OBO-Edit 2.3.1
23:11:2018 15:56
variation_ontology
1.2
med-mnv
A Variation Ontology
definition
database_cross_reference
has_exact_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence.
variation_ontology
adjacent_to
adjacent_to
A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence.
SO:ke
variation_ontology
associated_with
This relationship is vague and up for discussion.
associated_with
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.
variation_ontology
complete_evidence_for_feature
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
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
'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'.
variation_ontology
contains
The inverse relationship to "part of".
contains
'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'.
PSI-MOD:ref
variation_ontology
derives_from
derives_from
B is evidence_for_feature A, if an instance of B supports the existence of A.
variation_ontology
evidence_for_feature
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
B is evidence_for_feature A, if an instance of B supports the existence of A.
SO:ke
variation_ontology
genome_of
genome_of
'Entity A' has_functional_parent 'Entity B' implies that 'Entity B' has at least one chacteristic group from which 'Entity A' can be derived by functional modification.
variation_ontology
has_functional_parent
This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent.
has functional parent
'Entity A' has_functional_parent 'Entity B' implies that 'Entity B' has at least one chacteristic group from which 'Entity A' can be derived by functional modification.
PSI-MOD:ref
variation_ontology
has_origin
has_origin
variation_ontology
has_part
has_part
variation_ontology
has_quality
The relationship between a feature and an attribute.
has_quality
variation_ontology
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
variation_ontology
negatively_regulates
negatively_regulates
A relationship between a pseudogenic feature and its functional ancestor.
variation_ontology
non_functional_homolog_of
non_functional_homolog_of
A relationship between a pseudogenic feature and its functional ancestor.
SO:ke
variation_ontology
part_of
part_of
B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
variation_ontology
partial_evidence_for_feature
partial_evidence_for_feature
B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
SO:ke
variation_ontology
position_of
position_of
variation_ontology
positively_regulates
positively_regulates
variation_ontology
regulates
regulates
variation_ontology
sequence_of
sequence_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.
variation_ontology
variant_of
Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.
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
Alteration in DNA, RNA or protein.
variation_ontology
VariO:0001
variation
VariO:0001
Alteration in DNA, RNA or protein.
VariO:mv
Effects of a variation on protein level.
variation_ontology
VariO:0002
variation affecting protein
VariO:0002
Effects of a variation on protein level.
VariO:mv
Effect of variation on protein function.
variation_ontology
VariO:0003
variation affecting protein function
VariO:0003
Effect of variation on protein function.
VariO:mv
Effect of variation on the movement of a protein along filament of a polymeric molecule.
variation_ontology
VariO:0004
effect on protein movement
VariO:0004
Effect of variation on the movement of a protein along filament of a polymeric molecule.
VariO:mv
Effect of variation on storage protein. Storage proteins are cellular sources of amino acids and metal ions.
variation_ontology
VariO:0005
effect on protein storage
VariO:0005
Effect of variation on storage protein. Storage proteins are cellular sources of amino acids and metal ions.
VariO:mv
Effect of variation on structural role of protein. Structural proteins are fibrous and involved in increasing rigidity and stiffness of biological systems.
variation_ontology
VariO:0006
effect on structural protein
VariO:0006
Effect of variation on structural role of protein. Structural proteins are fibrous and involved in increasing rigidity and stiffness of biological systems.
VariO:mv
Effect of variation on selective non-covalent interaction of protein.
variation_ontology
VariO:0007
effect on protein recognition
VariO:0007
Effect of variation on selective non-covalent interaction of protein.
VariO:mv
Effect of variation on catalytic function of protein.
variation_ontology
VariO:0008
effect on catalytic protein function
VariO:0008
Effect of variation on catalytic function of protein.
VariO:mv
Effect of variation on transport function of protein in facilitating passage of an atom or molecule through membrane.
variation_ontology
VariO:0009
effect on transport function of protein
VariO:0009
Effect of variation on transport function of protein in facilitating passage of an atom or molecule through membrane.
VariO:mv
Variation affecting abundance of produced RNA molecules.
variation_ontology
VariO:0010
effect on RNA abundance
VariO:0010
Variation affecting abundance of produced RNA molecules.
VariO:mv
Effect of variation on information transfer by protein to control activity of specific processes in cells, tissues or organs.
variation_ontology
VariO:0011
effect on protein information transfer
VariO:0011
Effect of variation on information transfer by protein to control activity of specific processes in cells, tissues or organs.
VariO:mv
Type of protein variation. Describes origin and classification of a variant.
variation_ontology
VariO:0012
protein variation type
VariO:0012
Type of protein variation. Describes origin and classification of a variant.
VariO:mv
Protein variation that has genetic origin.
variation_ontology
VariO:0013
protein variation of genetic origin
VariO:0013
Protein variation that has genetic origin.
VariO:mv
Removal of one or more continuous amino acids from protein.
variation_ontology
VariO:0014
amino acid deletion
VariO:0014
Removal of one or more continuous amino acids from protein.
VariO:mv
Shortening of protein sequence from terminus.
variation_ontology
VariO:0015
protein truncation
VariO:0015
Shortening of protein sequence from terminus.
VariO:mv
Deletion of one or more amino acids from a protein, without affecting the sequence after deletion.
variation_ontology
VariO:0016
sequence retaining amino acid deletion
VariO:0016
Deletion of one or more amino acids from a protein, without affecting the sequence after deletion.
VariO:mv
mRNA variation leading to amino acid change in translated protein. The variant alters the codon so that it encodes another amino acid.
med-mnv
2015-06-04T13:23:24Z
variation_ontology
VariO:0017
nonsynonymous variation
VariO:0017
mRNA variation leading to amino acid change in translated protein. The variant alters the codon so that it encodes another amino acid.
Vario:mv
Addition of one or more amino acids to protein sequence.
variation_ontology
VariO:0018
amino acid insertion
VariO:0018
Addition of one or more amino acids to protein sequence.
VariO:mv
Insertion of one or more amino acids to protein with sequence completely changed after the insertion position. Caused by insertion of number of RNA nucleotides not divisible by three leading to frame shift of mRNA reading frame.
variation_ontology
VariO:0019
amphigoric amino acid insertion
VariO:0019
Insertion of one or more amino acids to protein with sequence completely changed after the insertion position. Caused by insertion of number of RNA nucleotides not divisible by three leading to frame shift of mRNA reading frame.
VariO:mv
Insertion of one or more amino acids to the protein without affecting the sequence after insertion.
variation_ontology
VariO:0020
sequence retaining amino acid insertion
VariO:0020
Insertion of one or more amino acids to the protein without affecting the sequence after insertion.
VariO:mv
Substitution of an amino acid in protein.
SO:0001606
variation_ontology
VariO:0021
amino acid substitution
VariO:0021
Substitution of an amino acid in protein.
VariO:mv
A complex protein variation consisting of both amino acid insertion(s) and deletion(s).
variation_ontology
VariO:0022
amino acid indel
VariO:0022
A complex protein variation consisting of both amino acid insertion(s) and deletion(s).
VariO:mv
Amino acid indel with sequence completely changed after the indel position. Caused by indel of number of RNA nucleotides not divisible by three leading to frameshift of reading frame.
Mauno Vihinen
2013-03-06T10:59:41Z
variation_ontology
VariO:0023
amphigoric amino acid indel
VariO:0023
Amino acid indel with sequence completely changed after the indel position. Caused by indel of number of RNA nucleotides not divisible by three leading to frameshift of reading frame.
VariO:mv
Protein variation that does not have genetic origin being modified at protein level.
variation_ontology
VariO:0024
variation emerging at protein level
VariO:0024
Protein variation that does not have genetic origin being modified at protein level.
VariO:mv
Heritable protein variation of non-genetic origin.
variation_ontology
VariO:0025
epigenetic protein variation
VariO:0025
Heritable protein variation of non-genetic origin.
VariO:mv
Inheritance of protein or protein complex structure without involvement of genetic information.
variation_ontology
VariO:0026
protein structural inheritance
VariO:0026
Inheritance of protein or protein complex structure without involvement of genetic information.
VariO:mv
Protein conformation change induced by structurally modified protein.
variation_ontology
VariO:0027
proteinaceous infection
VariO:0027
Protein conformation change induced by structurally modified protein.
VariO:mv
Protein molecule chemically modified after translation.
variation_ontology
VariO:0028
post translational modification
VariO:0028
Protein molecule chemically modified after translation.
VariO:mv
Amino acid indel without affecting the sequence after the indel position.
Mauno Vihinen
2013-03-06T11:04:21Z
variation_ontology
VariO:0029
sequence retaining amino acid indel
VariO:0029
Amino acid indel without affecting the sequence after the indel position.
VariO:mv
RNA indel not affecting reading frame after indel position.
Mauno Vihinen
2013-06-14T10:03:57Z
variation_ontology
VariO:0030
in-frame indel
VariO:0030
RNA indel not affecting reading frame after indel position.
VariO:mv
RNA indel containing a number of nucleotides not divisible by three and therefore causing change to reading frame.
Mauno Vihinen
2013-06-14T10:03:57Z
variation_ontology
VariO:0031
out-of-frame indel
VariO:0031
RNA indel containing a number of nucleotides not divisible by three and therefore causing change to reading frame.
VariO:mv
Variation affecting characteristic property of protein.
variation_ontology
VariO:0032
variation affecting protein property
VariO:0032
Variation affecting characteristic property of protein.
VariO:mv
Effect of variation on the targeting of a protein within a cell or cellular compartment.
variation_ontology
VariO:0033
effect on protein subcellular localization
VariO:0033
Effect of variation on the targeting of a protein within a cell or cellular compartment.
VariO:mv
Effect of variation on stability of protein.
variation_ontology
VariO:0034
effect on protein stability
VariO:0034
Effect of variation on stability of protein.
VariO:mv
Effect of variation on the potential of protein to dissolve in a liquid.
variation_ontology
VariO:0035
effect on protein solubility
VariO:0035
Effect of variation on the potential of protein to dissolve in a liquid.
VariO:mv
Variation affecting the formation of particles of aggregated proteins.
GO:0016234
variation_ontology
VariO:0036
effect on protein inclusion body formation
VariO:0036
Variation affecting the formation of particles of aggregated proteins.
VariO:mv
Variation at a covarying sequence position.
Mauno Vihinen
2014-01-16T14:03:51Z
variation_ontology
VariO:0037
covariant position
VariO:0037
Variation at a covarying sequence position.
VariO:mv
Variation affecting protein aggregation tendency.
variation_ontology
VariO:0038
effect on protein aggregation
VariO:0038
Variation affecting protein aggregation tendency.
VariO:mv
Type of protein function affecting variation.
variation_ontology
VariO:0039
protein function change
VariO:0039
Type of protein function affecting variation.
VariO:mv
Effect of variation causing new or enhanced protein activity.
variation_ontology
VariO:0040
protein gain of function
VariO:0040
Effect of variation causing new or enhanced protein activity.
VariO:mv
Variation generates new protein function.
variation_ontology
VariO:0041
neomorphic protein variation
VariO:0041
Variation generates new protein function.
VariO:mv
Dominant variation that acts to opposite direction than the normal protein.
dominant negative protein variation
variation_ontology
VariO:0042
antimorphic protein variation
VariO:0042
Dominant variation that acts to opposite direction than the normal protein.
VariO:mv
Effect of variation reducing or abolishing protein activity.
variation_ontology
VariO:0043
protein loss of function
VariO:0043
Effect of variation reducing or abolishing protein activity.
VariO:mv
Effect of variation to the accessibility of protein region to solvent.
variation_ontology
VariO:0044
effect on protein accessibility
VariO:0044
Effect of variation to the accessibility of protein region to solvent.
VariO:mv
Variation exposing buried region.
variation_ontology
VariO:0045
variation exposing buried region
VariO:0045
Variation exposing buried region.
VariO:mv
Variation leading to burying of exposed region.
variation_ontology
VariO:0046
variation burying exposed region
VariO:0046
Variation leading to burying of exposed region.
VariO:mv
Implication of a protein variant to pathogenicity.
variation_ontology
VariO:0047
association of protein variation to pathogenicity
VariO:0047
Implication of a protein variant to pathogenicity.
VariO:mv
Effect of variation on charge in protein.
variation_ontology
VariO:0048
effect on protein charge
VariO:0048
Effect of variation on charge in protein.
VariO:mv
Variation affecting electrostatics of the protein surface.
variation_ontology
VariO:0049
effect on protein electrostatics
VariO:0049
Variation affecting electrostatics of the protein surface.
VariO:mv
Variation changing protein isoelectric point.
variation_ontology
VariO:0050
effect on protein isoelectric point
VariO:0050
Variation changing protein isoelectric point.
VariO:mv
Effect of variation on degradation of protein.
variation_ontology
VariO:0051
effect on protein degradation
VariO:0051
Effect of variation on degradation of protein.
VariO:mv
Variation affecting abundance of produced protein molecules.
variation_ontology
VariO:0052
effect on protein abundance
VariO:0052
Variation affecting abundance of produced protein molecules.
VariO:mv
Effect of variation on activity of protein.
variation_ontology
VariO:0053
effect on protein activity
VariO:0053
Effect of variation on activity of protein.
VariO:mv
Effect of variation on protein affinity to binding molecule(s).
variation_ontology
VariO:0054
effect on protein affinity
VariO:0054
Effect of variation on protein affinity to binding molecule(s).
VariO:mv
Effect of variation on substrate binding specificity of protein.
variation_ontology
VariO:0055
effect on protein specificity
VariO:0055
Effect of variation on substrate binding specificity of protein.
VariO:mv
Effect of variation to enzyme reaction kinetics.
variation_ontology
VariO:0056
effect on enzyme reaction kinetics
VariO:0056
Effect of variation to enzyme reaction kinetics.
VariO:mv
Conservation of the variant site in related protein sequences.
variation_ontology
VariO:0057
conservation of protein variation site
VariO:0057
Conservation of the variant site in related protein sequences.
VariO:mv
Effect of variation on the interaction of protein with its partner.
variation_ontology
VariO:0058
effect on protein interaction
VariO:0058
Effect of variation on the interaction of protein with its partner.
VariO:mv
Effect of variation on contact energy between interacting molecules.
variation_ontology
VariO:0059
effect on protein contact energy
VariO:0059
Effect of variation on contact energy between interacting molecules.
VariO:mv
Variation affecting structure of protein.
variation_ontology
VariO:0060
variation affecting protein structure
VariO:0060
Variation affecting structure of protein.
VariO:mv
Hereditary protein structure modification of non-genetic origin.
variation_ontology
VariO:0061
epigenetic protein modification
VariO:0061
Hereditary protein structure modification of non-genetic origin.
VariO:mv
Variation affecting the formation of infectious protein having misfolded structure.
variation_ontology
VariO:0062
prion formation
VariO:0062
Variation affecting the formation of infectious protein having misfolded structure.
VariO:mv
Variation affecting heritable protein complex structure.
variation_ontology
VariO:0063
epigenetic protein complex structure
VariO:0063
Variation affecting heritable protein complex structure.
VariO:mv
Variation affecting protein three dimensional structure.
variation_ontology
VariO:0064
effect on protein 3D structure
VariO:0064
Variation affecting protein three dimensional structure.
VariO:mv
Variation affecting dynamics in protein structure.
variation_ontology
VariO:0065
effect on protein dynamics
VariO:0065
Variation affecting dynamics in protein structure.
VariO:mv
Variation affecting protein structural flexibility.
variation_ontology
VariO:0066
effect on structural flexibility
VariO:0066
Variation affecting protein structural flexibility.
VariO:mv
Variation affecting induced fit of protein binding to its partner.
variation_ontology
VariO:0067
effect on induced fit
VariO:0067
Variation affecting induced fit of protein binding to its partner.
VariO:mv
Variation affecting protein structural disorder.
variation_ontology
VariO:0068
effect on structural disorder
VariO:0068
Variation affecting protein structural disorder.
VariO:mv
Variation in affecting protein allosteric site.
variation_ontology
VariO:0069
effect on allosteric site
VariO:0069
Variation in affecting protein allosteric site.
VariO:mv
Variation affecting protein three dimensional structure.
variation_ontology
VariO:0070
effect on protein tertiary structure
VariO:0070
Variation affecting protein three dimensional structure.
VariO:mv
Variation affecting rate of protein folding.
variation_ontology
VariO:0071
effect on protein folding rate
VariO:0071
Variation affecting rate of protein folding.
VariO:mv
Variation effect on nonchromosomal DNA.
Mauno Vihinen
2012-11-09T14:16:30Z
variation_ontology
VariO:0072
extrachromosomal DNA affected
VariO:0072
Variation effect on nonchromosomal DNA.
VariO:mv
Variation affecting protein tertiary structure.
variation_ontology
VariO:0073
effect to protein fold
VariO:0073
Variation affecting protein tertiary structure.
VariO:mv
Variation changing protein conformation.
variation_ontology
VariO:0074
protein conformational change
VariO:0074
Variation changing protein conformation.
VariO:mv
Variation causing large overall protein conformational change.
variation_ontology
VariO:0075
global protein conformation change
VariO:0075
Variation causing large overall protein conformational change.
VariO:mv
Variation causing local and minor conformational change.
variation_ontology
VariO:0076
local protein conformation change
VariO:0076
Variation causing local and minor conformational change.
VariO:mv
Variation affecting protein structure due to alteration to domain orientation.
variation_ontology
VariO:0077
changed domain orientation
VariO:0077
Variation affecting protein structure due to alteration to domain orientation.
VariO:mv
Variation affecting formation of intramolecular disulphide bonds.
variation_ontology
VariO:0078
effect on protein disulphide formation
VariO:0078
Variation affecting formation of intramolecular disulphide bonds.
VariO:mv
Variation affecting protein secondary structural element of local ordered structure.
variation_ontology
VariO:0079
effect on protein secondary structural element
VariO:0079
Variation affecting protein secondary structural element of local ordered structure.
VariO:mv
Variation affecting secondary structure conformation where the peptide backbone forms a coil.
variation_ontology
VariO:0080
effect on protein helix
VariO:0080
Variation affecting secondary structure conformation where the peptide backbone forms a coil.
VariO:mv
Variation affecting protein left handed helix turning anticlockwise.
variation_ontology
VariO:0081
effect on left handed protein helix
VariO:0081
Variation affecting protein left handed helix turning anticlockwise.
VariO:mv
Variation affecting protein right handed helix where the coiled conformation turns in a clockwise, right handed screw.
variation_ontology
VariO:0082
effect on right handed protein helix
VariO:0082
Variation affecting protein right handed helix where the coiled conformation turns in a clockwise, right handed screw.
VariO:mv
Variation affecting protein helix having 4.1 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
variation_ontology
VariO:0083
effect on pi helix
VariO:0083
Variation affecting protein helix having 4.1 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
VariO:mv
Variation affecting protein helix having 3 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
variation_ontology
VariO:0084
effect on three ten helix
VariO:0084
Variation affecting protein helix having 3 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
VariO:mv
Variation affecting protein helix having 3.6 residues per turn. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
variation_ontology
VariO:0085
effect on alpha helix
VariO:0085
Variation affecting protein helix having 3.6 residues per turn. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
VariO:mv
Variation affecting extended protein backbone structure.
variation_ontology
VariO:0086
effect on protein beta strand
VariO:0086
Variation affecting extended protein backbone structure.
VariO:mv
Variation affecting beta strand forming part of antiparallel beta sheet. Hydrogen bonds are formed with another region of protein running in the opposite direction. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees).
variation_ontology
VariO:0087
Range.
effect on protein antiparallel beta strand
VariO:0087
Variation affecting beta strand forming part of antiparallel beta sheet. Hydrogen bonds are formed with another region of protein running in the opposite direction. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees).
VariO:mv
Variation affecting beta strand forming part of parallel beta sheet. Hydrogen bonds are formed with another region of protein running in the same direction. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees).
variation_ontology
VariO:0088
Range.
effect on protein parallel beta strand
VariO:0088
Variation affecting beta strand forming part of parallel beta sheet. Hydrogen bonds are formed with another region of protein running in the same direction. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees).
VariO:mv
Variation affecting protein backbone turn motif.
variation_ontology
VariO:0089
effect on protein turn motif
VariO:0089
Variation affecting protein backbone turn motif.
VariO:mv
Variation affecting protein 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.
variation_ontology
VariO:0090
effect on protein alpha beta motif
VariO:0090
Variation affecting protein 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.
VariO:mv
Variation affecting protein 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 is used to sub-categorize the turns.
variation_ontology
VariO:0091
effect on protein beta turn
VariO:0091
Variation affecting protein 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 is used to sub-categorize the turns.
VariO:mv
Variation affecting protein motif of five consecutive residues and two H-bonds, where residue(i) is either serine or threonine. Side chain O of residue(i) is H-bonded to the main chain NH of residue(i+2) or (i+3), and main chain CO or residue(i) is H-bonded to the main chain NH or residue(i+3) or (i+4).
variation_ontology
VariO:0092
effect on protein st motif
VariO:0092
Variation affecting protein motif of five consecutive residues and two H-bonds, where residue(i) is either serine or threonine. Side chain O of residue(i) is H-bonded to the main chain NH of residue(i+2) or (i+3), and main chain CO or residue(i) is H-bonded to the main chain NH or residue(i+3) or (i+4).
VariO:mv
Variation affecting protein motif of four or five consecutive residues and one H-bond in which residue(i) is serine or threonine, the side chain OH of residue(i) is H-bonded to the main chain CO or residue(i-3) or (i-4), and phi angles of residues(i-1), (i-2) and (i-3) are negative.
variation_ontology
VariO:0093
effect on protein st staple
VariO:0093
Variation affecting protein motif of four or five consecutive residues and one H-bond in which residue(i) is serine or threonine, the side chain OH of residue(i) is H-bonded to the main chain CO or residue(i-3) or (i-4), and phi angles of residues(i-1), (i-2) and (i-3) are negative.
VariO:mv
Variation affecting protein turn 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.
variation_ontology
VariO:0094
effect on protein gamma turn
VariO:0094
Variation affecting protein turn 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.
VariO:mv
Variation affecting protein motif of three consecutive residues and one H-bond in which: residue(i) is serine or threonine, the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
variation_ontology
VariO:0095
effect on protein st turn
VariO:0095
Variation affecting protein motif of three consecutive residues and one H-bond in which: residue(i) is serine or threonine, the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
VariO:mv
Variation affecting protein motif of six or seven consecutive residues that contains two H-bonds.
variation_ontology
VariO:0096
effect on protein schellman loop
VariO:0096
Variation affecting protein motif of six or seven consecutive residues that contains two H-bonds.
VariO:mv
Variation affecting protein motif of two consecutive residues. Dihedral angles are used to sub-categorise the nests. Nest does not contain proline.
variation_ontology
VariO:0097
effect on protein nest motif
VariO:0097
Variation affecting protein motif of two consecutive residues. Dihedral angles are used to sub-categorise the nests. Nest does not contain proline.
VariO:mv
Variation affecting a protein motif of three consecutive residues. Dihedral angles are used to sub-categorise the niche motifs.
variation_ontology
VariO:0098
effect on protein niche motif
VariO:0098
Variation affecting a protein motif of three consecutive residues. Dihedral angles are used to sub-categorise the niche motifs.
VariO:mv
Variation affecting protein 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).
variation_ontology
VariO:0099
effect on protein asx motif
VariO:0099
Variation affecting protein 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).
VariO:mv
Variation affecting protein 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.
variation_ontology
VariO:0100
effect on protein beta bulge
VariO:0100
Variation affecting protein 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.
VariO:mv
Variation affecting protein 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).
variation_ontology
VariO:0101
effect on protein asx turn
VariO:0101
Variation affecting protein 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).
VariO:mv
Variation affecting protein motif of three residues within a beta-sheet consisting of two H-bonds.
variation_ontology
VariO:0102
effect on protein beta bulge loop
VariO:0102
Variation affecting protein motif of three residues within a beta-sheet consisting of two H-bonds.
VariO:mv
Variation affecting irregular, unstructured region of protein.
variation_ontology
VariO:0103
effect on protein coil
VariO:0103
Variation affecting irregular, unstructured region of protein.
VariO:mv
Variation altering membrane spanning protein.
variation_ontology
VariO:0104
effect on transmembrane polypeptide
VariO:0104
Variation altering membrane spanning protein.
VariO:mv
Variation affecting region not traversing the lipid bilayer in a membrane protein.
variation_ontology
VariO:0105
effect on membrane protein extramembrane region
VariO:0105
Variation affecting region not traversing the lipid bilayer in a membrane protein.
VariO:mv
Variation affecting region present in the lipid bilayer in a membrane protein.
variation_ontology
VariO:0106
effect on membrane protein intramembrane region
VariO:0106
Variation affecting region present in the lipid bilayer in a membrane protein.
VariO:mv
Variation affecting the covalent alteration of protein amino acid by post translational process.
variation_ontology
VariO:0107
effect on protein post translational modification
VariO:0107
Variation affecting the covalent alteration of protein amino acid by post translational process.
VariO:mv
Variation causing deletion of a post translational modification site.
variation_ontology
VariO:0108
deletion of a post translational modification site
VariO:0108
Variation causing deletion of a post translational modification site.
VariO:mv
Variation affecting site of protein maturation by cleavage of peptide bond(s).
variation_ontology
VariO:0109
effect on protein processing
VariO:0109
Variation affecting site of protein maturation by cleavage of peptide bond(s).
VariO:mv
Variation affecting post-translational removal of peptide sequences from within a protein sequence.
variation_ontology
VariO:0110
effect on protein splicing
VariO:0110
Variation affecting post-translational removal of peptide sequences from within a protein sequence.
VariO:mv
Variation that generates a novel protein processing site.
variation_ontology
VariO:0111
variation generating a novel protein processing site
VariO:0111
Variation that generates a novel protein processing site.
VariO:mv
Variation causing prevention of polypeptide processing.
variation_ontology
VariO:0112
variation preventing polypeptide processing
VariO:0112
Variation causing prevention of polypeptide processing.
VariO:mv
Variation generating a novel post translational modification site.
variation_ontology
VariO:0113
generation of a novel post translational modification site
VariO:0113
Variation generating a novel post translational modification site.
VariO:mv
Variation affecting amino acid side chain size.
variation_ontology
VariO:0114
effect on amino acid size
VariO:0114
Variation affecting amino acid side chain size.
VariO:mv
Variation affecting amino acid packing in folded protein.
variation_ontology
VariO:0115
effect on protein packing
VariO:0115
Variation affecting amino acid packing in folded protein.
VariO:mv
Variation causing formation of a cavity to protein core due to replacement of a side chain by a smaller one.
variation_ontology
VariO:0116
protein cavity formation
VariO:0116
Variation causing formation of a cavity to protein core due to replacement of a side chain by a smaller one.
VariO:mv
Variation causing over packing of amino acids due to replacement by larger amino acid side chain.
variation_ontology
VariO:0117
protein overpacking
VariO:0117
Variation causing over packing of amino acids due to replacement by larger amino acid side chain.
VariO:mv
Variation affecting ligand binding amino acid(s) in protein.
variation_ontology
VariO:0118
effect on protein interaction site
VariO:0118
Variation affecting ligand binding amino acid(s) in protein.
VariO:mv
Variation affecting region on the surface of a protein that interacts with another molecule.
variation_ontology
VariO:0119
effect on protein binding site
VariO:0119
Variation affecting region on the surface of a protein that interacts with another molecule.
VariO:mv
Variation affecting amino acid(s) in protein catalytic site.
variation_ontology
VariO:0120
effect on protein catalytic site
VariO:0120
Variation affecting amino acid(s) in protein catalytic site.
VariO:mv
Variation affecting three dimensional structure of a protein complex.
variation_ontology
VariO:0121
effect on protein quaternary structure
VariO:0121
Variation affecting three dimensional structure of a protein complex.
VariO:mv
Variation affecting interaction between protein subunits in quaternary structure.
variation_ontology
VariO:0122
effect on protein quaternary structure forming interaction
VariO:0122
Variation affecting interaction between protein subunits in quaternary structure.
VariO:mv
Complex change of protein three dimensional structure.
variation_ontology
VariO:0123
complex 3D structural change
VariO:0123
Complex change of protein three dimensional structure.
VariO:mv
Variation prolonging protein chain at an end.
variation_ontology
VariO:0124
protein elongation
VariO:0124
Variation prolonging protein chain at an end.
VariO:mv
Addition of one or more amino acids to protein C-terminus.
variation_ontology
VariO:0125
C-terminal protein elongation
VariO:0125
Addition of one or more amino acids to protein C-terminus.
VariO:mv
Addition of one or more amino acids to protein N-terminus.
variation_ontology
VariO:0126
N-terminal protein elongation
VariO:0126
Addition of one or more amino acids to protein N-terminus.
VariO:mv
Origin of DNA variation.
Mauno Vihinen
2013-10-11T08:46:32Z
variation_ontology
VariO:0127
DNA variation origin
VariO:0127
Origin of DNA variation.
VariO:mv
Effects of a variation on DNA level.
variation_ontology
VariO:0128
variation affecting DNA
VariO:0128
Effects of a variation on DNA level.
VariO:mv
Type of DNA variation. Describes origin and classification of a variant.
variation_ontology
VariO:0129
DNA variation type
VariO:0129
Type of DNA variation. Describes origin and classification of a variant.
VariO:mv
DNA variation that has genetic origin.
variation_ontology
VariO:0130
DNA variation of genetic origin
VariO:0130
DNA variation that has genetic origin.
VariO:mv
Variation of genomic level.
variation_ontology
VariO:0131
genomic variation
VariO:0131
Variation of genomic level.
VariO:mv
Variation at chromosomal level.
variation_ontology
VariO:0132
chromosomal variation
VariO:0132
Variation at chromosomal level.
VariO:mv
Variation affecting chromosome number.
variation_ontology
aneuploidy
VariO:0133
variation of chromosome number
VariO:0133
Variation affecting chromosome number.
VariO:mv
Variation affecting structure of chromosome.
variation_ontology
VariO:0134
variation of chromosome structure
VariO:0134
Variation affecting structure of chromosome.
VariO:mv
Variation at DNA chain.
variation_ontology
VariO:0135
DNA chain variation
VariO:0135
Variation at DNA chain.
VariO:mv
Substitution of a DNA nucleotide.
variation_ontology
VariO:0136
DNA substitution
VariO:0136
Substitution of a DNA nucleotide.
VariO:mv
Variation affecting RNA tertiary structure.
med-mnv
2018-04-26T12:45:52Z
variation_ontology
VariO:0137
effect on RNA tertiary structure
VariO:0137
Variation affecting RNA tertiary structure.
VariO:mv
A genetic character, organism or individual with a difference to reference state.
Mauno Vihinen
2012-11-11T19:43:00Z
variation_ontology
VariO:0138
variant
VariO:0138
A genetic character, organism or individual with a difference to reference state.
VariO:mv
Any process generating variation.
Mauno Vihinen
2012-11-11T19:43:39Z
variation_ontology
VariO:0139
mutation
VariO:0139
Any process generating variation.
VariO:mv
The observed feature is not changed in relation to the wild type form.
Mauno Vihinen
2012-11-11T19:46:40Z
variation_ontology
VariO:0140
not changed
VariO:0140
The observed feature is not changed in relation to the wild type form.
VariO:mv
Removal of one or more continuous nucleotides from DNA sequence.
nucleotide deletion
variation_ontology
VariO:0141
DNA deletion
VariO:0141
Removal of one or more continuous nucleotides from DNA sequence.
VariO:mv
Addition of one or more nucleotides between two adjacent nucleotides in the DNA sequence.
nucleotide insertion
variation_ontology
VariO:0142
DNA insertion
VariO:0142
Addition of one or more nucleotides between two adjacent nucleotides in the DNA sequence.
VariO:mv
A complex DNA variation consisting of both nucleotide insertion(s) and deletion(s).
variation_ontology
VariO:0143
DNA indel
VariO:0143
A complex DNA variation consisting of both nucleotide insertion(s) and deletion(s).
VariO:mv
A continuous stretch of DNA sequence moved to a new position within a chromosome.
MI:0593
SO:0000199
variation_ontology
VariO:0144
DNA translocation
VariO:0144
A continuous stretch of DNA sequence moved to a new position within a chromosome.
VariO:mv
A continuous stretch of DNA sequence inserted to the same position in reverse orientation.
SO:1000036
variation_ontology
VariO:0145
DNA inversion
VariO:0145
A continuous stretch of DNA sequence inserted to the same position in reverse orientation.
VariO:mv
DNA variation that does not have genetic origin.
variation_ontology
VariO:0146
DNA variation of non-genetic origin
VariO:0146
DNA variation that does not have genetic origin.
VariO:mv
Heritable DNA variation of non-genetic origin.
variation_ontology
VariO:0147
epigenetic DNA variation
VariO:0147
Heritable DNA variation of non-genetic origin.
VariO:mv
Variation having effect on DNA function and usage.
variation_ontology
VariO:0148
variation affecting DNA function
VariO:0148
Variation having effect on DNA function and usage.
VariO:mv
Variation affecting transcription, synthesis of either RNA on a template of DNA or DNA on a template of RNA.
variation_ontology
VariO:0149
effect on transcription
VariO:0149
Variation affecting transcription, synthesis of either RNA on a template of DNA or DNA on a template of RNA.
VariO:mv
Variation affecting information transfer of DNA.
variation_ontology
VariO:0150
effect on DNA information transfer
VariO:0150
Variation affecting information transfer of DNA.
VariO:mv
Variation affecting the process of restoring DNA after damage.
GO:0006281
Wikipedia:DNA_repair
variation_ontology
VariO:0151
effect on DNA repair
VariO:0151
Variation affecting the process of restoring DNA after damage.
VariO:mv
Variation affecting regulatory function of DNA.
variation_ontology
VariO:0152
effect on regulatory function of DNA
VariO:0152
Variation affecting regulatory function of DNA.
VariO:mv
Variation affecting chromatin.
med-mnv
2018-03-05T16:05:29Z
variation_ontology
VariO:0153
chromatin variation
VariO:0153
Variation affecting chromatin.
VariO:mv
Variation originating from semi conservative DNA strand synthesis. The template for replication is either DNA or RNA molecule.
variation_ontology
VariO:0154
effect on DNA replication
VariO:0154
Variation originating from semi conservative DNA strand synthesis. The template for replication is either DNA or RNA molecule.
VariO:mv
Variation affecting structure of DNA.
variation_ontology
VariO:0155
variation affecting DNA structure
VariO:0155
Variation affecting structure of DNA.
VariO:mv
Hereditary variation of DNA not affecting primary sequence.
variation_ontology
VariO:0156
epigenetic DNA modification
VariO:0156
Hereditary variation of DNA not affecting primary sequence.
VariO:mv
Inheritable cytosine or adenosine pyrimidine ring methylation regulating gene expression.
variation_ontology
VariO:0157
epigenetic DNA methylation
VariO:0157
Inheritable cytosine or adenosine pyrimidine ring methylation regulating gene expression.
VariO:mv
Positioning of nucleosomes to DNA strand.
chromatin modeling
chromatin remodelling
variation_ontology
VariO:0158
nucleosome positioning
VariO:0158
Positioning of nucleosomes to DNA strand.
VariO:mv
chromatin modeling
GO:0006338
chromatin remodelling
GO:0006338
Affected level of DNA.
variation_ontology
VariO:0159
affected DNA level
VariO:0159
Affected level of DNA.
VariO:mv
Variation effect on DNA level.
variation_ontology
VariO:0160
DNA chain affected
VariO:0160
Variation effect on DNA level.
VariO:mv
Variation located in intron.
SO:0001627
variation_ontology
VariO:0161
variation in intron
VariO:0161
Variation located in intron.
VariO:mv
Variation located in exon.
variation_ontology
VariO:0162
variation in exon
VariO:0162
Variation located in exon.
VariO:mv
Variation located in intergenic DNA.
SO:0001628
variation_ontology
VariO:0163
variation at intergenic DNA
VariO:0163
Variation located in intergenic DNA.
VariO:mv
Variation effect on chromosome level.
variation_ontology
VariO:0164
chromosome affected
VariO:0164
Variation effect on chromosome level.
VariO:mv
Variation effect on genome level.
variation_ontology
VariO:0165
genome affected
VariO:0165
Variation effect on genome level.
VariO:mv
Somatic recombination combining gene segments in antibody, immunoglobulin B and T cell receptor and MCH coding genes.
med-mnv
2015-09-22T19:10:52Z
variation_ontology
VariO:0166
immunological receptor gene rearrangement
VariO:0166
Somatic recombination combining gene segments in antibody, immunoglobulin B and T cell receptor and MCH coding genes.
VariO:mv
Variation affecting DNA structural form.
med-mnv
2017-01-16T12:52:26Z
variation_ontology
VariO:0167
effect on DNA form
VariO:0167
Variation affecting DNA structural form.
VariO:mv
Immunoglobulin diversification mechanism by producing variations to antigen variable regions.
med-mnv
2015-09-22T19:12:51Z
variation_ontology
VariO:0168
somatic hypermutation
VariO:0168
Immunoglobulin diversification mechanism by producing variations to antigen variable regions.
VariO:mv
Switching of immunoglobulin M to other isotype by changing a portion of a region coding for heavy chain.
med-mnv
2015-09-22T19:12:51Z
variation_ontology
VariO:0169
class switch recombination
VariO:0169
Switching of immunoglobulin M to other isotype by changing a portion of a region coding for heavy chain.
VariO:mv
Secondary immunological receptor diversification by replacing a DNA stretch by a homologous sequence.
med-mnv
2015-09-22T19:12:51Z
variation_ontology
VariO:0170
immunological receptor gene conversion
VariO:0170
Secondary immunological receptor diversification by replacing a DNA stretch by a homologous sequence.
VariO:mv
Variation affecting DNA tertiary structure.
variation_ontology
VariO:0171
effect on DNA tertiary structure
VariO:0171
Variation affecting DNA tertiary structure.
VariO:mv
Variation generated on purpose by e.g. chemical or physical treatment or artificial modification of DNA.
Mauno Vihinen
2012-11-16T08:44:55Z
variation_ontology
VariO:0172
artificial DNA variation
VariO:0172
Variation generated on purpose by e.g. chemical or physical treatment or artificial modification of DNA.
VariO:mv
Variation affecting G-quadruplex of four stranded nucleic acid structure. The structure can be intramolecular, bimolecular or tetramolecular.
variation_ontology
VariO:0173
effect on nucleic acid G-quadruplex
VariO:0173
Variation affecting G-quadruplex of four stranded nucleic acid structure. The structure can be intramolecular, bimolecular or tetramolecular.
VariO:mv
Variation affecting cytosine rich DNA domain where strands associate both inter- and intramolecularly.
variation_ontology
VariO:0174
effect on i motif
VariO:0174
Variation affecting cytosine rich DNA domain where strands associate both inter- and intramolecularly.
VariO:mv
Variation affecting DNA helix formed of three strands.
variation_ontology
VariO:0175
effect on DNA triple helix
VariO:0175
Variation affecting DNA helix formed of three strands.
VariO:mv
Variation affecting chromosome.
SO:0000240
variation_ontology
VariO:0176
chromosome variation
VariO:0176
Variation affecting chromosome.
VariO:mv
Variation affecting length of telomere sequence.
variation_ontology
VariO:0177
telomere length change
VariO:0177
Variation affecting length of telomere sequence.
VariO:mv
Variation shortening length of telomere sequence.
variation_ontology
VariO:0178
telomere shortening
VariO:0178
Variation shortening length of telomere sequence.
VariO:mv
Variation extending length of telomere sequence.
variation_ontology
VariO:0179
telomere extension
VariO:0179
Variation extending length of telomere sequence.
VariO:mv
Variation affecting structure of chromosome.
SO:1000183
variation_ontology
VariO:0180
chromosome structure variation
VariO:0180
Variation affecting structure of chromosome.
VariO:mv
Chromosome lacking one arm with duplication of the other arm.
variation_ontology
VariO:0181
isochromosome
VariO:0181
Chromosome lacking one arm with duplication of the other arm.
VariO:mv
Circular chromosome with ends joined.
SO:1000045
variation_ontology
VariO:0182
ring chromosome
VariO:0182
Circular chromosome with ends joined.
VariO:mv
Increase in the frequency of a chromosomal region.
variation_ontology
VariO:0183
chromosomal amplification
VariO:0183
Increase in the frequency of a chromosomal region.
VariO:mv
Copies of a chromosomal region of length greater than one scattered to genome sequence.
SO:0000658
variation_ontology
VariO:0184
interspersed repeat
VariO:0184
Copies of a chromosomal region of length greater than one scattered to genome sequence.
VariO:mv
Adjacent copies of a chromosomal region of length greater than 1.
SO:0000705
variation_ontology
VariO:0185
tandem repeat
VariO:0185
Adjacent copies of a chromosomal region of length greater than 1.
VariO:mv
Tandem repetitive sequence consisting of units in length from seven to few tens of base pairs.
variation_ontology
VariO:0186
minisatellite
VariO:0186
Tandem repetitive sequence consisting of units in length from seven to few tens of base pairs.
VariO:mv
Increase or decrease of the number of copies of a chromosomal region. Sizes of copy number variations range from about 1 kilobase to several megabases.
SO:0001019
variation_ontology
VariO:0187
copy number variation
VariO:0187
Increase or decrease of the number of copies of a chromosomal region. Sizes of copy number variations range from about 1 kilobase to several megabases.
VariO:mv
Tandem repetitive sequence consisting of units of two to six base pair.
variation_ontology
VariO:0188
microsatellite
VariO:0188
Tandem repetitive sequence consisting of units of two to six base pair.
VariO:mv
Tandem repetitive sequence consisting of three nucleotide units.
variation_ontology
VariO:0189
trinucleotide expansion
VariO:0189
Tandem repetitive sequence consisting of three nucleotide units.
VariO:mv
Tandem repetitive sequence consisting of one nucleotide type.
variation_ontology
VariO:0190
mononucleotide expansion
VariO:0190
Tandem repetitive sequence consisting of one nucleotide type.
VariO:mv
Tandem repetitive sequence consisting of four nucleotide units.
variation_ontology
VariO:0191
tetranucleotide expansion
VariO:0191
Tandem repetitive sequence consisting of four nucleotide units.
VariO:mv
Mobile genetic element incorporated into chromosome.
variation_ontology
VariO:0192
DNA mobile genetic element insertion
VariO:0192
Mobile genetic element incorporated into chromosome.
VariO:mv
Deletion of chromosomal region.
variation_ontology
VariO:0193
chromosomal deletion
VariO:0193
Deletion of chromosomal region.
VariO:mv
Deletion of chromosomal region not including terminus.
variation_ontology
VariO:0194
interstitial deletion
VariO:0194
Deletion of chromosomal region not including terminus.
VariO:mv
Deletion of chromosomal region from the end of chromosome arm.
variation_ontology
VariO:0195
terminal deletion
VariO:0195
Deletion of chromosomal region from the end of chromosome arm.
VariO:mv
Chromosome structure variation with four or more breakpoints.
SO:1000146
variation_ontology
VariO:0196
complex chromosomal variation
VariO:0196
Chromosome structure variation with four or more breakpoints.
SO:ke
VariO:mv
Translocation of chromosomal region.
SO:0000199
variation_ontology
VariO:0197
chromosomal translocation
VariO:0197
Translocation of chromosomal region.
VariO:mv
Translocation of chromosomal region within a chromosome.
variation_ontology
VariO:0198
intrachromosomal translocation
VariO:0198
Translocation of chromosomal region within a chromosome.
VariO:mv
Intrachromosomal variation where a chromosomal region is inserted in reverse direction.
variation_ontology
VariO:0199
chromosomal inversion
VariO:0199
Intrachromosomal variation where a chromosomal region is inserted in reverse direction.
VariO:mv
Chromosomal inversion within a chromosome arm.
SO:1000047
variation_ontology
VariO:0200
paracentric inversion
VariO:0200
Chromosomal inversion within a chromosome arm.
VariO:mv
Chromosomal inversion including centromere.
SO:1000046
variation_ontology
VariO:0201
pericentric inversion
VariO:0201
Chromosomal inversion including centromere.
VariO:mv
Translocation of chromosomal region to another chromosome.
variation_ontology
VariO:0202
interchromosomal translocation
VariO:0202
Translocation of chromosomal region to another chromosome.
VariO:mv
Switching of chromosomal regions between nonhomologous chromosomes.
SO:1000048
variation_ontology
VariO:0203
reciprocal chromosomal translocation
VariO:0203
Switching of chromosomal regions between nonhomologous chromosomes.
VariO:mv
Fusion of long arms of two acrocentric chromosomes having very short p arms.
SO:1000043
variation_ontology
VariO:0204
Robertsonian translocation
VariO:0204
Fusion of long arms of two acrocentric chromosomes having very short p arms.
VariO:mv
Tandem repetitive sequence consisting of two nucleotide units.
med-mnv
2015-09-17T10:53:06Z
variation_ontology
VariO:0205
dinucleotide expansion
VariO:0205
Tandem repetitive sequence consisting of two nucleotide units.
VariO:mv
Variation affecting the number of chromosomes.
aneuploidy
variation_ontology
VariO:0206
chromosome number variation
VariO:0206
Variation affecting the number of chromosomes.
VariO:mv
Three copies of a chromosome in a cell or organism.
variation_ontology
VariO:0207
trisomy
VariO:0207
Three copies of a chromosome in a cell or organism.
VariO:mv
Two copies of a chromosome in a cell or organism .
variation_ontology
VariO:0208
disomy
VariO:0208
Two copies of a chromosome in a cell or organism .
VariO:mv
Both copies of a chromosome or a part of it in diploid cell or organism are from one parent.
variation_ontology
VariO:0209
uniparental disomy
VariO:0209
Both copies of a chromosome or a part of it in diploid cell or organism are from one parent.
VariO:mv
Uniparental disomy with duplication of a single chromosome from one parent.
variation_ontology
VariO:0210
isodisomy
VariO:0210
Uniparental disomy with duplication of a single chromosome from one parent.
VariO:mv
Pair of non-identical chromosomes inherited from one parent.
variation_ontology
VariO:0211
heterodisomy
VariO:0211
Pair of non-identical chromosomes inherited from one parent.
VariO:mv
No copies of a chromosome in a cell or organism.
variation_ontology
VariO:0212
nullisomy
VariO:0212
No copies of a chromosome in a cell or organism.
VariO:mv
Four copies of a chromosome in a cell or organism.
variation_ontology
VariO:0213
tetrasomy
VariO:0213
Four copies of a chromosome in a cell or organism.
VariO:mv
One copy of a chromosome in a cell or organism.
variation_ontology
VariO:0214
monosomy
VariO:0214
One copy of a chromosome in a cell or organism.
VariO:mv
Variation affecting number of entire chromosome sets.
euploidy
variation_ontology
VariO:0215
chromosome set number variation
VariO:0215
Variation affecting number of entire chromosome sets.
VariO:mv
Variation with two sets of chromosomes.
variation_ontology
VariO:0216
diploidy
VariO:0216
Variation with two sets of chromosomes.
VariO:mv
Variation with four sets of chromosomes.
Mauno
2011-03-04T12:19:35Z
variation_ontology
VariO:0217
tetraploidy
VariO:0217
Variation with four sets of chromosomes.
VariO:mv
Variation with several sets of chromosomes.
variation_ontology
VariO:0218
polyploidy
VariO:0218
Variation with several sets of chromosomes.
VariO:mv
Variation with several sets of chromosomes originating from the same organism.
variation_ontology
VariO:0219
autopolyploidy
VariO:0219
Variation with several sets of chromosomes originating from the same organism.
VariO:mv
Variation with several sets of chromosomes originating from a different organism.
variation_ontology
VariO:0220
allopolyploidy
VariO:0220
Variation with several sets of chromosomes originating from a different organism.
VariO:mv
Variation without chromosomes.
variation_ontology
VariO:0221
nulliploidy
VariO:0221
Variation without chromosomes.
VariO:mv
Variation with three sets of chromosomes.
variation_ontology
VariO:0222
triploidy
VariO:0222
Variation with three sets of chromosomes.
VariO:mv
Variation with five sets of chromosomes.
variation_ontology
VariO:0223
pentaploidy
VariO:0223
Variation with five sets of chromosomes.
VariO:mv
Variation with six sets of chromosomes.
variation_ontology
VariO:0224
hexaploidy
VariO:0224
Variation with six sets of chromosomes.
VariO:mv
Variation with a single set of chromosomes.
haploidy
variation_ontology
VariO:0225
monoploidy
VariO:0225
Variation with a single set of chromosomes.
VariO:mv
Variation affecting structure of chromatin the complex of chromosomal DNA and histone proteins.
variation_ontology
VariO:0226
chromatin structure variation
VariO:0226
Variation affecting structure of chromatin the complex of chromosomal DNA and histone proteins.
VariO:mv
Variation affecting characteristic property of DNA.
variation_ontology
VariO:0227
variation affecting DNA property
VariO:0227
Variation affecting characteristic property of DNA.
VariO:mv
Fusion of two protein chains. Produced from fusion gene of two joined genes.
Mauno Vihinen
2012-12-11T08:59:44Z
variation_ontology
VariO:0228
protein fusion
VariO:0228
Fusion of two protein chains. Produced from fusion gene of two joined genes.
VariO:mv
Implication of a DNA variant to pathogenicity.
variation_ontology
VariO:0229
association of DNA variation to pathogenicity
VariO:0229
Implication of a DNA variant to pathogenicity.
VariO:mv
Variation affecting interaction of DNA with its partner.
variation_ontology
VariO:0230
effect on DNA interaction
VariO:0230
Variation affecting interaction of DNA with its partner.
VariO:mv
Conservation of the variation site in related DNA sequences.
variation_ontology
VariO:0231
conservation of DNA variation site
VariO:0231
Conservation of the variation site in related DNA sequences.
VariO:mv
Attributes define and modulate terms at other levels.
variation_ontology
VariO:0232
variation attribute
VariO:0232
Attributes define and modulate terms at other levels.
VariO:mv
Sequence conservation attribute.
variation_ontology
VariO:0233
conservation
VariO:0233
Sequence conservation attribute.
VariO:mv
Variation at a region of sequence similarity in multiple sequence alignment of related sequences.
variation_ontology
VariO:0234
conserved region
VariO:0234
Variation at a region of sequence similarity in multiple sequence alignment of related sequences.
VariO:mv
Variation at invariant sequence region in multiple sequence alignment of related sequences.
variation_ontology
VariO:0235
invariant region
VariO:0235
Variation at invariant sequence region in multiple sequence alignment of related sequences.
VariO:mv
Mutual or reciprocal action or influence that happens at a given place and time between participating molecules.
variation_ontology
VariO:0236
interaction
VariO:0236
Mutual or reciprocal action or influence that happens at a given place and time between participating molecules.
VariO:mv
src_code:NR
Two genes A and B "genetically interact" when the phenotype generated as the result of variations in both genes (double variant ab) is unexpectedly not just a combination of the phenotypes of the two single variants a and b.
MI:0208
variation_ontology
VariO:0237
genetic interaction
VariO:0237
Two genes A and B "genetically interact" when the phenotype generated as the result of variations in both genes (double variant ab) is unexpectedly not just a combination of the phenotypes of the two single variants a and b.
PMID:16527956
VariO:mv
Two genes A and B present a genetic interaction defined by inequality if the phenotypes of the two single variants a and b, the double variant ab and the wild-type can be measured quantitatively and described relative to each other by an inequality relationship.
MI:0931
genetic inequality
variation_ontology
VariO:0238
genetic interaction defined by inequality
VariO:0238
Two genes A and B present a genetic interaction defined by inequality if the phenotypes of the two single variants a and b, the double variant ab and the wild-type can be measured quantitatively and described relative to each other by an inequality relationship.
PMID:14755292
VariO:mv
genetic inequality
MI:0931
The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g. WT > a > ab > b.
MI:0800
single nonmonotonic
single nonmonotonic genetic interaction (sensu inequality)
variation_ontology
VariO:0239
single nonmonotonic genetic interaction defined by inequality
VariO:0239
The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g. WT > a > ab > b.
PMID:15833125
single nonmonotonic
MI:0800
single nonmonotonic genetic interaction (sensu inequality)
MI:0800
Variation preventing protein translation because of e. g. initiation codon variation or mRNA surveillance mechanism.
Mauno Vihinen
2012-12-11T13:07:02Z
variation_ontology
VariO:0240
missing protein
VariO:0240
Variation preventing protein translation because of e. g. initiation codon variation or mRNA surveillance mechanism.
VariO:mv
A continuous stretch of RNA sequence moved to a new position.
Mauno Vihinen
2012-12-18T16:17:33Z
variation_ontology
VariO:0241
RNA translocation
VariO:0241
A continuous stretch of RNA sequence moved to a new position.
VariO:mv
The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b variant has an effect only in the a background. A has an effect only in the b background, or the b variant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab.
MI:0798
conditional
conditional genetic interaction (sensu inequality)
variation_ontology
VariO:0242
conditional genetic interaction defined by inequality
VariO:0242
The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b variant has an effect only in the a background. A has an effect only in the b background, or the b variant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab.
PMID:15833125
VariO:mv
conditional
MI:0798
conditional genetic interaction (sensu inequality)
MI:0798
Single-variant phenotype effects combine to give a double-variant effect different from the wild type and different from single variant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b.
MI:0799
additive
additive genetic interaction (sensu inequality)
variation_ontology
VariO:0243
additive genetic interaction defined by inequality
VariO:0243
Single-variant phenotype effects combine to give a double-variant effect different from the wild type and different from single variant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b.
PMID:15833125
VariO:mv
additive
MI:0799
additive genetic interaction (sensu inequality)
MI:0799
A continuous stretch of RNA sequence inserted to the same position in reverse orientation.
Mauno Vihinen
2012-12-18T16:17:33Z
variation_ontology
VariO:0244
RNA inversion
VariO:0244
A continuous stretch of RNA sequence inserted to the same position in reverse orientation.
VriO:mv
Variation preventing transcription e. g. because of impaired transcription machinery or variation in the transcription regulation or start site.
Mauno Vihinen
2013-01-04T09:23:09Z
variation_ontology
VariO:0245
missing RNA
VariO:0245
Variation preventing transcription e. g. because of impaired transcription machinery or variation in the transcription regulation or start site.
VariO:mv
Protein variation generated on purpose.
gerard
2013-02-01T11:24:30Z
variation_ontology
VariO:0246
artificial protein variation
VariO:0246
Protein variation generated on purpose.
VariO:mv
RNA variation generated on purpose.
gerard
2013-02-01T11:27:07Z
variation_ontology
VariO:0247
artificial RNA variation
VariO:0247
RNA variation generated on purpose.
VariO:mv
The phenotype of the double variant ab is weaker than expected from the combination of the individual effects of a and b.
MI:0935
positive gent int
variation_ontology
VariO:0248
positive genetic interaction
VariO:0248
The phenotype of the double variant ab is weaker than expected from the combination of the individual effects of a and b.
PMID:14755292
VariO:mv
positive gent int
MI:0935
The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other variant gene. E.g. WT >= ab > a >= b.
MI:0801
double nonmonotonic
double nonmonotonic genetic interaction (sensu inequality)
variation_ontology
VariO:0249
double nonmonotonic genetic interaction defined by inequality
VariO:0249
The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other variant gene. E.g. WT >= ab > a >= b.
PMID:15833125
VariO:mv
double nonmonotonic
MI:0801
double nonmonotonic genetic interaction (sensu inequality)
MI:0801
The genetic interaction between a group of genes, in which the effects of an allele of one member gene of the group hide the effects of alleles of other genes in the group.
MI:0930
epistatis
variation_ontology
VariO:0250
epistatic genetic interaction
VariO:0250
The genetic interaction between a group of genes, in which the effects of an allele of one member gene of the group hide the effects of alleles of other genes in the group.
PMID:11988766
epistatis
MI:0930
The phenotype resulting from genetic perturbation of A and B have different effects (in terms of direction or magnitude) on the wild-type background and the double variant has the same phenotype as either A or B (for example, A < WT < B = AB).
MI:0797
epistatic
epistatic genetic interaction (sensu inequality)
variation_ontology
VariO:0251
epistatic genetic interaction defined by inequality
VariO:0251
The phenotype resulting from genetic perturbation of A and B have different effects (in terms of direction or magnitude) on the wild-type background and the double variant has the same phenotype as either A or B (for example, A < WT < B = AB).
PMID:15833125
VariO:mv
epistatic
MI:0797
epistatic genetic interaction (sensu inequality)
MI:0797
The phenotype resulting from genetic perturbation of A alone, B alone and AB combined have the same effect on the WT background. E. g., WT > a = b = ab.
MI:0795
asynthetic
asynthetic genetic interaction (sensu inequality)
variation_ontology
VariO:0252
asynthetic genetic interaction defined by inequality
VariO:0252
The phenotype resulting from genetic perturbation of A alone, B alone and AB combined have the same effect on the WT background. E. g., WT > a = b = ab.
PMID:15833125
asynthetic
MI:0795
asynthetic genetic interaction (sensu inequality)
MI:0795
The phenotype resulting from genetic perturbation of A has an effect on WT, but that effect is abolished by adding the suppressor b, which itself shows no single-variant effect. E. g., WT = b = ab > a.
MI:0796
suppression
suppressive genetic interaction (sensu inequality)
variation_ontology
VariO:0253
suppressive genetic interaction defined by inequality
VariO:0253
The phenotype resulting from genetic perturbation of A has an effect on WT, but that effect is abolished by adding the suppressor b, which itself shows no single-variant effect. E. g., WT = b = ab > a.
PMID:15833125
VariO:mv
suppression
MI:0796
suppressive genetic interaction (sensu inequality)
MI:0796
The phenotype of the double variant ab is equal to the phenotype expected from the combination of the individual effects of a and b.
MI:0934
neutral gent int
variation_ontology
VariO:0254
neutral genetic interaction
VariO:0254
The phenotype of the double variant ab is equal to the phenotype expected from the combination of the individual effects of a and b.
PMID:14755292
VariO:mv
neutral gent int
MI:0934
Variation that has no effect in the WT and b backgrounds, or b has no effect in the a and WT backgrounds, or both hold true. E. g., WT = a > b = ab.
MI:0932
noninteractive
noninteractive genetic interaction (sensu inequality)
variation_ontology
VariO:0255
noninteractive genetic interaction defined by inequality
VariO:0255
Variation that has no effect in the WT and b backgrounds, or b has no effect in the a and WT backgrounds, or both hold true. E. g., WT = a > b = ab.
PMID:15833125
VariO:mv
noninteractive
MI:0932
noninteractive genetic interaction (sensu inequality)
MI:0932
The phenotype of the double variant ab is stronger than expected from the combination of the individual effects of a and b.
MI:0933
negative gen int
variation_ontology
VariO:0256
negative genetic interaction
VariO:0256
The phenotype of the double variant ab is stronger than expected from the combination of the individual effects of a and b.
PMID:14755292
VariO:mv
negative gen int
MI:0933
The phenotype resulting from genetic perturbation a and the phenotype resulting from genetic perturbation b have no effect on the WT background, but the combined genetic perturbation of A and B has a phenotypic effect. E. g., WT = a = b > ab.
MI:0794
synthetic
synthetic genetic interaction (sensu inequality)
variation_ontology
VariO:0257
synthetic genetic interaction defined by inequality
VariO:0257
The phenotype resulting from genetic perturbation a and the phenotype resulting from genetic perturbation b have no effect on the WT background, but the combined genetic perturbation of A and B has a phenotypic effect. E. g., WT = a = b > ab.
PMID:15833125
synthetic
MI:0794
synthetic genetic interaction (sensu inequality)
MI:0794
Molecular structural level of interaction.
variation_ontology
VariO:0258
structural level of interaction
VariO:0258
Molecular structural level of interaction.
VariO:mv
Interaction between molecules.
variation_ontology
VariO:0259
intermolecular interaction
VariO:0259
Interaction between molecules.
VariO:mv
Interaction within a molecule.
variation_ontology
VariO:0260
intramolecular interaction
VariO:0260
Interaction within a molecule.
VariO:mv
Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
MI:0403
variation_ontology
VariO:0261
colocalization
VariO:0261
Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
PMID:14755292
Entity participating in a physical or functional interaction.
SBO:0000336
variation_ontology
VariO:0262
interactor
VariO:0262
Entity participating in a physical or functional interaction.
SBO:0000336
Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
MI:0328
variation_ontology
VariO:0263
small molecule
VariO:0263
Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
PMID:14755292
Metal atom.
CHEBI:33521
variation_ontology
VariO:0264
metal
VariO:0264
Metal atom.
CHEBI:33521
A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
CHEBI:46787
variation_ontology
VariO:0265
solvent
VariO:0265
A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
CHEBI:46787
An inorganic hydroxy compound that has formula H2O.
CHEBI:15377
variation_ontology
VariO:0266
water
VariO:0266
An inorganic hydroxy compound that has formula H2O.
CHEBI:15377
Set of interacting molecules that can be copurified.
MI:0314
variation_ontology
VariO:0267
complex
VariO:0267
Set of interacting molecules that can be copurified.
PMID:14755292
A macromolecular complex containing both protein and RNA molecules.
MI:0316
ribonucleoprot compl
variation_ontology
VariO:0268
ribonucleoprotein complex
VariO:0268
A macromolecular complex containing both protein and RNA molecules.
PMID:14755292
ribonucleoprot compl
MI:0316
A stable set of interacting proteins that can be copurified and operate as a functional unit.
GO:0043234
MI:0315
protein-protein complex
variation_ontology
VariO:0269
protein complex
VariO:0269
A stable set of interacting proteins that can be copurified and operate as a functional unit.
PMID:14755292
protein-protein complex
GO:0043234
A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
MI:0233
variation_ontology
VariO:0270
protein dna complex
VariO:0270
A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
PMID:14755292
Any type of molecule, including complexes, that may be observed but not identified.
MI:0329
variation_ontology
VariO:0271
unknown participant
VariO:0271
Any type of molecule, including complexes, that may be observed but not identified.
PMID:14755292
Interactor of genetic interaction.
MI:0250
variation_ontology
VariO:0272
gene
VariO:0272
Interactor of genetic interaction.
MI:0000704
Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
MI:0383
variation_ontology
VariO:0273
biopolymer
VariO:0273
Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
PMID:14577292
Linear polymer of nucleotides, linked by 3',5' phosphodiester linkages.
GO:0005561
MI:0318
variation_ontology
VariO:0274
nucleic acid
VariO:0274
Linear polymer of nucleotides, linked by 3',5' phosphodiester linkages.
PMID:14755292
Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues.
MI:0327
oligopeptide
polypeptide
variation_ontology
VariO:0275
peptide
VariO:0275
Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues.
PMID:14755292
oligopeptide
MI:0327
polypeptide
MI:0327
A polysaccharide is a complex polymer of carbohydrate monomers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules.
MI:0904
variation_ontology
VariO:0276
polysaccharide
VariO:0276
A polysaccharide is a complex polymer of carbohydrate monomers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules.
PMID:14755292
A linear polymer of amino acids joined by peptide bonds in a specific sequence.
GO:0003675
MI:0326
variation_ontology
VariO:0277
protein
VariO:0277
A linear polymer of amino acids joined by peptide bonds in a specific sequence.
PMID:14755292
Molecules that are experimentally shown to be associated potentially by sharing just one interactor. Often associated molecules are co-purified by a pull-down or coimmunoprecipitation and share the same bait molecule.
MI:0914
variation_ontology
VariO:0278
association
VariO:0278
Molecules that are experimentally shown to be associated potentially by sharing just one interactor. Often associated molecules are co-purified by a pull-down or coimmunoprecipitation and share the same bait molecule.
PMID:14755292
Interaction physical force.
variation_ontology
VariO:0279
interaction physical force
VariO:0279
Interaction physical force.
VariO:mv
A chemical link between two atoms in which electrons are shared between them.
variation_ontology
VariO:0280
covalent bond
VariO:0280
A chemical link between two atoms in which electrons are shared between them.
http://chemistry.about.com/od/chemistryglossary/a/covalentbonddef.htm
The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain.
SO:0001088
variation_ontology
VariO:0281
disulphide bridge
VariO:0281
The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain.
EBIBS:GAR
UniProt:curation_manual
VariO:mv
Interaction between biochemical entities that results in the formation of a non-covalent bond.
SBO:0000177
variation_ontology
VariO:0282
non covalent bond
VariO:0282
Interaction between biochemical entities that results in the formation of a non-covalent bond.
VariO:mv
Attractive interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom.
FIX:0000503
http://chemistry.about.com/od/chemistryglossary/g/hbond.htm
variation_ontology
H-bond
VariO:0283
hydrogen bond
VariO:0283
Attractive interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom.
VariO:mv
H-bond
FIX:0000503
Network of interactions formed by several hydrogen bonds.
variation_ontology
VariO:0284
hydrogen bond network
VariO:0284
Network of interactions formed by several hydrogen bonds.
VariO:mv
Interaction of nonpolar (un-ionizable) hydrocarbon molecules forced together because of stronger water-water interaction.
variation_ontology
VariO:0285
hydrophobic interaction
VariO:0285
Interaction of nonpolar (un-ionizable) hydrocarbon molecules forced together because of stronger water-water interaction.
http://medical-dictionary.thefreedictionary.com/Hydrophobic+Interaction
Interaction between charged groups.
variation_ontology
VariO:0286
salt bridge
VariO:0286
Interaction between charged groups.
VariO:mv
Weak attractive electrical force between neutral groups or molecules.
FIX:0000506
variation_ontology
VariO:0287
van der Waals interaction
VariO:0287
Weak attractive electrical force between neutral groups or molecules.
VariO:mv
Attraction between two electrically charged groups or molecules.
variation_ontology
VariO:0288
electrostatic interaction
VariO:0288
Attraction between two electrically charged groups or molecules.
VariO:mv
Quantity attribute.
variation_ontology
VariO:0289
quantity change
VariO:0289
Quantity attribute.
VariO:mv
The observed feature is decreased compared to that in the wild type (slower, weaker, lower, smaller, etc.).
APO:0000003
variation_ontology
VariO:0290
decreased
VariO:0290
The observed feature is decreased compared to that in the wild type (slower, weaker, lower, smaller, etc.).
SGD:curators
The observed feature is increased compared to that in the wild type (faster, stronger, higher, larger, etc.).
APO:0000004
variation_ontology
VariO:0291
increased
VariO:0291
The observed feature is increased compared to that in the wild type (faster, stronger, higher, larger, etc.).
SGD:curators
The observed feature is missing compared to that in the wild type.
variation_ontology
VariO:0292
missing
VariO:0292
The observed feature is missing compared to that in the wild type.
VariO:mv
Pathogenicity attribute.
variation_ontology
VariO:0293
pathogenicity association
VariO:0293
Pathogenicity attribute.
VariO:mv
Variation is causative of disease.
variation_ontology
VariO:0294
disease causing
VariO:0294
Variation is causative of disease.
VariO:mv
Variation is not related to clinical phenotype.
variation_ontology
VariO:0295
not related to clinical phenotype
VariO:0295
Variation is not related to clinical phenotype.
VariO:mv
Variation is disease related.
variation_ontology
VariO:0296
disease associated
VariO:0296
Variation is disease related.
VariO:mv
Effects of a variation on RNA level.
variation_ontology
VariO:0297
variation affecting RNA
VariO:0297
Effects of a variation on RNA level.
VariO:mv
Variation affecting characteristic property of RNA.
variation_ontology
VariO:0298
variation affecting RNA property
VariO:0298
Variation affecting characteristic property of RNA.
VariO:mv
Variation affecting degradation of RNA.
variation_ontology
VariO:0299
effect on RNA degradation
VariO:0299
Variation affecting degradation of RNA.
VariO:mv
Variation affecting folding of RNA.
variation_ontology
VariO:0300
effect on RNA folding
VariO:0300
Variation affecting folding of RNA.
VariO:mv
Variation affecting stability of transcript.
SO:0001546
variation_ontology
VariO:0301
effect on RNA stability
VariO:0301
Variation affecting stability of transcript.
VariO:mv
Conservation of the variation site in related RNA sequences.
variation_ontology
VariO:0302
conservation of RNA variation site
VariO:0302
Conservation of the variation site in related RNA sequences.
VariO:mv
An excess of a particular chromosome in a cell or organism.
gerard
2013-02-01T11:30:39Z
variation_ontology
VariO:0303
polysomy
VariO:0303
An excess of a particular chromosome in a cell or organism.
VariO:mv
Implication of an RNA variant to pathogenicity.
variation_ontology
VariO:0304
association of RNA variation to pathogenicity
VariO:0304
Implication of an RNA variant to pathogenicity.
VariO:mv
Variation affecting interaction of RNA with its partner.
variation_ontology
VariO:0305
effect on RNA interaction
VariO:0305
Variation affecting interaction of RNA with its partner.
VariO:mv
Type of RNA variation. Describes origin and classification of a variant.
variation_ontology
VariO:0306
RNA variation type
VariO:0306
Type of RNA variation. Describes origin and classification of a variant.
VariO:mv
RNA variation that has genetic origin.
variation_ontology
VariO:0307
RNA variation of genetic origin
VariO:0307
RNA variation that has genetic origin.
VariO:mv
Nucleotide change in the mRNA triplet codon codes for another amino acid.
variation_ontology
VariO:0308
missense variation
VariO:0308
Nucleotide change in the mRNA triplet codon codes for another amino acid.
VariO:mv
RNA nucleotide change in termination codon.
SO:0001590
variation_ontology
VariO:0309
termination codon change
VariO:0309
RNA nucleotide change in termination codon.
VariO:mv
Nucleotide change in the mRNA codon triplet creates a terminator codon.
variation_ontology
VariO:0310
nonsense variation
VariO:0310
Nucleotide change in the mRNA codon triplet creates a terminator codon.
VariO:mv
A complex RNA variation consisting of both nucleotide insertion(s) and deletion(s).
variation_ontology
VariO:0311
RNA indel
VariO:0311
A complex RNA variation consisting of both nucleotide insertion(s) and deletion(s).
VariO:mv
Substitution of RNA nucleotide.
variation_ontology
VariO:0312
RNA substitution
VariO:0312
Substitution of RNA nucleotide.
VariO:mv
Change of a pyrimidine nucleotide, C or T (or U), into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.
variation_ontology
VariO:0313
transition
VariO:0313
Change of a pyrimidine nucleotide, C or T (or U), into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.
VariO:mv
A substitution of a pyrimidine, C or T (or U), for another pyrimidine.
variation_ontology
VariO:0314
pyrimidine transition
VariO:0314
A substitution of a pyrimidine, C or T (or U), for another pyrimidine.
VariO:mv
A substitution of a purine, A or G, for another purine.
variation_ontology
VariO:0315
purine transition
VariO:0315
A substitution of a purine, A or G, for another purine.
VariO:mv
Change of a pyrimidine nucleotide, C or T (or U), into a purine nucleotide, A or G, or vice versa.
http://en.wikipedia.org/wiki/Transversion
variation_ontology
VariO:0316
transversion
VariO:0316
Change of a pyrimidine nucleotide, C or T (or U), into a purine nucleotide, A or G, or vice versa.
VariO:mv
http://en.wikipedia.org/wiki/Transversion
wiki
RNA nucleotide change in the initiation codon.
SO:0001582
variation_ontology
VariO:0317
initiation codon change
VariO:0317
RNA nucleotide change in the initiation codon.
VariO:mv
RNA variation that does not change the encoded amino acid.
variation_ontology
VariO:0318
silent variation
VariO:0318
RNA variation that does not change the encoded amino acid.
VariO:mv
One or more continuous nucleotides are missing from RNA sequence.
variation_ontology
VariO:0319
RNA deletion
VariO:0319
One or more continuous nucleotides are missing from RNA sequence.
VariO:mv
Deletion of nucleotides in multiples of three so that the mRNA coding sequence frame is retained.
variation_ontology
VariO:0320
in-frame deletion
VariO:0320
Deletion of nucleotides in multiples of three so that the mRNA coding sequence frame is retained.
VariO:mv
Deletion of nucleotide(s) causing alteration of mRNA coding sequence frame.
variation_ontology
VariO:0321
out-of-frame deletion
VariO:0321
Deletion of nucleotide(s) causing alteration of mRNA coding sequence frame.
VariO:mv
Classification of DNA variation.
Mauno Vihinen
2013-10-11T08:46:32Z
variation_ontology
VariO:0322
DNA variation classification
VariO:0322
Classification of DNA variation.
VariO:mv
Origin of protein variation.
Mauno Vihinen
2013-10-11T08:53:23Z
variation_ontology
VariO:0323
protein variation origin
VariO:0323
Origin of protein variation.
VariO:mv
Origin of RNA variation.
2013-10-11T09:04:23Z
variation_ontology
VariO:0324
RNA variation origin
VariO:0324
Origin of RNA variation.
VariO:mv
Classification of protein variation.
Mauno Vihinen
2013-10-11T08:59:04Z
variation_ontology
VariO:0325
protein variation classification
VariO:0325
Classification of protein variation.
VariO:mv
Addition of one or more nucleotides between adjacent nucleotides in RNA sequence.
variation_ontology
VariO:0326
RNA insertion
VariO:0326
Addition of one or more nucleotides between adjacent nucleotides in RNA sequence.
VariO:mv
Insertion of nucleotide(s) causing alteration of mRNA reading frame.
variation_ontology
VariO:0327
out-of-frame insertion
VariO:0327
Insertion of nucleotide(s) causing alteration of mRNA reading frame.
VariO:mv
Classification of RNA variation.
Mauno Vihinen
2013-10-11T09:05:02Z
variation_ontology
VariO:0328
RNA variation classification
VariO:0328
Classification of RNA variation.
VariO:mv
RNA variation due to defective fidelity of transcription.
2014-10-23T00:29:53Z
variation_ontology
VariO:0329
alternative RNA form
VariO:0329
RNA variation due to defective fidelity of transcription.
VariO:mv
Protein variation due to defective fidelity of translation.
Mauno Vihinen
2014-10-23T00:31:56Z
variation_ontology
VariO:0330
mistranslated protein
VariO:0330
Protein variation due to defective fidelity of translation.
VariO:mv
Alternative form of mRNA molecule.
med-mnv
2018-04-26T14:47:12Z
variation_ontology
VariO:0331
alternative form of mRNA
VariO:0331
Alternative form of mRNA molecule.
VariO:mv
Insertion of nucleotides in multiples of three so that the reading frame is retained.
variation_ontology
VariO:0332
in-frame insertion
VariO:0332
Insertion of nucleotides in multiples of three so that the reading frame is retained.
VariO:mv
RNA variation that does not have genetic origin being modified at RNA level.
variation_ontology
VariO:0333
RNA variation of non-genetic origin
VariO:0333
RNA variation that does not have genetic origin being modified at RNA level.
VariO:mv
Change to RNA splicing.
variation_ontology
VariO:0334
RNA splicing change
VariO:0334
Change to RNA splicing.
VariO:mv
RNA molecule destroyed due to appearance of a premature termination codon.
variation_ontology
VariO:0335
decayed RNA
VariO:0335
RNA molecule destroyed due to appearance of a premature termination codon.
VariO:mv
Post transcriptionally modified RNA.
variation_ontology
VariO:0336
modified RNA
VariO:0336
Post transcriptionally modified RNA.
VariO:mv
DNA variation due to biological, chemical, physical or other modification.
Mauno Vihinen
2014-10-23T00:42:47Z
variation_ontology
VariO:0337
modified DNA
VariO:0337
DNA variation due to biological, chemical, physical or other modification.
VariO:mv
Variation affecting structure of RNA.
variation_ontology
VariO:0338
variation affecting RNA structure
VariO:0338
Variation affecting structure of RNA.
VariO:mv
mRNA variation not affecting the sequence of the translated protein.
med-mnv
2015-06-04T13:23:24Z
variation_ontology
VariO:0343
synonymous variation
VariO:0343
mRNA variation not affecting the sequence of the translated protein.
VariO:mv
Affected type of RNA.
variation_ontology
VariO:0349
affected RNA type
VariO:0349
Affected type of RNA.
VariO:mv
Variation affecting RNA not coding for protein.
ncRNA
non-coding RNA
ncRNA
variation_ontology
VariO:0350
non-protein coding RNA
VariO:0350
Variation affecting RNA not coding for protein.
VariO:mv
RNA coding for protein.
variation_ontology
VariO:0351
protein coding RNA
VariO:0351
RNA coding for protein.
VariO:mv
Variation affecting region coding for protein in protein coding RNA.
variation_ontology
VariO:0352
coding region of mRNA
VariO:0352
Variation affecting region coding for protein in protein coding RNA.
VariO:mv
Variation affecting region not coding for protein in protein coding mRNA.
variation_ontology
VariO:0353
non-coding region of mRNA
VariO:0353
Variation affecting region not coding for protein in protein coding mRNA.
VariO:mv
Variation affecting post transcriptional RNA modification.
variation_ontology
VariO:0354
effect on post transcriptional RNA modification
VariO:0354
Variation affecting post transcriptional RNA modification.
VariO:mv
Polyadenylation of mRNA molecule at alternative site.
variation_ontology
VariO:0356
alternatively polyadenylated mRNA
VariO:0356
Polyadenylation of mRNA molecule at alternative site.
VariO:mv
Post transcriptional modification of RNA nucleoside sugar.
variation_ontology
VariO:0361
RNA sugar variation
VariO:0361
Post transcriptional modification of RNA nucleoside sugar.
VariO:mv
Effect to process where introns in mRNA are cut away from exons.
SO:0001568
variation_ontology
VariO:0362
effect on RNA splicing
VariO:0362
Effect to process where introns in mRNA are cut away from exons.
VariO:mv
Variation affecting cellular localization of RNA.
med-mnv
2018-05-07T11:20:14Z
variation_ontology
VariO:0363
effect on RNA localization
VariO:0363
Variation affecting cellular localization of RNA.
VariO:mv
Variation affecting aggregation tendency of RNA.
med-mnv
2018-05-07T11:20:14Z
variation_ontology
VariO:0364
effect on RNA aggregation
VariO:0364
Variation affecting aggregation tendency of RNA.
VariO:mv
Intronic splicing within an RNA molecule.
variation_ontology
VariO:0365
effect on cis splicing
VariO:0365
Intronic splicing within an RNA molecule.
VariO:mv
Variation affecting splicing at recursive splice site which subdivides a large intron.
variation_ontology
VariO:0366
variation at recursive splice site
VariO:0366
Variation affecting splicing at recursive splice site which subdivides a large intron.
VariO:mv
Variation affecting intronic region bordering exon or retained RNA region, at the five prime end of the intron.
variation_ontology
VariO:0367
variation at five prime splice site
VariO:0367
Variation affecting intronic region bordering exon or retained RNA region, at the five prime end of the intron.
VariO:mv
Variation affecting canonical prime splice site at five prime end.
variation_ontology
VariO:0368
variation at canonical five prime splice site
VariO:0368
Variation affecting canonical prime splice site at five prime end.
VariO:mv
Variation affecting non canonical splice site at five prime end.
variation_ontology
VariO:0369
variation at non canonical five prime splice site
VariO:0369
Variation affecting non canonical splice site at five prime end.
VariO:mv
Variation affecting intronic region bordering the exon or retained RNA region, at the 3' edge of the intron.
variation_ontology
VariO:0370
variation at three prime splice site
VariO:0370
Variation affecting intronic region bordering the exon or retained RNA region, at the 3' edge of the intron.
VariO:mv
Variation affecting non canonical splice site at three prime end.
variation_ontology
VariO:0371
variation at non canonical three prime splice site
VariO:0371
Variation affecting non canonical splice site at three prime end.
VariO:mv
Variation affecting canonical splice site at three prime end.
variation_ontology
VariO:0372
variation at canonical three prime splice site
VariO:0372
Variation affecting canonical splice site at three prime end.
VariO:mv
Activation of new splice site.
SO:0001569
variation_ontology
VariO:0373
cryptic splice site activation
VariO:0373
Activation of new splice site.
VariO:mv
Activation of new splice donor site.
SO:0001571
variation_ontology
VariO:0374
cryptic splice donor activation
VariO:0374
Activation of new splice donor site.
VariO:mv
Activation of new splice acceptor site.
SO:0001570
variation_ontology
VariO:0375
cryptic splice acceptor activation
VariO:0375
Activation of new splice acceptor site.
VariO:mv
Variation affecting splicing and ligation different RNA molecules.
variation_ontology
VariO:0376
effect on trans splicing
VariO:0376
Variation affecting splicing and ligation different RNA molecules.
VariO:mv
Insertion of retrotransposon into chromosome. Retrotransposon is transcribed from DNA to RNA, and then reverse transcribed to DNA.
med-mnv
2015-08-26T12:50:29Z
variation_ontology
VariO:0377
retrotransposon insertion
VariO:0377
Insertion of retrotransposon into chromosome. Retrotransposon is transcribed from DNA to RNA, and then reverse transcribed to DNA.
VariO:mv
Insertion of a DNA transposable element into chromosome.
med-mnv
2015-08-26T12:50:29Z
variation_ontology
VariO:0378
DNA transposon
VariO:0378
Insertion of a DNA transposable element into chromosome.
VariO:mv
Long interspersed nuclear element generated by retrotransposition.
med-mnv
2015-08-26T12:51:03Z
variation_ontology
VariO:0379
LINE
VariO:0379
Long interspersed nuclear element generated by retrotransposition.
VariO:mv
Short interspersed nuclear element generated by retrotransposition. Length below 500 bp.
med-mnv
2015-08-26T12:51:03Z
variation_ontology
VariO:0380
SINE
VariO:0380
Short interspersed nuclear element generated by retrotransposition. Length below 500 bp.
VariO:mv
Variation affecting RNA double helix.
med-mnv
2018-05-07T11:22:31Z
variation_ontology
VariO:0381
effect on RNA double helix
VariO:0381
Variation affecting RNA double helix.
VariO:mv
Variation affecting RNA secondary structure.
variation_ontology
VariO:0382
effect on RNA secondary structure
VariO:0382
Variation affecting RNA secondary structure.
VariO:mv
Variation affecting closed RNA structure in which at least two double stranded regions meet.
variation_ontology
VariO:0383
effect on RNA multiloop
VariO:0383
Variation affecting closed RNA structure in which at least two double stranded regions meet.
VariO:mv
Variation affecting RNA structure in which nucleotides in one strand do not form base pairs.
variation_ontology
VariO:0384
effect on RNA bulge
VariO:0384
Variation affecting RNA structure in which nucleotides in one strand do not form base pairs.
VariO:mv
Variation affecting RNA structure in which both the strands do not form base pairs.
variation_ontology
VariO:0385
effect on RNA interior loop
VariO:0385
Variation affecting RNA structure in which both the strands do not form base pairs.
VariO:mv
Variation effecting hydrogen bonding in contiguous nested base pairs in RNA.
variation_ontology
VariO:0386
effect on RNA stem
VariO:0386
Variation effecting hydrogen bonding in contiguous nested base pairs in RNA.
VariO:mv
Variation affecting loop connecting adjacent regions forming helix in RNA.
variation_ontology
VariO:0387
effect on RNA hairpin loop
VariO:0387
Variation affecting loop connecting adjacent regions forming helix in RNA.
VariO:mv
Retrotransposon that has long terminal repeat sequences. Sizes from about 100 bp to over 5 kb.
med-mnv
2015-08-26T12:51:03Z
variation_ontology
VariO:0388
LTR
VariO:0388
Retrotransposon that has long terminal repeat sequences. Sizes from about 100 bp to over 5 kb.
VariO:mv
Tandem repetitive sequence consisting of five nucleotide units.
med-mnv
2015-09-17T10:55:04Z
variation_ontology
VariO:0389
pentanucleotide expansion
VariO:0389
Tandem repetitive sequence consisting of five nucleotide units.
VariO:mv
Variation affecting DNA double helical structure.
med-mnv
2017-01-16T12:53:57Z
variation_ontology
VariO:0390
effect on DNA double helix
VariO:0390
Variation affecting DNA double helical structure.
VariO:mv
Variation effect on independently replicating small DNA molecule.
med-mnv
2015-09-18T20:15:22Z
variation_ontology
VariO:0391
plasmid affected
VariO:0391
Variation effect on independently replicating small DNA molecule.
VariO:mv
Simple, relatively short transposable element. IS elements contain only transposition related genes.
med-mnv
2015-09-18T20:28:19Z
variation_ontology
VariO:0392
insertion sequence
VariO:0392
Simple, relatively short transposable element. IS elements contain only transposition related genes.
VariO:mv
RNA variation of epigenetic origin.
med-mnv
2018-05-07T11:43:50Z
variation_ontology
VariO:0393
epigenetic RNA variation
VariO:0393
RNA variation of epigenetic origin.
VariO:mv
Variation affecting double stranded DNA structure that contains in both strands at corresponding positions a single stranded base pairing forming stem and a connecting loop.
med-mnv
2015-09-18T20:44:08Z
variation_ontology
VariO:0394
effect on DNA cruciform
VariO:0394
Variation affecting double stranded DNA structure that contains in both strands at corresponding positions a single stranded base pairing forming stem and a connecting loop.
VariO:mv
Variation having effect on RNA function and usage.
variation_ontology
VariO:0396
variation affecting RNA function
VariO:0396
Variation having effect on RNA function and usage.
VariO:mv
Variation affecting splicing function of RNA.
variation_ontology
VariO:0397
effect on RNA splicing function
VariO:0397
Variation affecting splicing function of RNA.
VariO:mv
Variation affecting catalytic function of RNA.
variation_ontology
VariO:0398
effect on catalytic RNA activity
VariO:0398
Variation affecting catalytic function of RNA.
VariO:mv
Variation affecting translation of protein.
variation_ontology
VariO:0399
effect on translation
VariO:0399
Variation affecting translation of protein.
VariO:mv
Variation affecting regulatory function of RNA.
variation_ontology
VariO:0400
effect on regulatory function of RNA
VariO:0400
Variation affecting regulatory function of RNA.
VariO:mv
Variation affecting RNA function in amino acid transfer.
variation_ontology
VariO:0401
effect on amino acid transfer of RNA
VariO:0401
Variation affecting RNA function in amino acid transfer.
VariO:mv
Variation affecting information transfer by RNA.
variation_ontology
VariO:0402
effect on RNA information transfer
VariO:0402
Variation affecting information transfer by RNA.
VariO:mv
Transposable element coding for self-splicing ribozyme when transcribed. Splicing is initiated by nucleophilic attack of an exogenous GTP or guanosine.
med-mnv
2015-09-21T10:06:37Z
variation_ontology
VariO:0403
group I intron
VariO:0403
Transposable element coding for self-splicing ribozyme when transcribed. Splicing is initiated by nucleophilic attack of an exogenous GTP or guanosine.
VariO:mv
Transposable element coding for a self-splicing ribozyme when transcribed. Intron excision does not require GTP.
med-mnv
2015-09-21T10:06:37Z
variation_ontology
VariO:0404
group II intron
VariO:0404
Transposable element coding for a self-splicing ribozyme when transcribed. Intron excision does not require GTP.
VariO:mv
Fusion of two chromosome segments both containing a centromere.
med-mnv
2015-09-22T19:15:03Z
variation_ontology
VariO:0405
dicentric translocation
VariO:0405
Fusion of two chromosome segments both containing a centromere.
VariO:mv
Variation generated by chromosome editing.
med-mnv
2015-09-22T19:20:45Z
variation_ontology
VariO:0407
edited DNA
VariO:0407
Variation generated by chromosome editing.
VariO:mv
Fusion transcript of exons from two or more genes.
med-mnv
2015-09-24T13:21:02Z
variation_ontology
VariO:0408
RNA chimera
VariO:0408
Fusion transcript of exons from two or more genes.
VariO:mv
Transcript with -1 or +1 frameshift due to slipping back or skipping a nucleotide on a ribosome.
med-mnv
2015-09-24T13:21:02Z
variation_ontology
VariO:0409
frameshifted RNA
VariO:0409
Transcript with -1 or +1 frameshift due to slipping back or skipping a nucleotide on a ribosome.
VariO:mv
Variation affecting single stranded DNA structure.
med-mnv
2018-11-08T10:04:23Z
variation_ontology
VariO:0410
effect on single stranded DNA structure
VariO:0410
Variation affecting single stranded DNA structure.
VariO:mv
mRNA molecule matured by splicing at an alternative site.
med-mnv
2015-10-13T19:36:23Z
variation_ontology
VariO:0411
alternatively spliced RNA
VariO:0411
mRNA molecule matured by splicing at an alternative site.
VariO:mv
Variation affecting catalytic function of DNA.
med-mnv
2016-11-29T11:11:11Z
variation_ontology
VariO:0412
effect on catalytic DNA activity
VariO:0412
Variation affecting catalytic function of DNA.
VariO:mv
Variation affecting A form of right-handed DNA.
med-mnv
2017-01-16T12:55:40Z
variation_ontology
VariO:0413
effect on A DNA
VariO:0413
Variation affecting A form of right-handed DNA.
VariO:mv
Variation affecting B form of right-handed DNA.
med-mnv
2017-01-16T12:55:40Z
variation_ontology
VariO:0414
effect on B DNA
VariO:0414
Variation affecting B form of right-handed DNA.
VariO:mv
Variation affecting C form of right-handed DNA.
med-mnv
2017-01-16T12:55:40Z
variation_ontology
VariO:0415
effect on C DNA
VariO:0415
Variation affecting C form of right-handed DNA.
VariO:mv
Variation affecting L form of right-handed DNA.
med-mnv
2017-01-16T12:55:40Z
variation_ontology
VariO:0416
effect on L DNA
VariO:0416
Variation affecting L form of right-handed DNA.
VariO:mv
Variation affecting S form of right-handed DNA.
med-mnv
2017-01-16T12:55:40Z
variation_ontology
VariO:0417
effect on S DNA
VariO:0417
Variation affecting S form of right-handed DNA.
VariO:mv
Variation affecting D form of right-handed DNA.
med-mnv
2017-01-16T13:10:01Z
variation_ontology
VariO:0418
effect on D DNA
VariO:0418
Variation affecting D form of right-handed DNA.
VariO:mv
Variation affecting H form of intramolecular triple helical DNA.
med-mnv
2017-01-16T13:14:56Z
variation_ontology
VariO:0419
effect on H DNA
VariO:0419
Variation affecting H form of intramolecular triple helical DNA.
VariO:mv
Variation affecting four-stranded DNA.
med-mnv
2017-01-16T13:17:51Z
variation_ontology
VariO:0420
effect on four-stranded DNA
VariO:0420
Variation affecting four-stranded DNA.
VariO:mv
Variation affecting Z form of left-handed DNA.
med-mnv
2017-01-16T13:20:36Z
variation_ontology
VariO:0421
effect on Z DNA
VariO:0421
Variation affecting Z form of left-handed DNA.
VariO:mv
Variation affecting triple helical DNA structure where the third strand is provided by one of the strands forming the duplex.
med-mnv
2017-01-16T13:22:35Z
variation_ontology
VariO:0422
effect on intramolecular DNA triple helix
VariO:0422
Variation affecting triple helical DNA structure where the third strand is provided by one of the strands forming the duplex.
VariO:mv
Variation affecting triple helical DNA structure where the third strand is from a second DNA molecule.
med-mnv
2017-01-16T13:24:18Z
variation_ontology
VariO:0423
effect on intermolecular DNA triple helix
VariO:0423
Variation affecting triple helical DNA structure where the third strand is from a second DNA molecule.
VariO:mv
Variation affecting DNA-RNA hybrid.
med-mnv
2017-01-16T13:29:46Z
variation_ontology
VariO:0424
effect on DNA-RNA hybrid
VariO:0424
Variation affecting DNA-RNA hybrid.
VariO:mv
Variation affecting RNA helix formed of three strands.
med-mnv
2017-01-16T13:48:49Z
variation_ontology
VariO:0425
effect on RNA triple helix
VariO:0425
Variation affecting RNA helix formed of three strands.
VariO:mv
Variation affecting four-stranded RNA.
med-mnv
2017-01-16T13:48:49Z
variation_ontology
VariO:0426
effect on four-stranded RNA
VariO:0426
Variation affecting four-stranded RNA.
VariO:mv
Classification of chromosomal amplification type.
med-mnv
2017-01-17T09:34:30Z
variation_ontology
VariO:0427
type of chromosomal amplification
VariO:0427
Classification of chromosomal amplification type.
VariO:mv
Variation affecting genome.
med-mnv
2017-01-23T09:01:36Z
variation_ontology
VariO:0428
genome variation
VariO:0428
Variation affecting genome.
VariO:mv
Chromosome structure variation due to several breakpoints.
med-mnv
2017-01-23T09:03:57Z
variation_ontology
VariO:0429
complex genomic variation
VariO:0429
Chromosome structure variation due to several breakpoints.
VariO:mv
Repetitive sequence consisting of one more nucleotide units.
med-mnv
2017-01-23T09:09:22Z
variation_ontology
VariO:0430
nucleotide expansion
VariO:0430
Repetitive sequence consisting of one more nucleotide units.
VariO:mv
Effect on DNA-RNA R loop structure of short RNA-DNA hybrid and the displaced single stranded DNA.
med-mnv
2017-01-23T09:32:22Z
variation_ontology
VariO:0431
effect on R loop
VariO:0431
Effect on DNA-RNA R loop structure of short RNA-DNA hybrid and the displaced single stranded DNA.
VariO:mv
Effect on DNA-RNA T loop structure formed by single-stranded 3' strand looping back to anneal with double-stranded repeats. Appears in telomere end-replication.
med-mnv
2017-01-23T09:34:30Z
variation_ontology
VariO:0432
effect on T loop
VariO:0432
Effect on DNA-RNA T loop structure formed by single-stranded 3' strand looping back to anneal with double-stranded repeats. Appears in telomere end-replication.
VariO:mv
Effect on DNA displacement loop where two double-stranded DNA molecules are separated locally by a third strand of DNA or RNA.
med-mnv
2017-01-23T09:45:49Z
variation_ontology
VariO:0433
effect on D loop
VariO:0433
Effect on DNA displacement loop where two double-stranded DNA molecules are separated locally by a third strand of DNA or RNA.
VariO:mv
Replacement of the deoxyribonucleoside monophosphate by ribonucleoside monophosphate in the DNA backbone.
med-mnv
2017-03-23T10:54:09Z
variation_ontology
VariO:0434
DNA sugar variation
VariO:0434
Replacement of the deoxyribonucleoside monophosphate by ribonucleoside monophosphate in the DNA backbone.
VariO:mv
Effect of variation to protein reaction kinetics.
med-mnv
2017-04-28T14:52:51Z
variation_ontology
VariO:0435
effect on protein reaction kinetics
VariO:0435
Effect of variation to protein reaction kinetics.
VariO:mv
Completely processed RNA molecule.
med-mnv
2017-04-28T14:58:30Z
variation_ontology
VariO:0436
mature RNA
VariO:0436
Completely processed RNA molecule.
VariO:mv
RNA variation causing alternative translation initiation.
med-mnv
2017-04-28T16:01:26Z
variation_ontology
VariO:0437
alternatively initiated mRNA
VariO:0437
RNA variation causing alternative translation initiation.
VariO:mv
Epigenetic modification of RNA.
med-mnv
2018-05-07T14:40:53Z
variation_ontology
VariO:0438
epigenetic RNA modification
VariO:0438
Epigenetic modification of RNA.
VariO:mv
Effect of variation on RNA activity.
med-mnv
2017-04-28T16:23:47Z
variation_ontology
VariO:0439
effect on RNA activity
VariO:0439
Effect of variation on RNA activity.
VariO:mv
Effect of variation on RNA reaction kinetics.
med-mnv
2017-04-28T16:26:01Z
variation_ontology
VariO:0440
effect on RNA reaction kinetics
VariO:0440
Effect of variation on RNA reaction kinetics.
VariO:mv
Effect of variation on RNA affinity to binding molecule(s).
med-mnv
2017-04-28T16:26:01Z
variation_ontology
VariO:0441
effect on RNA affinity
VariO:0441
Effect of variation on RNA affinity to binding molecule(s).
VariO:mv
Effect of variation on substrate binding specificity of RNA.
med-mnv
2017-04-28T16:26:01Z
variation_ontology
VariO:0442
effect on RNA specificity
VariO:0442
Effect of variation on substrate binding specificity of RNA.
VariO:mv
Protein variant originating from alternative translation initiation.
med-mnv
2017-05-03T09:09:05Z
variation_ontology
VariO:0443
alternatively initiated protein
VariO:0443
Protein variant originating from alternative translation initiation.
VariO:mv
Variation that has emerged in a germ cell on one of the parents or in the fertilized egg during early embryogenesis.
med-mnv
2018-01-08T11:31:50Z
variation_ontology
VariO:0444
de novo variation
VariO:0444
Variation that has emerged in a germ cell on one of the parents or in the fertilized egg during early embryogenesis.
VariO:mv
Variation that has been inherited from a germline cell.
med-mnv
2017-12-15T09:58:57Z
variation_ontology
germline variation
VariO:0445
germinal variation
VariO:0445
Variation that has been inherited from a germline cell.
VariO:mv
Variation that has its origin in a cell in soma.
med-mnv
2017-12-15T09:58:57Z
variation_ontology
VariO:0446
somatic variation
VariO:0446
Variation that has its origin in a cell in soma.
VariO:mv
Processes that recombine and modify genes coding for immunological recognition molecules (antigens, B- and T-cell receptors, MCH type I and II molecules).
med-mnv
2017-12-15T10:47:27Z
variation_ontology
VariO:0447
immunological recognition molecule diversification
VariO:0447
Processes that recombine and modify genes coding for immunological recognition molecules (antigens, B- and T-cell receptors, MCH type I and II molecules).
VariO:mv
Variation effect on DNA within cellular compartment.
med-mnv
2018-02-01T12:42:12Z
variation_ontology
VariO:0448
organellar DNA affected
VariO:0448
Variation effect on DNA within cellular compartment.
VariO:mv
Circular DNA molecule not part of the chromosomes.
med-mnv
2018-02-01T12:47:35Z
variation_ontology
VariO:0449
extrachromosomal circular DNA
VariO:0449
Circular DNA molecule not part of the chromosomes.
VariO:mv
Variation affecting DNA within mitochondria.
med-mnv
2018-02-01T12:52:27Z
variation_ontology
VariO:0450
mitochondrial DNA affected
VariO:0450
Variation affecting DNA within mitochondria.
VariO:mv
Variation affecting DNA within plastids e.g. chloroplasts.
med-mnv
2018-02-01T12:53:15Z
variation_ontology
VariO:0451
plastid DNA affected
VariO:0451
Variation affecting DNA within plastids e.g. chloroplasts.
VariO:mv
Tandem repetitive sequence consisting of six nucleotide units.
med-mnv
2018-02-01T14:49:25Z
variation_ontology
VariO:0452
heptanucleotide expansion
VariO:0452
Tandem repetitive sequence consisting of six nucleotide units.
VariO:mv
Epigenetic modification of histone.
med-mnv
2018-02-06T09:08:59Z
variation_ontology
VariO:0453
histone modification
VariO:0453
Epigenetic modification of histone.
VariO:mv
Variation affecting topology associating domain (TAD).
med-mnv
2018-03-05T16:55:07Z
variation_ontology
VariO:0454
variation at topology associating domain
VariO:0454
Variation affecting topology associating domain (TAD).
VariO:mv
med-mnv
2018-11-08T10:05:56Z
variation_ontology
VariO:0455
effect on A motif
VariO:0455
Genome composed of RNA molecule.
RNA genome
Genome for a RNA virus.
RNA virus genome
Genome for an infectious particle.
viroid genome
Genome for a subviral agent.
satelletite genome
Unprocessed mRNA.
pre-mRNA
Mature mRNA.
mRNA
Covalently closed single-stranded RNA chain.
circRNA
circular RNA
Single-stranded non-coding RNA compelementary to a mRNA or part of it.
antisense RNA
Single-stranded noncoding RNA overlapping with mRNA but not coding for a protein.
non-coding sense RNA
Non-coding RNA with a function.
functional non-coding RNA
RNA intermediate of a retrotransposon.
class I transposable element
transposon via RNA intermediate
retrotransposon RNA intermediate
RNA involved in protein synthesis.
translation related non-coding RNA
Transfer RNA involved in protein synthesis. Modiefied tRNA contains amino acid and carries it to ribosome.
tRNA
transfer RNA
Non-coding RNA that is a constituent of the large ribosomal subunit.
LSU RNA
large subunit ribosomal RNA
Non-coding RNA that is a constituent of the small ribosomal unit.
SSU RNA
small subunit ribosomal RNA
Intervening region ithat is spliced off during RNA maturation.
intron
Intron with an intrinsic splicing activity.
self-splicing intron
Intron removed by spliceosome.
spliceosomal intron
Inclusion intron sequence to mRNA.
intron retention
targeting RNA
Non-coding RNA component of telomerase.
telomerase RNA
RNA with catalytic activity.
catalytic RNA
RNA with regulatory activity.
regulatory RNA
Short non-coding RNA that binds to complementary region in mRNA and silences and regulates gene expression.
miRNA
microRNA
Short double-stranded non-coding RNA regulating gene expresion by causing degration of mRNA with complementary sequence.
siRNA
small intervening RNA
Non-coding RNA binding to piwi-superfamily Argonaute proteins to silence transposons, repeat-derived transcripts and genetic elements.
piRNA
piwi-interacting RNA
Non-coding RNA component of signal recognition particle.
signal recognition particle RNA
Non-coding RNA component of X-inactivation center.
X-chromosome inactivation center RNA
Non-coding RNA component of editosome complex.
RNA editing related RNA
Non-coding RNA component of DNA editing complex.
DNA editing related RNA
Non-coding RNA component of spliceosome.
spliceosomal RNA
location or origin of non-coding RNA
Non-coding RNA in nucleus.
nuclear non-coding RNA
Non-coding RNA in mitochondrion.
mitochondrial non-coding RNA
Non-coding RNA related to chromatin.
chromatin related non-coding RNA
Non-coding RNA related to centromere.
centromeric non-coding RNA
Classification of non-coding RNA based on the length.
size of non-coding RNA
Non-coding RNA shorter than 200 nucleotides or base pairs.
small non-coding RNA
sRNA
short non-coding RNA
Non-coding RNA constituent of ribosome.
rRNA
ribosomal RNA
Non-coding RNA longer than 200 nucleotides or base pairs.
large non-coding RNA
lncRNA
long non-coding RNA
Non-coding RNA longer than 10 kb.
vlnicRNA
very long non-coding RNA
Transcript region that is part in mature mRNA.
exon
Variation causing alternative mRNA termination.
alternatively terminated mRNA
Variation affecting post transcriptional RNA modification.
effect on RNA modification
Post transcriptionally modified nucleotide in mRNA.
modified mRNA nucleotide
Variation affecting RNA stucture containing at teast two stem loops where part of one stem is intercalated to the other stem.
effect on RNA pseudoknot
RNA produced by degradation of processing of an RNA molecule.
RNA fragment
Variation where an exon is completele cleaved out from a mature transcript.
exon skipping
Transcript from which part of an exon is missing.
loss of exon fragment
Transcript that includes a cryptic exon from the middle of intron.
inclusion of cryptic exon
Transcript that contains and additional stretch from intron.
inclusion of intron fragment
Type of variation affecting splice site.
affected splice site
Variation affecting the type of RNA splicing.
effect on mode of splicing
Variation affecting splicing occurring simultnaeously with transcription.
effect on co-transcriptional splicing
Variation affecting splicing that does not occur in sequential order.
effect on non-sequential splicing
Variation affecting intron splicing that occurs in several splicing events.
effect on recursive splicing
Only one of two exons is incluided into mRNA.
snoRNA
mutually exclusive exon
http://purl.obolibrary.org/obo/vario.owl
OBO-Edit 2.3.1
23:11:2018 15:56
variation_ontology
1.2
med-mnv
A Variation Ontology