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 has quantity 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 biological macromolecule. variation_ontology VariO:0001 variation Alteration in biological macromolecule. VariO:mv Effects of a variation on protein level. variation_ontology VariO:0002 variation affecting protein Effects of a variation on protein level. VariO:mv Effect of variation on protein function. variation_ontology VariO:0003 variation affecting protein function Effect of variation on protein function. VariO:mv Effect of variation on the movement of a protein within or along protein filament. variation_ontology VariO:0004 effect on protein movement Effect of variation on the movement of a protein within or along protein filament. 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 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 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 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 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 or between body parts. variation_ontology VariO:0009 effect on transport function of protein Effect of variation on transport function of protein in facilitating passage of an atom or molecule through membrane or between body parts. VariO:mv Variation affecting abundance of produced RNA molecules. variation_ontology VariO:0010 effect on RNA abundance 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 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 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 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 Removal of one or more continuous amino acids from protein. VariO:mv Shortening of protein sequence from terminus. variation_ontology VariO:0015 protein truncation 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 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 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 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 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 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 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 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 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 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 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 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 Protein conformation change induced by structurally modified protein. VariO:mv Protein molecule chemically modified after translation. variation_ontology VariO:0028 post translational modification 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 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 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 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 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 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 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 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 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 Variation at a covarying sequence position. VariO:mv Variation affecting protein aggregation tendency. variation_ontology VariO:0038 effect on protein aggregation Variation affecting protein aggregation tendency. VariO:mv Type of protein function affecting variation. variation_ontology VariO:0039 protein function change 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 Effect of variation causing new or enhanced protein activity. VariO:mv Variation generates new protein function. variation_ontology VariO:0041 neomorphic protein variation 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 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 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 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 Variation exposing buried region. VariO:mv Variation leading to burying of exposed region. variation_ontology VariO:0046 variation burying exposed region 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 Implication of a protein variant to pathogenicity. VariO:mv Effect of variation on charge in protein. variation_ontology VariO:0048 effect on protein charge Effect of variation on charge in protein. VariO:mv Variation affecting electrostatics of the protein surface. variation_ontology VariO:0049 effect on protein electrostatics Variation affecting electrostatics of the protein surface. VariO:mv Variation changing protein isoelectric point. variation_ontology VariO:0050 effect on protein isoelectric point Variation changing protein isoelectric point. VariO:mv Effect of variation on degradation of protein. variation_ontology VariO:0051 effect on protein degradation Effect of variation on degradation of protein. VariO:mv Variation affecting abundance of produced protein molecules. variation_ontology VariO:0052 effect on protein abundance Variation affecting abundance of produced protein molecules. VariO:mv Effect of variation on activity of protein. variation_ontology VariO:0053 effect on protein activity 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 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 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 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 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 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 Effect of variation on contact energy between interacting molecules. VariO:mv Variation affecting structure of protein. variation_ontology VariO:0060 variation affecting protein structure Variation affecting structure of protein. VariO:mv Hereditary protein structure modification of non-genetic origin. variation_ontology VariO:0061 epigenetic protein modification 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 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 Variation affecting heritable protein complex structure. VariO:mv Variation affecting protein three dimensional structure. variation_ontology VariO:0064 effect on protein 3D structure Variation affecting protein three dimensional structure. VariO:mv Variation affecting dynamics in protein structure. variation_ontology VariO:0065 effect on protein dynamics Variation affecting dynamics in protein structure. VariO:mv Variation affecting protein structural flexibility. variation_ontology VariO:0066 effect on structural flexibility 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 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 Variation affecting protein structural disorder. VariO:mv Variation in affecting protein allosteric site. variation_ontology VariO:0069 effect on allosteric site Variation in affecting protein allosteric site. VariO:mv Variation affecting protein three dimensional structure. variation_ontology VariO:0070 effect on protein tertiary structure Variation affecting protein three dimensional structure. VariO:mv Variation affecting rate of protein folding. variation_ontology VariO:0071 effect on protein folding rate 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 Variation effect on nonchromosomal DNA. VariO:mv Variation affecting protein tertiary structure. variation_ontology VariO:0073 effect to protein fold Variation affecting protein tertiary structure. VariO:mv Variation changing protein conformation. variation_ontology VariO:0074 protein conformational change Variation changing protein conformation. VariO:mv Variation causing large overall protein conformational change. variation_ontology VariO:0075 global protein conformation change Variation causing large overall protein conformational change. VariO:mv Variation causing local and minor conformational change. variation_ontology VariO:0076 local protein conformation change 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Variation affecting irregular, unstructured region of protein. VariO:mv Variation altering membrane spanning protein. variation_ontology VariO:0104 effect on transmembrane polypeptide 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 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 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 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 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 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 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 Variation that generates a novel protein processing site. VariO:mv Variation causing prevention of polypeptide processing. variation_ontology VariO:0112 variation preventing polypeptide processing 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 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 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 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 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 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 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 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 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 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 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 Complex change of protein three dimensional structure. VariO:mv Variation prolonging protein chain at an end. variation_ontology VariO:0124 protein elongation 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 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 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 Origin of DNA variation. VariO:mv Effects of a variation on DNA level. variation_ontology VariO:0128 variation affecting DNA Effects of a variation on DNA level. VariO:mv DNA variation that has genetic origin. variation_ontology VariO:0130 DNA variation of genetic origin DNA variation that has genetic origin. VariO:mv Variation of genomic level. variation_ontology VariO:0131 genomic variation Variation of genomic level. VariO:mv Variation at chromosomal level. variation_ontology VariO:0132 chromosomal variation Variation at chromosomal level. VariO:mv Variation at DNA chain. variation_ontology VariO:0135 DNA chain variation Variation at DNA chain. VariO:mv Substitution of a DNA nucleotide. variation_ontology VariO:0136 DNA substitution 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 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 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 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 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 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 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 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 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 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 DNA variation that does not have genetic origin. VariO:mv Heritable DNA variation of non-genetic origin. variation_ontology VariO:0147 epigenetic DNA variation Heritable DNA variation of non-genetic origin. 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 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 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 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 Variation affecting regulatory function of DNA. 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 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 Variation affecting structure of DNA. VariO:mv Hereditary variation of DNA not affecting primary sequence. variation_ontology VariO:0156 epigenetic DNA modification 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 Inheritable cytosine or adenosine pyrimidine ring methylation regulating gene expression. VariO:mv Variation affecting nucleosome positioning to DNA strand. chromatin modeling chromatin remodelling variation_ontology VariO:0158 variation at nucleosome positioning Variation affecting nucleosome positioning to DNA strand. VariO:mv chromatin modeling GO:0006338 chromatin remodelling GO:0006338 Affected level of DNA. variation_ontology VariO:0159 affected DNA level Affected level of DNA. VariO:mv Variation effect on DNA level. variation_ontology VariO:0160 DNA chain affected Variation effect on DNA level. VariO:mv Variation located in intron. SO:0001627 variation_ontology VariO:0161 variation in intron Variation located in intron. VariO:mv Variation located in exon. variation_ontology VariO:0162 variation in exon Variation located in exon. VariO:mv Variation located in intergenic DNA. SO:0001628 variation_ontology VariO:0163 variation at intergenic DNA Variation located in intergenic DNA. 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 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 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 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 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 Secondary immunological receptor diversification by replacing a DNA stretch by a homologous sequence. 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 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 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 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 Variation affecting DNA helix formed of three strands. VariO:mv Variation affecting chromosome. SO:0000240 variation_ontology VariO:0176 chromosome variation Variation affecting chromosome. VariO:mv Variation affecting length of telomere sequence. variation_ontology VariO:0177 telomere length change Variation affecting length of telomere sequence. VariO:mv Variation shortening length of telomere sequence. variation_ontology VariO:0178 telomere shortening Variation shortening length of telomere sequence. VariO:mv Variation extending length of telomere sequence. variation_ontology VariO:0179 telomere extension Variation extending length of telomere sequence. VariO:mv Variation affecting structure of chromosome. SO:1000183 variation_ontology VariO:0180 chromosome structure variation Variation affecting structure of chromosome. VariO:mv Chromosome lacking one arm with duplication of the other arm. variation_ontology VariO:0181 isochromosome 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 Circular chromosome with ends joined. VariO:mv Increase in the frequency of a chromosomal region. variation_ontology VariO:0183 chromosomal amplification 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 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 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 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 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 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 Tandem repetitive sequence consisting of three nucleotide units. VariO:mv Tandem repetitive sequence consisting of one nucleotide type. variation_ontology VariO:0190 mononucleotide expansion Tandem repetitive sequence consisting of one nucleotide type. VariO:mv Tandem repetitive sequence consisting of four nucleotide units. variation_ontology VariO:0191 tetranucleotide expansion 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 Mobile genetic element incorporated into chromosome. VariO:mv Deletion of chromosomal region. variation_ontology VariO:0193 chromosomal deletion Deletion of chromosomal region. VariO:mv Deletion of chromosomal region not including terminus. variation_ontology VariO:0194 interstitial deletion 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 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 Chromosome structure variation with four or more breakpoints. SO:ke VariO:mv Translocation of chromosomal region. SO:0000199 variation_ontology VariO:0197 chromosomal translocation Translocation of chromosomal region. VariO:mv Translocation of chromosomal region within a chromosome. variation_ontology VariO:0198 intrachromosomal translocation 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 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 Chromosomal inversion within a chromosome arm. VariO:mv Chromosomal inversion including centromere. SO:1000046 variation_ontology VariO:0201 pericentric inversion Chromosomal inversion including centromere. VariO:mv Translocation of chromosomal region to another chromosome. variation_ontology VariO:0202 interchromosomal translocation 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 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 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 Tandem repetitive sequence consisting of two nucleotide units. VariO:mv Variation affecting the number of chromosomes. aneuploidy variation_ontology VariO:0206 chromosome number variation Variation affecting the number of chromosomes. VariO:mv Three copies of a chromosome in a cell or organism. variation_ontology VariO:0207 trisomy 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 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 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 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 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 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 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 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 Variation affecting number of entire chromosome sets. VariO:mv Variation with two sets of chromosomes. variation_ontology VariO:0216 diploidy 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 Variation with four sets of chromosomes. VariO:mv Variation with several sets of chromosomes. variation_ontology VariO:0218 polyploidy Variation with several sets of chromosomes. VariO:mv Variation with several sets of chromosomes originating from the same organism. variation_ontology VariO:0219 autopolyploidy 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 Variation with several sets of chromosomes originating from a different organism. VariO:mv Variation without chromosomes. variation_ontology VariO:0221 nulliploidy Variation without chromosomes. VariO:mv Variation with three sets of chromosomes. variation_ontology VariO:0222 triploidy Variation with three sets of chromosomes. VariO:mv Variation with five sets of chromosomes. variation_ontology VariO:0223 pentaploidy Variation with five sets of chromosomes. VariO:mv Variation with six sets of chromosomes. variation_ontology VariO:0224 hexaploidy Variation with six sets of chromosomes. VariO:mv Variation with a single set of chromosomes. haploidy variation_ontology VariO:0225 monoploidy Variation with a single set of chromosomes. VariO:mv Variation affecting structure of chromatin the complex of chromosomal DNA and proteins. variation_ontology VariO:0226 chromatin structure variation Variation affecting structure of chromatin the complex of chromosomal DNA and proteins. 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 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 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 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 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 Attributes define and modulate terms at other levels. VariO:mv Sequence conservation attribute. variation_ontology VariO:0233 conservation 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 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 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 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 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 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 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 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 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 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 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 A continuous stretch of RNA sequence inserted to the same position in reverse orientation. VriO:mv Protein variation generated on purpose. gerard 2013-02-01T11:24:30Z variation_ontology VariO:0246 artificial protein variation 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 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 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 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 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 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 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 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 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 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 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 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 Molecular structural level of interaction. VariO:mv Interaction between molecules. variation_ontology VariO:0259 intermolecular interaction Interaction between molecules. VariO:mv Interaction within a molecule. variation_ontology VariO:0260 intramolecular interaction 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 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 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 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 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 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 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 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 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 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 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 Any type of molecule, including complexes, that may be observed but not identified. PMID:14755292 A continuous stretch of polynucleotide sequence, consecutive segments, or connected segments joined together to code for a functional gene product or products variation_ontology VariO:0272 gene Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds. MI:0383 variation_ontology VariO:0273 biopolymer 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 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 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 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 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 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 Interaction physical force. VariO:mv A chemical link between two atoms in which electrons are shared between them. variation_ontology VariO:0280 covalent bond 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 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 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 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 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 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 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 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 Attraction between two electrically charged groups or molecules. VariO:mv Quantity attribute. variation_ontology VariO:0289 quantity change 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 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 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 The observed feature is missing compared to that in the wild type. VariO:mv Pathogenicity attribute. variation_ontology VariO:0293 pathogenicity association Pathogenicity attribute. VariO:mv Variation is causative of disease. variation_ontology VariO:0294 disease causing Variation is causative of disease. VariO:mv Variation is not related to clinical phenotype. variation_ontology VariO:0295 not related to clinical phenotype Variation is not related to clinical phenotype. VariO:mv Variation is disease related. variation_ontology VariO:0296 disease associated Variation is disease related. VariO:mv Effects of a variation on RNA level. variation_ontology VariO:0297 variation affecting RNA Effects of a variation on RNA level. VariO:mv Variation affecting characteristic property of RNA. variation_ontology VariO:0298 variation affecting RNA property Variation affecting characteristic property of RNA. VariO:mv Variation affecting degradation of RNA. variation_ontology VariO:0299 effect on RNA degradation Variation affecting degradation of RNA. VariO:mv Variation affecting folding of RNA. variation_ontology VariO:0300 effect on RNA folding Variation affecting folding of RNA. VariO:mv Variation affecting stability of transcript. SO:0001546 variation_ontology VariO:0301 effect on RNA stability 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 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 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 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 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 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 RNA variation that has genetic origin. VariO:mv Substitution in the mRNA coding region that leads to amino acid substitution in the coded protein. variation_ontology VariO:0308 missense variation Substitution in the mRNA coding region that leads to amino acid substitution in the coded protein. VariO:mv RNA nucleotide change in termination codon. SO:0001590 variation_ontology VariO:0309 termination codon change RNA nucleotide change in termination codon. VariO:mv Substitution in the mRNA coding region that creates a terminator codon. variation_ontology VariO:0310 nonsense variation Substitution in the mRNA coding region that 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 A complex RNA variation consisting of both nucleotide insertion(s) and deletion(s). VariO:mv Substitutions of RNA nucleotide. VariO:0312 RNA subsitution 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 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 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 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 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 Substitution in mRNA coding region that does not change the encoded amino acid. synonymous variation variation_ontology VariO:0318 silent variation Substitution in mRNA coding region that does not change the encoded amino acid. VariO:mv One or more continuous nucleotides missing from RNA sequence. VariO:0319 RNA deletion Origin of protein variation. Mauno Vihinen 2013-10-11T08:53:23Z variation_ontology VariO:0323 protein variation origin Origin of protein variation. VariO:mv Origin of RNA variation. 2013-10-11T09:04:23Z variation_ontology VariO:0324 RNA variation origin Origin of RNA variation. VariO:mv Classification of protein variation. Mauno Vihinen 2013-10-11T08:59:04Z variation_ontology VariO:0325 protein variation classification Classification of protein variation. VariO:mv Addition of one or more nucleotides between adjacent nucleotides in RNA sequence. variation_ontology VariO:0326 RNA insertion 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 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 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 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 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 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 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 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 Change to RNA splicing. VariO:mv RNA molecule destroyed due to appearance of a premature termination codon. variation_ontology VariO:0335 decayed RNA RNA molecule destroyed due to appearance of a premature termination codon. VariO:mv Post transcriptionally modified RNA. variation_ontology VariO:0336 modified RNA 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 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 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 mRNA variation not affecting the sequence of the translated protein. VariO:mv Affected type of RNA. variation_ontology VariO:0349 affected RNA type 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 Variation affecting RNA not coding for protein. VariO:mv RNA coding for protein. variation_ontology VariO:0351 protein coding RNA RNA coding for protein. VariO:mv Variation affecting region coding for protein in protein coding RNA. variation_ontology VariO:0352 coding region of mRNA 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 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 Variation affecting post transcriptional RNA modification. VariO:mv Polyadenylation of mRNA molecule at alternative site. variation_ontology VariO:0356 alternatively polyadenylated mRNA Polyadenylation of mRNA molecule at alternative site. VariO:mv Post transcriptional modification of RNA nucleoside sugar. variation_ontology VariO:0361 RNA sugar variation 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 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 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 Variation affecting aggregation tendency of RNA. VariO:mv Intronic splicing within an RNA molecule. variation_ontology VariO:0365 effect on cis splicing 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 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 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 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 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 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 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 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 Activation of new splice site. VariO:mv Activation of new splice donor site. SO:0001571 variation_ontology VariO:0374 cryptic splice donor activation Activation of new splice donor site. VariO:mv Activation of new splice acceptor site. SO:0001570 variation_ontology VariO:0375 cryptic splice acceptor activation Activation of new splice acceptor site. VariO:mv Variation affecting splicing and ligation different RNA molecules. variation_ontology VariO:0376 effect on trans splicing 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 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 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 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 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 Variation affecting RNA double helix. VariO:mv Variation affecting RNA secondary structure. variation_ontology VariO:0382 effect on RNA secondary structure 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Variation affecting splicing function of RNA. VariO:mv Variation affecting catalytic function of RNA. variation_ontology VariO:0398 effect on catalytic RNA activity Variation affecting catalytic function of RNA. VariO:mv Variation affecting translation of protein. variation_ontology VariO:0399 effect on translation Variation affecting translation of protein. VariO:mv Variation affecting regulatory function of RNA. variation_ontology VariO:0400 effect on regulatory function of RNA 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Classification of chromosomal amplification type. VariO:mv Variation affecting genome. med-mnv 2017-01-23T09:01:36Z variation_ontology VariO:0428 genome variation 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 hexanucleotide expansion 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 Epigenetic modification of histone. VariO:mv Variation affecting topology associating domain (TAD) with local high interaction frequency . med-mnv 2018-03-05T16:55:07Z variation_ontology VariO:0454 variation at topologically associating domain Variation affecting topology associating domain (TAD) with local high interaction frequency . VariO:mv med-mnv 2018-11-08T10:05:56Z variation_ontology VariO:0455 effect on A motif 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 Variation affecting large structure formed by numerous macromolecules, especially in membraneless cellular organelle. effect on macromolecular assembly Double-stranded highly specific DNA endonuclease coded by either an intron or intein and facilitates their mobility. VariO:0530 homing endonuclease effect on ion channel activity effect on ion channel gating-pore current effect on ion channel modulation effect on ion channel selectivity effect on ion channel peak current effect on ion channel persistent current effect on ion channel rate of activation (tau activation) effect on ion channel rate of deactivation effect on ion channel rate of fast inactivation (tau activation) effect on ion channel recovery from fast inactivation effect on ion channel resurgent current effect on ion channel slow inactivation effect on ion channel subthreshold current effect on ion channel voltage dependence of activation effect on ion channel voltage dependence of fast inactivation effect on ion channel ramp current effect on ion channel use dependence effect on ion channel voltage dependence of slow inactivation effect on ion channel rate of slow inactivation (tau inactivation) effect on ion channel recovery from slow inactivation effect on ion channel slope of slow inactivation effect on ion chanel shift of voltage dependence of activation (V1/2) effect on ion channel slope factor of activation (k) severity benign mild moderate severe very severe functional effect gain of function loss of function mixed gain and loss of function The collective genomic component of microorganisms in a systems such as an organism. VariO:0574 microbiome Inheritable cytosine hydroxymethylation regulating gene expression VariO:0577 epigenetic DNA hydroxymethylation Inheritable modification of DNA sugar moieity. VariO:0578 epigenetic DNA sugar modification Variation in sex chromosome region that that homologous counterpart in another sex chromosome and where genetic recombination is possible between the different sex chromosomes. VariO:0583 pseudoautosomal region effect on activation effect of fast ion channel fast inactivation effect on ion channel voltage dependence of fast inactivation (V1/2) effect on ion channel slope factor of fast inactivation (k) effect on slope factor or slow inactivation (k) Variation affecting number of copies of a gene present in a genome. variation in gene dosage Sex determination system that is based on the dosage of genome. Males are haploid and produced from unfertilized eggs and diploid females from fertilized eggs haplodiploidy Reproductive system where males develop from fertilized eggs, but pass to offspring only the maternally inherited haplotype. paternal genome elimination Chromosome diminution or deletion in somatic cells. programmed genome rearrangement The entirety genomic material of all strains in a species. pangenome The common genetic material of all strains in a speicies. core genome Diffent numbers of genomes in different cells within an organism. mixoploidy Effect on protein that contains a non-peptide component. effect on protein chemical composition Effect on protein that consists only of amino acids. effect on simple protein Effect on protein that contains a non-peptide component. effect on protein conjugation Effect on a conjugated protein that contains a heme. effect on cytochrome Effect on a conjugated protein that contains covalently bound or tightly attached flavin component. effect on flavoprotein Effect on a conjugated protein that contains covalently bound carbohydrate component. effect on glycoprotein Effect on a conjugated protein that contains heme as the prosthetic group. effect on hemoprotein Effect on a conjugated protein that contains a lipid component. effect on lipoprotein Effect on a conjugated protein that contains a nucleic acid component. effect on nucleoprotein Effect on a conjugated protein that contains a visual pigment. effect on opsin Effect on a conjugated protein that contains a phosphoric acid component. effect on phosphoprotein Effect on a conjugated protein that contains a covalently bound linear tetrapyrrolic prosthetic group as a chromophore. effect on phytochrome Effect on a conjugated protein that contains a covalently bound glycosaminoglycan component. effect on proteoglycan Effect on a conjugated protein that contains a pigmented prosthetic group. effect on chromoprotein effect on protein shape Effect on elongated or fibrous protein. effect on fibrous protein Effect on spherical protein. effect on globular protein Effect on protein that is attached or spans through a membrane. effect on membrane protein Effect on membrane protein that spans through the lipid bilayer of a membrane. effect on integral membrane protein Effect on membrane protein that interacts with the surface of the lipid bilayer of a membrane. effect on peripheral membrane protein Effect on protein that does not have a fixed three-dimensional structure. effect on intrinsically disordered protein Elimination of entire chromosome. chromosome elimination Preferential elimination of a chromosome from one parent. uniparental chromosome elimination Programmed elimination of parts of chromosomes during mitosis. chromatin diminution Variation affecting chromatin structure formed by closely located genomic loci that in the sequence are far apart. variation at chromatin loop Variation affecting chromatin structure in which architectural proteins (cohesin, CTCF) facilitate loop formation. variation at extruded loop Variation affecting chromatin structure in which regulatory components (transcription factor, heterechromatin protein, polycomb) facilitate loop formation. variation at regulatory component-related loop variation at chromatin domain Variation affecting chromatin structure formed by segregation of active and inactive chromatin, without involvement of CTCF. variation at compartmental domain Variation affecting chromatin structure associated with nuclear lamina. variation at lamina-associated domain Variation affecting large chromatin structure of several megabases. variation at chromatin macrostructure Chromosome that is part of the karyotype of an organism. essential chromosome Gene which product is protein. protein coding gene Gene which product is not protein. non-protein coding gene The combined genome of a host and its symbiotic microbes. hologenome Total genetic material in a sample. Refers often to environmental samples. metagenome Genetic constitution of an organism or cell. genotype Observable characteristic of an organism. phenotype Genetically determined charactistic of an organism or cell. trait Genetic constitution of an organisms or cell. Variant in a gene. allele Classification of DNA variation. VariO:0322 DNA variation classification Type of DNA variation. Describes origin and classification of a variant. variation_ontology VariO:0129 DNA variation type Variation having effect on DNA function and usage. variation_ontology variation affecting DNA function Variation affecting DNA tertiary structure. VariO:0171 effect on DNA tertiary structure Variation affecting chromatin. VariO:0153 chromatin variation Variation to the complete epigenetic variome. VariO:0579 epigenome editing Variation affecting chromosome number. VariO:0133 variation of chromosome number Variation affecting structure of chromosome. VariO:0134 variation of chromosome structure Variation affecting characteristic property of DNA. VariO:0227 variation affecting DNA property Variation preventing transcription e.g. because of impaired transcription machinery or variation in the transcription regulation, start site or due to degradation because of containing premature stop codon. VariO:0245 missing RNA RNA nucletide change in the initiation codon. VariO:0317 initiation codon change Deletion of nucleotides in multiples of three so that the mRNA coding sequence frame is retained. VariO:0320 in-frame deletion Deletion of nucleotide(s) causing alteration of mRNA coding sequence frame. VariO:0321 out-of-frame deletion Substitution in mRNA coding region that affects gene expression and protein production without introducing a stop codon in the variation site. VariO:0514 unsense variation The complete genomic material in an organism. VariO:0516 genome Linear or circular nucleic acid chain that contains genetic material and associated protein molecules. VariO:0517 chromosome Nucleic acid segment that resembles a functional gene but which is defective. VariO:0519 variation in pseudogene Intronless pseudogene. VariO:0520 processed pseudogene Intron(s) containing pseudogene. VariO:0521 unprocessed pseudogene Pseudogene without functional gene copy. VariO:0522 unitary pseudogene Gene that is nonfunctional pseudogene in the reference sequence but functional gene in some individual(s). VariO:0523 polymorphic pseudogene VariO:0524 selfish genetic element Genetic segment that can enhance its own transmission even at the expense of the organism. VariO:0525 over-replicating element Nucleotide region capable of moving within genome. VariO:0526 mobile genetic element Independently replicating linear or circular extrachromosomal DNA or RNA chain. plasmid VariO:0527 Infectious agent that replicates inside cells of other species. Retroviruses act as selfish genetic element. VariO:0528 virus Self-splicing group I intron that codes for endnuclease and that cuts specific sites within the genome, typically uninserted homologous sequence. VariO:0529 biased gene converter Genetic element that distorts transmission of genes or chromosomes to offspring. VariO:0531 homing endonuclease transmission distorter Non-essential chromosome in some individuals within a species. accessory chromosome supernumerary chromosome dispensable chromosome lineage-specific chromosome VariO:0532 B chromosome Chromosome drive that affects fair segregation. VariO:0533 driving chromosome Sex chromosome drive that affects fair segregation. VariO:0534 driving sex chromosome Intracellular symbiotic organism or organelle. VariO:0570 endosymbiont Heritable intracellular symbiotic microbe. VariO:0571 heritable microbe Heritable intracellular organelle. VariO:0572 heritable organelle Ultra-selfish DNA sequence that kills meiotic products that do not contain the killer DNA element. VariO:0573 killer meiotic driver Different protein forms originating from a single gene. Proteoforms originate due to changes at DNA, RNA and protein levels. VariO:0575 proteoform VariO:0576 Variation affecting reservoir of genetic material. effect on reservoir of genetic material Reorganization of DNA chromatin packing. VariO:0580 chromatin remodeling Protein variant ending from alternative translation termination. VariO:0581 alternatively terminated protein Structural form of double-stranded DNA supercoiling. VariO:0582 DNA topoisomer Hybridization between distantly related species. genomic allopolyploidy true allopolyploidy Hybridization within a species, between genomes that differ in several regions. segmental allopolyploidy Genome doubling after allopolyploid formation. autoallopolyploidy Hybridization within a species deu to genome duplication or fusion of gamets from similar individuals. strict autopolyploidy Hybridization within a species between genetically distinct and structurally similar chromosomes. interracial autopolyploidy Description of general genetic concept. VariO:0515 genetic concept