individual regions are in the same orientation.
SO:1000039
direct tandem duplication
sequence
A tandem duplication where the individual regions are in the same orientation.
SO:ke
inverted_tandem_duplication
A tandem duplication where the individual regions are not in the same orientation.
SO:1000040
inverted tandem duplication
mirror duplication
sequence
A tandem duplication where the individual regions are not in the same orientation.
SO:ke
intrachromosomal_transposition
(Drosophila)Tp
A chromosome structure variation whereby a transposition occurred within a chromosome.
SO:1000041
intrachromosomal transposition
sequence
A chromosome structure variation whereby a transposition occurred within a chromosome.
SO:ke
compound_chromosome
A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms.
SO:1000042
compound chromosome
sequence
A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms.
SO:ke
Robertsonian_fusion
A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere.
Robertsonian fusion
SO:1000043
centric-fusion translocations
http://en.wikipedia.org/wiki/Robertsonian_fusion
sequence
whole-arm translocations
A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere.
http://en.wikipedia.org/wiki/Robertsonian_translocation
wiki
http://en.wikipedia.org/wiki/Robertsonian_fusion
chromosomal_translocation
(Drosophila)T
(fungi)T
An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations.
SO:1000044
chromosomal translocation
http://en.wikipedia.org/wiki/Chromosomal_translocation
sequence
wiki
http://en.wikipedia.org/wiki/Chromosomal_translocation
An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations.
FB:reference_manual
ring_chromosome
(Drosophila)R
(fungi)C
A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome.
SO:1000045
http://en.wikipedia.org/wiki/Ring_chromosome
ring chromosome
sequence
wiki
http://en.wikipedia.org/wiki/Ring_chromosome
A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome.
http://en.wikipedia.org/wiki/Ring_chromosome
pericentric_inversion
A chromosomal inversion that includes the centromere.
SO:1000046
pericentric inversion
sequence
A chromosomal inversion that includes the centromere.
FB:reference_manual
paracentric_inversion
A chromosomal inversion that does not include the centromere.
SO:1000047
paracentric inversion
sequence
A chromosomal inversion that does not include the centromere.
FB:reference_manual
reciprocal_chromosomal_translocation
A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged.
SO:1000048
reciprocal chromosomal translocation
sequence
A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged.
FB:reference_manual
sequence_variation_affecting_transcript
Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001576
SO:1000049
SO:1000177
SO:1000179
mutation affecting transcript
mutation causing partially characterised change in transcript
mutation causing uncharacterised change in transcript
sequence
sequence variant causing partially characterised change in transcript
sequence variant causing uncharacterised change in transcript
sequence variation affecting transcript
sequence_variant_causing_partially_characterised_change_in_transcript
sequence_variant_causing_uncharacterised_change_in_transcript
true
Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_causing_no_change_in_transcript
No effect on the state of the RNA.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term.
SO:1000050
mutation causing no change in transcript
sequence
sequence variant causing no change in transcript
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
No effect on the state of the RNA.
sequence_variation_affecting_coding_sequence
Any of the amino acid coding triplets of a gene are affected by the DNA mutation.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001580
SO:1000054
mutation affecting coding sequence
sequence
sequence variation affecting coding sequence
true
Any of the amino acid coding triplets of a gene are affected by the DNA mutation.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_causing_initiator_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001582
SO:1000055
The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used.
mutation causing initiator codon change in transcript
sequence
sequence variant causing initiator codon change in transcript
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used.
sequence_variant_causing_amino_acid_coding_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001606
SO:1000056
The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons.
mutaton causing amino acid coding codon change in transcript
sequence
sequence variant causing amino acid coding codon change in transcript
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons.
sequence_variant_causing_synonymous_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001819
SO:1000057
The changed codon has the same translation product as the original codon.
mutation causing synonymous codon change in transcript
sequence
sequence variant causing synonymous codon change in transcript
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The changed codon has the same translation product as the original codon.
sequence_variant_causing_non_synonymous_codon_change_in_transcript
A DNA point mutation that causes a substitution of an amino acid by an other.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001583
SO:1000058
mutation causing non synonymous codon change in transcript
non-synonymous codon change in transcript
sequence
sequence variant causing non synonymous codon change in transcript
true
A DNA point mutation that causes a substitution of an amino acid by an other.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_causing_missense_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001583
SO:1000059
The nucleotide change in the codon leads to a new codon coding for a new amino acid.
mutation causing missense codon change in transcript
sequence
sequence variant causing missense codon change in transcript
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The nucleotide change in the codon leads to a new codon coding for a new amino acid.
sequence_variant_causing_conservative_missense_codon_change_in_transcript
SO:0001585
SO:1000060
The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position.
The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
mutation causing conservative missense codon change in transcript
sequence
sequence variant causing conservative missense codon change in transcript
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position.
sequence_variant_causing_nonconservative_missense_codon_change_in_transcript
SO:0001586
SO:1000061
The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position.
The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
mutation causing nonconservative missense codon change in transcript
sequence
sequence variant causing nonconservative missense codon change in transcript
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position.
sequence_variant_causing_nonsense_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001587
SO:1000062
The nucleotide change in the codon triplet creates a terminator codon.
mutation causing nonsense codon change in transcript
sequence
sequence variant causing nonsense codon change in transcript
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The nucleotide change in the codon triplet creates a terminator codon.
sequence_variant_causing_terminator_codon_change_in_transcript
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001590
SO:1000063
The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence.
mutation causing terminator codon change in transcript
sequence
sequence variant causing terminator codon change in transcript
true
SO:ke
The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence.
sequence_variation_affecting_reading_frame
An umbrella term for terms describing an effect of a sequence variation on the frame of translation.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000064
mutation affecting reading frame
sequence
sequence variation affecting reading frame
true
An umbrella term for terms describing an effect of a sequence variation on the frame of translation.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
frameshift_sequence_variation
A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.
SO:1000065
frameshift mutation
frameshift sequence variation
http://en.wikipedia.org/wiki/Frameshift_mutation
out of frame mutation
sequence
true
A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.
SO:ke
wiki
http://en.wikipedia.org/wiki/Frameshift_mutation
sequence_variant_causing_plus_1_frameshift_mutation
A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001594
SO:1000066
plus 1 frameshift mutation
sequence
sequence variant causing plus 1 frameshift mutation
true
A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide.
SO:ke
sequence_variant_causing_minus_1_frameshift
A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001592
SO:1000067
minus 1 frameshift mutation
sequence
sequence variant causing minus 1 frameshift
true
A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide.
SO:ke
sequence_variant_causing_plus_2_frameshift
A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001595
SO:1000068
plus 2 frameshift mutation
sequence
sequence variant causing plus 2 frameshift
true
A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides.
SO:ke
sequence_variant_causing_minus_2_frameshift
A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001593
SO:1000069
minus 2 frameshift mutation
sequence
sequence variant causing minus 2 frameshift
true
A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides.
SO:ke
sequence_variant_affecting_transcript_processing
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001543
SO:1000070
Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript.
mutation affecting transcript processing
sequence
sequence variant affecting transcript processing
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript.
sequence_variant_affecting_splicing
A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001568
SO:1000071
mutation affecting splicing
sequence
sequence variant affecting splicing
true
A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_affecting_splice_donor
A sequence_variant_effect that changes the splice donor sequence.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001575
SO:1000072
mutation affecting splice donor
sequence
sequence variant affecting splice donor
splice donor mutation
true
A sequence_variant_effect that changes the splice donor sequence.
SO:ke
sequence_variant_affecting_splice_acceptor
A sequence_variant_effect that changes the splice acceptor sequence.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001574
SO:1000073
mutation affecting splicing
sequence
sequence variant affecting splice acceptor
splice acceptor mutation
true
A sequence_variant_effect that changes the splice acceptor sequence.
SO:ke
sequence_variant_causing_cryptic_splice_activation
A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration.
A sequence variant causing a new (functional) splice site.
SO:0001569
SO:1000074
cryptic splice activator sequence variant
mutation causing cryptic splice activator
sequence
sequence variant causing cryptic splice activator
true
A sequence variant causing a new (functional) splice site.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_affecting_editing
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001544
SO:1000075
Sequence variant affects the editing of the transcript.
mutation affecting editing
sequence
sequence variant affecting editing
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
Sequence variant affects the editing of the transcript.
sequence_variant_affecting_transcription
Mutation affects the process of transcription, its initiation, progression or termination.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001549
SO:1000076
mutation affecting transcription
sequence
sequence variant affecting transcription
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
Mutation affects the process of transcription, its initiation, progression or termination.
sequence_variant_decreasing_rate_of_transcription
A sequence variation that decreases the rate a which transcription of the sequence occurs.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000078
mutation decreasing rate of transcription
sequence
sequence variation decreasing rate of transcription
true
A sequence variation that decreases the rate a which transcription of the sequence occurs.
SO:ke
sequence_variation_affecting_transcript_sequence
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000079
mutation affecting transcript sequence
sequence
sequence variation affecting transcript sequence
true
sequence_variant_increasing_rate_of_transcription
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000080
mutation increasing rate of transcription
sequence
sequence variation increasing rate of transcription
true
sequence_variant_affecting_rate_of_transcription
A mutation that alters the rate a which transcription of the sequence occurs.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001550
SO:1000081
mutation affecting rate of transcription
sequence
sequence variant affecting rate of transcription
true
A mutation that alters the rate a which transcription of the sequence occurs.
SO:ke
sequence variant_affecting_transcript_stability
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001546
SO:1000082
Sequence variant affects the stability of the transcript.
mutation affecting transcript stability
sequence
sequence variant affecting transcript stability
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
Sequence variant affects the stability of the transcript.
sequence_variant_increasing_transcript_stability
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000083
Sequence variant increases the stability (half-life) of the transcript.
mutation increasing transcript stability
sequence
sequence variant increasing transcript stability
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
Sequence variant increases the stability (half-life) of the transcript.
sequence_variant_decreasing_transcript_stability
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000084
Sequence variant decreases the stability (half-life) of the transcript.
mutation decreasing transcript stability
sequence
sequence variant decreasing transcript stability
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
Sequence variant decreases the stability (half-life) of the transcript.
sequence_variation_affecting_level_of_transcript
A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001540
SO:1000085
mutation affecting level of transcript
sequence
sequence variation affecting level of transcript
true
A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.
SO:ke
sequence_variation_decreasing_level_of_transcript
A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000086
mutation decreasing level of transcript
sequence
sequence variation decreasing level of transcript
true
A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.
SO:ke
sequence_variation_increasing_level_of_transcript
A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000087
mutation increasing level of transcript
sequence
sequence variation increasing level of transcript
true
A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.
SO:ke
sequence_variant_affecting_translational_product
A sequence variant causing a change in primary translation product of a transcript.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001553
SO:1000088
SO:1000090
SO:1000091
mutation affecting translational product
mutation causing partially characterised change of translational product
mutation causing uncharacterised change of translational product
sequence
sequence variant affecting translational product
sequence variant causing partially characterised change of translational product
sequence variant causing uncharacterised change of translational product
sequence_variant_causing_partially_characterised_change_of_translational_product
sequence_variant_causing_uncharacterised_change_of_translational_product
true
A sequence variant causing a change in primary translation product of a transcript.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_causing_no_change_of_translational_product
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term.
SO:1000089
The sequence variant at RNA level does not lead to any change in polypeptide.
mutation causing no change of translational product
sequence
sequence variant causing no change of translational product
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The sequence variant at RNA level does not lead to any change in polypeptide.
sequence_variant_causing_complex_change_of_translational_product
Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001539
SO:1000092
mutation causing complex change of translational product
sequence
sequence variant causing complex change of translational product
true
Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_causing_amino_acid_substitution
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001606
SO:1000093
The replacement of a single amino acid by another.
mutation causing amino acid substitution
sequence
sequence variant causing amino acid substitution
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The replacement of a single amino acid by another.
sequence_variant_causing_conservative_amino_acid_substitution
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001607
SO:1000094
mutation causing conservative amino acid substitution
sequence
sequence variant causing conservative amino acid substitution
true
sequence_variant_causing_nonconservative_amino_acid_substitution
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001607
SO:1000095
mutation causing nonconservative amino acid substitution
sequence
sequence variant causing nonconservative amino acid substitution
true
sequence_variant_causing_amino_acid_insertion
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001605
SO:1000096
The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.
mutation causing amino acid insertion
sequence
sequence variant causing amino acid insertion
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.
sequence_variant_causing_amino_acid_deletion
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001825
SO:1000097
The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.
mutation causing amino acid deletion
sequence
sequence variant causing amino acid deletion
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.
sequence_variant_causing_polypeptide_truncation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001587
SO:1000098
The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062).
mutation causing polypeptide truncation
sequence
sequence variant causing polypeptide truncation
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062).
sequence_variant_causing_polypeptide_elongation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001609
SO:1000099
The extension of the translational product at either (or both) the N-terminus and/or the C-terminus.
mutation causing polypeptide elongation
sequence
sequence variant causing polypeptide elongation
true
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
The extension of the translational product at either (or both) the N-terminus and/or the C-terminus.
mutation_causing_polypeptide_N_terminal_elongation
.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001611
SO:1000100
mutation causing polypeptide N terminal elongation
polypeptide N-terminal elongation
sequence
true
.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
mutation_causing_polypeptide_C_terminal_elongation
.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001610
SO:1000101
mutation causing polypeptide C terminal elongation
polypeptide C-terminal elongation
sequence
true
.
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_affecting_level_of_translational_product
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001553
SO:1000102
mutation affecting level of translational product
sequence
sequence variant affecting level of translational product
true
sequence_variant_decreasing_level_of_translation_product
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001555
SO:1000103
mutationdecreasing level of translation product
sequence
sequence variant decreasing level of translation product
true
sequence_variant_increasing_level_of_translation_product
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000104
mutationt increasing level of translation product
sequence
sequence variant increasing level of translation product
true
sequence_variant_affecting_polypeptide_amino_acid_sequence
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001603
SO:1000105
mutation affecting polypeptide amino acid sequence
sequence
sequence variant affecting polypeptide amino acid sequence
true
mutation_causing_inframe_polypeptide_N_terminal_elongation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001614
SO:1000106
inframe polypeptide N-terminal elongation
mutation causing inframe polypeptide N terminal elongation
sequence
true
mutation_causing_out_of_frame_polypeptide_N_terminal_elongation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001615
SO:1000107
mutation causing out of frame polypeptide N terminal elongation
out of frame polypeptide N-terminal elongation
sequence
true
mutaton_causing_inframe_polypeptide_C_terminal_elongation
SO:0001612
SO:1000108
inframe_polypeptide C-terminal elongation
mutaton causing inframe polypeptide C terminal elongation
sequence
true
mutation_causing_out_of_frame_polypeptide_C_terminal_elongation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001613
SO:1000109
mutation causing out of frame polypeptide C terminal elongation
out of frame polypeptide C-terminal elongation
sequence
true
frame_restoring_sequence_variant
A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame.
SO:1000110
frame restoring mutation
frame restoring sequence variant
sequence
true
A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame.
SO:ke
sequence_variant_affecting_3D_structure_of_polypeptide
A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001599
SO:1000111
SO:1000113
SO:1000114
mutation affecting 3D structure of polypeptide
mutation causing partially characterised 3D structural change
mutation causing uncharacterised 3D structural change
sequence
sequence variant affecting 3D structure of polypeptide
sequence variant affecting 3D-structure of polypeptide
sequence variant causing partially characterised 3D structural change
sequence variant causing uncharacterised 3D structural change
sequence_variant_causing_partially_characterised_3D_structural_change
sequence_variant_causing_uncharacterised_3D_structural_change
true
A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule.
SO:ke
sequence_variant_causing_no_3D_structural_change
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term.
SO:1000112
mutation causing no 3D structural change
sequence
sequence variant causing no 3D structural change
true
sequence_variant_causing_complex_3D_structural_change
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001600
SO:1000115
mutation causing complex 3D structural change
sequence
sequence variant causing complex 3D structural change
true
sequence_variant_causing_conformational_change
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001601
SO:1000116
mutation causing conformational change
sequence
sequence variant causing conformational change
true
sequence_variant_affecting_polypeptide_function
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001554
SO:1000117
mutation affecting polypeptide function
sequence
sequence variant affecting polypeptide function
true
sequence_variant_causing_loss_of_function_of_polypeptide
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001559
SO:1000118
loss of function of polypeptide
mutation causing loss of function of polypeptide
sequence
sequence variant causing loss of function of polypeptide
true
sequence_variant_causing_inactive_ligand_binding_site
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001560
SO:1000119
mutation causing inactive ligand binding site
sequence
sequence variant causing inactive ligand binding site
true
sequence_variant_causing_inactive_catalytic_site
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001618
SO:1000120
mutation causing inactive catalytic site
sequence
sequence variant causing inactive catalytic site
true
sequence_variant_causing_polypeptide_localization_change
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001558
SO:1000121
mutation causing polypeptide localization change
sequence
sequence variant causing polypeptide localization change
true
sequence_variant_causing_polypeptide_post_translational_processing_change
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001562
SO:1000122
mutation causing polypeptide post translational processing change
polypeptide post-translational processing affected
sequence
sequence variant causing polypeptide post translational processing change
true
polypeptide_post_translational_processing_affected
SO:1000123
polypeptide_post-translational_processing_affected
sequence
true
sequence_variant_causing_partial_loss_of_function_of_polypeptide
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001561
SO:1000124
mutation causing partial loss of function of polypeptide
partial loss of function of polypeptide
sequence
sequence variant causing partial loss of function of polypeptide
true
sequence_variant_causing_gain_of_function_of_polypeptide
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001557
SO:1000125
gain of function of polypeptide
mutation causing gain of function of polypeptide
sequence
sequence variant causing gain of function of polypeptide
true
sequence_variant_affecting_transcript_secondary_structure
A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001596
SO:1000126
mutation affecting transcript secondary structure
sequence
sequence variant affecting transcript secondary structure
true
A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule.
SO:ke
sequence_variant_causing_compensatory_transcript_secondary_structure_mutation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001597
SO:1000127
mutation causing compensatory transcript secondary structure mutation
sequence
sequence variant causing compensatory transcript secondary structure mutation
true
sequence_variant_effect
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
Updated after discussion with Peter Taschner - Feb 09.
SO:1000132
The effect of a change in nucleotide sequence.
sequence
sequence variant effect
true
SO:ke
The effect of a change in nucleotide sequence.
sequence_variant_causing_polypeptide_fusion
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001616
SO:1000134
mutation causing polypeptide fusion
sequence
sequence variant causing polypeptide fusion
true
autosynaptic_chromosome
(Drosophila)A
An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome.
SO:1000136
autosynaptic chromosome
sequence
An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome.
PMID:6804304
homo_compound_chromosome
A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved.
SO:1000138
homo compound chromosome
homo-compound chromosome
sequence
A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved.
SO:ke
hetero_compound_chromosome
A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them.
SO:1000140
hetero compound chromosome
hetero-compound chromosome
sequence
A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them.
FB:reference_manual
SO:ke
chromosome_fission
A chromosome that occurred by the division of a larger chromosome.
SO:1000141
chromosome fission
sequence
A chromosome that occurred by the division of a larger chromosome.
SO:ke
dexstrosynaptic_chromosome
An autosynaptic chromosome carrying the two right (D = dextro) telomeres.
SO:1000142
dexstrosynaptic chromosome
sequence
An autosynaptic chromosome carrying the two right (D = dextro) telomeres.
FB:manual
laevosynaptic_chromosome
LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres.
SO:1000143
laevosynaptic chromosome
sequence
FB:manual
LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres.
free_duplication
A chromosome structure variation whereby the duplicated sequences are carried as a free centric element.
SO:1000144
free duplication
sequence
A chromosome structure variation whereby the duplicated sequences are carried as a free centric element.
FB:reference_manual
free_ring_duplication
(Drosophila)R
A ring chromosome which is a copy of another chromosome.
SO:1000145
free ring duplication
sequence
A ring chromosome which is a copy of another chromosome.
SO:ke
complex_chromosomal_mutation
A chromosome structure variant with 4 or more breakpoints.
SO:1000146
complex chromosomal mutation
sequence
A chromosome structure variant with 4 or more breakpoints.
FB:reference_manual
SO:ke
deficient_translocation
(Drosophila)Df
(Drosophila)DfT
A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining.
SO:1000147
deficient translocation
sequence
A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining.
FB:reference_manual
inversion_cum_translocation
(Drosophila)InT
(Drosophila)T
A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break.
SO:1000148
inversion cum translocation
sequence
A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break.
FB:reference_manual
bipartite_duplication
(Drosophila)bDp
An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break.
SO:1000149
bipartite duplication
sequence
An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break.
FB:reference_manual
cyclic_translocation
A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third.
SO:1000150
cyclic translocation
sequence
A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third.
FB:reference_manual
bipartite_inversion
(Drosophila)bIn
A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed).
SO:1000151
bipartite inversion
sequence
A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed).
FB:reference_manual
uninverted_insertional_duplication
(Drosophila)eDp
An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.
SO:1000152
sequence
uninverted insertional duplication
An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.
FB:reference_manual
inverted_insertional_duplication
(Drosophila)iDp
An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.
SO:1000153
inverted insertional duplication
sequence
An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.
FB:reference_manual
insertional_duplication
(Drosophila)Dpp
A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication).
SO:1000154
insertional duplication
sequence
A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication).
SO:ke
interchromosomal_transposition
(Drosophila)Tp
A chromosome structure variation whereby a transposition occurred between chromosomes.
SO:1000155
interchromosomal transposition
sequence
A chromosome structure variation whereby a transposition occurred between chromosomes.
SO:ke
inverted_interchromosomal_transposition
(Drosophila)iTp
An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment.
SO:1000156
inverted interchromosomal transposition
sequence
An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment.
FB:reference_manual
uninverted_interchromosomal_transposition
(Drosophila)eTp
An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.
SO:1000157
sequence
uninverted interchromosomal transposition
An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.
FB:reference_manual
inverted_intrachromosomal_transposition
(Drosophila)iTp
An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.
SO:1000158
inverted intrachromosomal transposition
sequence
An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.
FB:reference_manual
uninverted_intrachromosomal_transposition
(Drosophila)eTp
An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.
SO:1000159
sequence
uninverted intrachromosomal transposition
An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.
FB:reference_manual
unoriented_insertional_duplication
(Drosophila)uDp
An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.
Flag - unknown in the definition.
SO:1000160
sequence
unoriented insertional duplication
An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.
FB:reference_manual
unoriented_interchromosomal_transposition
(Drosophila)uTp
An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.
FLAG - term describes an unknown.
SO:1000161
sequence
unorientated interchromosomal transposition
An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.
FB:reference_manual
unoriented_intrachromosomal_transposition
(Drosophila)uTp
An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.
FLAG - definition describes an unknown.
SO:1000162
sequence
unorientated intrachromosomal transposition
An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.
FB:reference_manual
uncharacterised_chromosomal_mutation
SO:1000170
sequence
uncharacterised chromosomal mutation
deficient_inversion
(Drosophila)Df
(Drosophila)DfIn
A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted.
SO:1000171
deficient inversion
sequence
A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted.
FB:reference_manual
SO:ke
tandem_duplication
A duplication consisting of 2 identical adjacent regions.
SO:1000173
erverted
sequence
tandem duplication
erverted
http://www.ncbi.nlm.nih.gov/dbvar/
A duplication consisting of 2 identical adjacent regions.
SO:ke
partially_characterised_chromosomal_mutation
SO:1000175
partially characterised chromosomal mutation
sequence
sequence_variant_affecting_gene_structure
A sequence_variant_effect that changes the gene structure.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001564
SO:1000180
mutation affecting gene structure
sequence
sequence variant affecting gene structure
true
A sequence_variant_effect that changes the gene structure.
SO:ke
sequence_variant_causing_gene_fusion
A sequence_variant_effect that changes the gene structure by causing a fusion to another gene.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001565
SO:1000181
mutation causing gene fusion
sequence
sequence variant causing gene fusion
true
A sequence_variant_effect that changes the gene structure by causing a fusion to another gene.
SO:ke
chromosome_number_variation
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.
SO:1000182
chromosome number variation
sequence
A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.
SO:ke
chromosome_structure_variation
SO:1000183
chromosome structure variation
sequence
sequence_variant_causes_exon_loss
A sequence variant affecting splicing and causes an exon loss.
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000184
mutation causes exon loss
sequence
sequence variant causes exon loss
true
A sequence variant affecting splicing and causes an exon loss.
SO:ke
sequence_variant_causes_intron_gain
A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072).
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:1000185
mutation causes intron gain
sequence
sequence variant causes intron gain
true
A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072).
EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
sequence_variant_causing_cryptic_splice_donor_activation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001571
SO:1000186
sequence
sequence variant causing cryptic splice donor activation
true
sequence_variant_causing_cryptic_splice_acceptor_activation
OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
SO:0001570
SO:1001186
sequence
sequence variant causing cryptic splice acceptor activation
true
alternatively_spliced_transcript
A transcript that is alternatively spliced.
SO:1001187
alternatively spliced transcript
sequence
A transcript that is alternatively spliced.
SO:xp
encodes_1_polypeptide
A gene that is alternately spliced, but encodes only one polypeptide.
SO:1001188
encodes 1 polypeptide
sequence
A gene that is alternately spliced, but encodes only one polypeptide.
SO:ke
encodes_greater_than_1_polypeptide
A gene that is alternately spliced, and encodes more than one polypeptide.
SO:1001189
encodes greater than 1 polypeptide
sequence
A gene that is alternately spliced, and encodes more than one polypeptide.
SO:ke
encodes_different_polypeptides_different_stop
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons.
SO:1001190
encodes different polypeptides different stop
sequence
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons.
SO:ke
encodes_overlapping_peptides_different_start
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons.
SO:1001191
encodes overlapping peptides different start
sequence
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons.
SO:ke
encodes_disjoint_polypeptides
A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences.
SO:1001192
encodes disjoint polypeptides
sequence
A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences.
SO:ke
encodes_overlapping_polypeptides_different_start_and_stop
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons.
SO:1001193
encodes overlapping polypeptides different start and stop
sequence
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons.
SO:ke
alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping
SO:1001194
sequence
true
encodes_overlapping_peptides
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences.
SO:1001195
encodes overlapping peptides
sequence
A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences.
SO:ke
cryptogene
A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence.
SO:1001196
sequence
A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence.
SO:ma
dicistronic_primary_transcript
A primary transcript that has the quality dicistronic.
SO:1001197
dicistronic primary transcript
sequence
A primary transcript that has the quality dicistronic.
SO:xp
member_of_regulon
SO:1001217
member of regulon
sequence
alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping
SO:1001244
alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping
sequence
true
CDS_independently_known
A CDS with the evidence status of being independently known.
CDS independently known
SO:1001246
sequence
A CDS with the evidence status of being independently known.
SO:xp
orphan_CDS
A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence.
SO:1001247
orphan CDS
sequence
A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence.
SO:ma
CDS_supported_by_domain_match_data
A CDS that is supported by domain similarity.
CDS supported by domain match data
SO:1001249
sequence
A CDS that is supported by domain similarity.
SO:xp
CDS_supported_by_sequence_similarity_data
A CDS that is supported by sequence similarity data.
CDS supported by sequence similarity data
SO:1001251
sequence
A CDS that is supported by sequence similarity data.
SO:xp
CDS_predicted
A CDS that is predicted.
CDS predicted
SO:1001254
sequence
A CDS that is predicted.
SO:ke
status_of_coding_sequence
SO:1001255
sequence
true
CDS_supported_by_EST_or_cDNA_data
A CDS that is supported by similarity to EST or cDNA data.
CDS supported by EST or cDNA data
SO:1001259
sequence
A CDS that is supported by similarity to EST or cDNA data.
SO:xp
internal_Shine_Dalgarno_sequence
A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria.
SO:1001260
internal Shine Dalgarno sequence
internal Shine-Dalgarno sequence
sequence
A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria.
PMID:12519954
SO:ke
recoded_mRNA
SO:1001261
The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.
recoded mRNA
sequence
The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract
minus_1_translationally_frameshifted
An attribute describing a translational frameshift of -1.
SO:1001262
minus 1 translationally frameshifted
sequence
An attribute describing a translational frameshift of -1.
SO:ke
plus_1_translationally_frameshifted
An attribute describing a translational frameshift of +1.
SO:1001263
plus 1 translationally frameshifted
sequence
An attribute describing a translational frameshift of +1.
SO:ke
mRNA_recoded_by_translational_bypass
A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.
SO:1001264
mRNA recoded by translational bypass
sequence
A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract
mRNA_recoded_by_codon_redefinition
A recoded_mRNA that was modified by an alteration of codon meaning.
SO:1001265
mRNA recoded by codon redefinition
sequence
A recoded_mRNA that was modified by an alteration of codon meaning.
SO:ma
stop_codon_redefinition_as_selenocysteine
SO:1001266
sequence
true
stop_codon_readthrough
SO:1001267
sequence
true
recoding_stimulatory_region
A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA.
SO:1001268
recoding stimulatory region
recoding stimulatory signal
sequence
A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract
four_bp_start_codon
4bp start codon
A non-canonical start codon with 4 base pairs.
SO:1001269
four bp start codon
sequence
A non-canonical start codon with 4 base pairs.
SO:ke
stop_codon_redefinition_as_pyrrolysine
SO:1001270
sequence
true
archaeal_intron
An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease.
Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism.
SO:1001271
archaeal intron
sequence
An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease.
PMID:9301331
SO:ma
tRNA_intron
An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification.
Could be a cross product with Gene ontology, GO:0006388.
SO:1001272
pre-tRNA intron
sequence
tRNA intron
An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification.
SO:ke
CTG_start_codon
A non-canonical start codon of sequence CTG.
CTG start codon
SO:1001273
sequence
A non-canonical start codon of sequence CTG.
SO:ke
SECIS_element
SECIS element
SO:1001274
The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes.
http://en.wikipedia.org/wiki/SECIS_element
sequence
wiki
http://en.wikipedia.org/wiki/SECIS_element
The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes.
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031
retron
SO:1001275
Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes.
sequence
SO:ma
Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes.
three_prime_recoding_site
SO:1001277
The recoding stimulatory signal located downstream of the recoding site.
sequence
three prime recoding site
SO:ke
The recoding stimulatory signal located downstream of the recoding site.
three_prime_stem_loop_structure
A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region.
SO:1001279
sequence
three prime stem loop structure
A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region.
PMID:12519954
SO:ke
five_prime_recoding_site
SO:1001280
The recoding stimulatory signal located upstream of the recoding site.
five prime recoding site
sequence
SO:ke
The recoding stimulatory signal located upstream of the recoding site.
flanking_three_prime_quadruplet_recoding_signal
Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons.
SO:1001281
flanking three prime quadruplet recoding signal
sequence
Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons.
PMID:12519954
SO:ke
UAG_stop_codon_signal
A stop codon signal for a UAG stop codon redefinition.
SO:1001282
UAG stop codon signal
sequence
A stop codon signal for a UAG stop codon redefinition.
SO:ke
UAA_stop_codon_signal
A stop codon signal for a UAA stop codon redefinition.
SO:1001283
UAA stop codon signal
sequence
A stop codon signal for a UAA stop codon redefinition.
SO:ke
regulon
A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal.
SO:1001284
http://en.wikipedia.org/wiki/Regulon
sequence
A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal.
ISBN:0198506732
wiki
http://en.wikipedia.org/wiki/Regulon
UGA_stop_codon_signal
A stop codon signal for a UGA stop codon redefinition.
SO:1001285
UGA stop codon signal
sequence
A stop codon signal for a UGA stop codon redefinition.
SO:ke
three_prime_repeat_recoding_signal
A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements.
SO:1001286
sequence
three prime repeat recoding signal
A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements.
PMID:12519954
SO:ke
distant_three_prime_recoding_signal
A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon.
SO:1001287
distant three prime recoding signal
sequence
A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon.
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract
stop_codon_signal
A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding.
SO:1001288
This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal.
sequence
stop codon signal
A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding.
PMID:12519954
SO:ke
databank_entry
SO:2000061
The sequence referred to by an entry in a databank such as GenBank or SwissProt.
accession
databank entry
sequence
SO:ke
The sequence referred to by an entry in a databank such as GenBank or SwissProt.
gene_segment
A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.
Requested by tracker 2021594, July 2008, by Alex.
SO:3000000
gene segment
sequence
A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.
GOC:add
2015-05-14