format-version: 1.2 date: 23:11:2018 15:56 saved-by: med-mnv auto-generated-by: OBO-Edit 2.3.1 default-namespace: variation_ontology remark: A Variation Ontology ontology: vario owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion( \"\")\n) [Term] id: VariO:0001 name: variation def: "Alteration in DNA, RNA or protein." [VariO:mv] [Term] id: VariO:0002 name: variation affecting protein def: "Effects of a variation on protein level." [VariO:mv] is_a: VariO:0001 ! variation [Term] id: VariO:0003 name: variation affecting protein function def: "Effect of variation on protein function." [VariO:mv] is_a: VariO:0002 ! variation affecting protein [Term] id: VariO:0004 name: effect on protein movement def: "Effect of variation on the movement of a protein along filament of a polymeric molecule." [VariO:mv] is_a: VariO:0003 ! variation affecting protein function [Term] id: VariO:0005 name: effect on protein storage def: "Effect of variation on storage protein. Storage proteins are cellular sources of amino acids and metal ions." [VariO:mv] is_a: VariO:0003 ! variation affecting protein function [Term] id: VariO:0006 name: effect on structural protein def: "Effect of variation on structural role of protein. Structural proteins are fibrous and involved in increasing rigidity and stiffness of biological systems." [VariO:mv] is_a: VariO:0003 ! variation affecting protein function [Term] id: VariO:0007 name: effect on protein recognition def: "Effect of variation on selective non-covalent interaction of protein." [VariO:mv] is_a: VariO:0003 ! variation affecting protein function [Term] id: VariO:0008 name: effect on catalytic protein function def: "Effect of variation on catalytic function of protein." [VariO:mv] is_a: VariO:0003 ! variation affecting protein function [Term] id: VariO:0009 name: effect on transport function of protein def: "Effect of variation on transport function of protein in facilitating passage of an atom or molecule through membrane." [VariO:mv] is_a: VariO:0003 ! variation affecting protein function [Term] id: VariO:0010 name: effect on RNA abundance def: "Variation affecting abundance of produced RNA molecules." [VariO:mv] is_a: VariO:0298 ! variation affecting RNA property [Term] id: VariO:0011 name: effect on protein information transfer def: "Effect of variation on information transfer by protein to control activity of specific processes in cells, tissues or organs." [VariO:mv] is_a: VariO:0003 ! variation affecting protein function [Term] id: VariO:0012 name: protein variation type def: "Type of protein variation. Describes origin and classification of a variant." [VariO:mv] is_a: VariO:0002 ! variation affecting protein [Term] id: VariO:0013 name: protein variation of genetic origin def: "Protein variation that has genetic origin." [VariO:mv] is_a: VariO:0323 ! protein variation origin [Term] id: VariO:0014 name: amino acid deletion def: "Removal of one or more continuous amino acids from protein." [VariO:mv] is_a: VariO:0325 ! protein variation classification [Term] id: VariO:0015 name: protein truncation def: "Shortening of protein sequence from terminus." [VariO:mv] is_a: VariO:0014 ! amino acid deletion [Term] id: VariO:0016 name: sequence retaining amino acid deletion def: "Deletion of one or more amino acids from a protein, without affecting the sequence after deletion." [VariO:mv] is_a: VariO:0014 ! amino acid deletion [Term] id: VariO:0017 name: nonsynonymous variation def: "mRNA variation leading to amino acid change in translated protein. The variant alters the codon so that it encodes another amino acid." [Vario:mv] is_a: VariO:0232 ! variation attribute created_by: med-mnv creation_date: 2015-06-04T13:23:24Z [Term] id: VariO:0018 name: amino acid insertion def: "Addition of one or more amino acids to protein sequence." [VariO:mv] is_a: VariO:0325 ! protein variation classification [Term] id: VariO:0019 name: amphigoric amino acid insertion def: "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] is_a: VariO:0018 ! amino acid insertion [Term] id: VariO:0020 name: sequence retaining amino acid insertion def: "Insertion of one or more amino acids to the protein without affecting the sequence after insertion." [VariO:mv] is_a: VariO:0018 ! amino acid insertion [Term] id: VariO:0021 name: amino acid substitution def: "Substitution of an amino acid in protein." [VariO:mv] xref: SO:0001606 is_a: VariO:0325 ! protein variation classification [Term] id: VariO:0022 name: amino acid indel def: "A complex protein variation consisting of both amino acid insertion(s) and deletion(s)." [VariO:mv] is_a: VariO:0325 ! protein variation classification [Term] id: VariO:0023 name: amphigoric amino acid indel def: "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] is_a: VariO:0022 ! amino acid indel created_by: Mauno Vihinen creation_date: 2013-03-06T10:59:41Z [Term] id: VariO:0024 name: variation emerging at protein level def: "Protein variation that does not have genetic origin being modified at protein level." [VariO:mv] is_a: VariO:0323 ! protein variation origin [Term] id: VariO:0025 name: epigenetic protein variation def: "Heritable protein variation of non-genetic origin." [VariO:mv] is_a: VariO:0024 ! variation emerging at protein level [Term] id: VariO:0026 name: protein structural inheritance def: "Inheritance of protein or protein complex structure without involvement of genetic information." [VariO:mv] is_a: VariO:0025 ! epigenetic protein variation [Term] id: VariO:0027 name: proteinaceous infection def: "Protein conformation change induced by structurally modified protein." [VariO:mv] is_a: VariO:0025 ! epigenetic protein variation [Term] id: VariO:0028 name: post translational modification def: "Protein molecule chemically modified after translation." [VariO:mv] is_a: VariO:0024 ! variation emerging at protein level [Term] id: VariO:0029 name: sequence retaining amino acid indel def: "Amino acid indel without affecting the sequence after the indel position." [VariO:mv] is_a: VariO:0022 ! amino acid indel created_by: Mauno Vihinen creation_date: 2013-03-06T11:04:21Z [Term] id: VariO:0030 name: in-frame indel def: "RNA indel not affecting reading frame after indel position." [VariO:mv] is_a: VariO:0311 ! RNA indel created_by: Mauno Vihinen creation_date: 2013-06-14T10:03:57Z [Term] id: VariO:0031 name: out-of-frame indel def: "RNA indel containing a number of nucleotides not divisible by three and therefore causing change to reading frame." [VariO:mv] is_a: VariO:0311 ! RNA indel created_by: Mauno Vihinen creation_date: 2013-06-14T10:03:57Z [Term] id: VariO:0032 name: variation affecting protein property def: "Variation affecting characteristic property of protein." [VariO:mv] is_a: VariO:0002 ! variation affecting protein [Term] id: VariO:0033 name: effect on protein subcellular localization def: "Effect of variation on the targeting of a protein within a cell or cellular compartment." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0034 name: effect on protein stability def: "Effect of variation on stability of protein." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0035 name: effect on protein solubility def: "Effect of variation on the potential of protein to dissolve in a liquid." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0036 name: effect on protein inclusion body formation def: "Variation affecting the formation of particles of aggregated proteins." [VariO:mv] xref: GO:0016234 is_a: VariO:0035 ! effect on protein solubility [Term] id: VariO:0037 name: covariant position def: "Variation at a covarying sequence position." [VariO:mv] is_a: VariO:0233 ! conservation created_by: Mauno Vihinen creation_date: 2014-01-16T14:03:51Z [Term] id: VariO:0038 name: effect on protein aggregation def: "Variation affecting protein aggregation tendency." [VariO:mv] is_a: VariO:0035 ! effect on protein solubility [Term] id: VariO:0039 name: protein function change def: "Type of protein function affecting variation." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0040 name: protein gain of function def: "Effect of variation causing new or enhanced protein activity." [VariO:mv] is_a: VariO:0039 ! protein function change [Term] id: VariO:0041 name: neomorphic protein variation def: "Variation generates new protein function." [VariO:mv] is_a: VariO:0040 ! protein gain of function [Term] id: VariO:0042 name: antimorphic protein variation def: "Dominant variation that acts to opposite direction than the normal protein." [VariO:mv] synonym: "dominant negative protein variation" EXACT [] is_a: VariO:0040 ! protein gain of function [Term] id: VariO:0043 name: protein loss of function def: "Effect of variation reducing or abolishing protein activity." [VariO:mv] is_a: VariO:0039 ! protein function change [Term] id: VariO:0044 name: effect on protein accessibility def: "Effect of variation to the accessibility of protein region to solvent." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0045 name: variation exposing buried region def: "Variation exposing buried region." [VariO:mv] is_a: VariO:0044 ! effect on protein accessibility [Term] id: VariO:0046 name: variation burying exposed region def: "Variation leading to burying of exposed region." [VariO:mv] is_a: VariO:0044 ! effect on protein accessibility [Term] id: VariO:0047 name: association of protein variation to pathogenicity def: "Implication of a protein variant to pathogenicity." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0048 name: effect on protein charge def: "Effect of variation on charge in protein." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0049 name: effect on protein electrostatics def: "Variation affecting electrostatics of the protein surface." [VariO:mv] is_a: VariO:0048 ! effect on protein charge [Term] id: VariO:0050 name: effect on protein isoelectric point def: "Variation changing protein isoelectric point." [VariO:mv] is_a: VariO:0048 ! effect on protein charge [Term] id: VariO:0051 name: effect on protein degradation def: "Effect of variation on degradation of protein." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0052 name: effect on protein abundance def: "Variation affecting abundance of produced protein molecules." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0053 name: effect on protein activity def: "Effect of variation on activity of protein." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0054 name: effect on protein affinity def: "Effect of variation on protein affinity to binding molecule(s)." [VariO:mv] is_a: VariO:0053 ! effect on protein activity [Term] id: VariO:0055 name: effect on protein specificity def: "Effect of variation on substrate binding specificity of protein." [VariO:mv] is_a: VariO:0053 ! effect on protein activity [Term] id: VariO:0056 name: effect on enzyme reaction kinetics def: "Effect of variation to enzyme reaction kinetics." [VariO:mv] is_a: VariO:0435 ! effect on protein reaction kinetics [Term] id: VariO:0057 name: conservation of protein variation site def: "Conservation of the variant site in related protein sequences." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0058 name: effect on protein interaction def: "Effect of variation on the interaction of protein with its partner." [VariO:mv] is_a: VariO:0032 ! variation affecting protein property [Term] id: VariO:0059 name: effect on protein contact energy def: "Effect of variation on contact energy between interacting molecules." [VariO:mv] is_a: VariO:0058 ! effect on protein interaction [Term] id: VariO:0060 name: variation affecting protein structure def: "Variation affecting structure of protein." [VariO:mv] is_a: VariO:0002 ! variation affecting protein [Term] id: VariO:0061 name: epigenetic protein modification def: "Hereditary protein structure modification of non-genetic origin." [VariO:mv] is_a: VariO:0060 ! variation affecting protein structure [Term] id: VariO:0062 name: prion formation def: "Variation affecting the formation of infectious protein having misfolded structure." [VariO:mv] is_a: VariO:0061 ! epigenetic protein modification [Term] id: VariO:0063 name: epigenetic protein complex structure def: "Variation affecting heritable protein complex structure." [VariO:mv] is_a: VariO:0061 ! epigenetic protein modification [Term] id: VariO:0064 name: effect on protein 3D structure def: "Variation affecting protein three dimensional structure." [VariO:mv] is_a: VariO:0060 ! variation affecting protein structure [Term] id: VariO:0065 name: effect on protein dynamics def: "Variation affecting dynamics in protein structure." [VariO:mv] is_a: VariO:0064 ! effect on protein 3D structure [Term] id: VariO:0066 name: effect on structural flexibility def: "Variation affecting protein structural flexibility." [VariO:mv] is_a: VariO:0065 ! effect on protein dynamics [Term] id: VariO:0067 name: effect on induced fit def: "Variation affecting induced fit of protein binding to its partner." [VariO:mv] is_a: VariO:0065 ! effect on protein dynamics [Term] id: VariO:0068 name: effect on structural disorder def: "Variation affecting protein structural disorder." [VariO:mv] is_a: VariO:0065 ! effect on protein dynamics [Term] id: VariO:0069 name: effect on allosteric site def: "Variation in affecting protein allosteric site." [VariO:mv] is_a: VariO:0065 ! effect on protein dynamics [Term] id: VariO:0070 name: effect on protein tertiary structure def: "Variation affecting protein three dimensional structure." [VariO:mv] is_a: VariO:0064 ! effect on protein 3D structure [Term] id: VariO:0071 name: effect on protein folding rate def: "Variation affecting rate of protein folding." [VariO:mv] is_a: VariO:0070 ! effect on protein tertiary structure [Term] id: VariO:0072 name: extrachromosomal DNA affected def: "Variation effect on nonchromosomal DNA." [VariO:mv] is_a: VariO:0159 ! affected DNA level created_by: Mauno Vihinen creation_date: 2012-11-09T14:16:30Z [Term] id: VariO:0073 name: effect to protein fold def: "Variation affecting protein tertiary structure." [VariO:mv] is_a: VariO:0070 ! effect on protein tertiary structure [Term] id: VariO:0074 name: protein conformational change def: "Variation changing protein conformation." [VariO:mv] is_a: VariO:0073 ! effect to protein fold [Term] id: VariO:0075 name: global protein conformation change def: "Variation causing large overall protein conformational change." [VariO:mv] is_a: VariO:0074 ! protein conformational change [Term] id: VariO:0076 name: local protein conformation change def: "Variation causing local and minor conformational change." [VariO:mv] is_a: VariO:0074 ! protein conformational change [Term] id: VariO:0077 name: changed domain orientation def: "Variation affecting protein structure due to alteration to domain orientation." [VariO:mv] is_a: VariO:0073 ! effect to protein fold [Term] id: VariO:0078 name: effect on protein disulphide formation def: "Variation affecting formation of intramolecular disulphide bonds." [VariO:mv] is_a: VariO:0073 ! effect to protein fold [Term] id: VariO:0079 name: effect on protein secondary structural element def: "Variation affecting protein secondary structural element of local ordered structure." [VariO:mv] is_a: VariO:0070 ! effect on protein tertiary structure [Term] id: VariO:0080 name: effect on protein helix def: "Variation affecting secondary structure conformation where the peptide backbone forms a coil." [VariO:mv] is_a: VariO:0079 ! effect on protein secondary structural element [Term] id: VariO:0081 name: effect on left handed protein helix def: "Variation affecting protein left handed helix turning anticlockwise." [VariO:mv] is_a: VariO:0080 ! effect on protein helix [Term] id: VariO:0082 name: effect on right handed protein helix def: "Variation affecting protein right handed helix where the coiled conformation turns in a clockwise, right handed screw." [VariO:mv] is_a: VariO:0080 ! effect on protein helix [Term] id: VariO:0083 name: effect on pi helix def: "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] is_a: VariO:0082 ! effect on right handed protein helix [Term] id: VariO:0084 name: effect on three ten helix def: "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] is_a: VariO:0082 ! effect on right handed protein helix [Term] id: VariO:0085 name: effect on alpha helix def: "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] is_a: VariO:0082 ! effect on right handed protein helix [Term] id: VariO:0086 name: effect on protein beta strand def: "Variation affecting extended protein backbone structure." [VariO:mv] is_a: VariO:0079 ! effect on protein secondary structural element [Term] id: VariO:0087 name: effect on protein antiparallel beta strand def: "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] comment: Range. is_a: VariO:0086 ! effect on protein beta strand [Term] id: VariO:0088 name: effect on protein parallel beta strand def: "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] comment: Range. is_a: VariO:0086 ! effect on protein beta strand [Term] id: VariO:0089 name: effect on protein turn motif def: "Variation affecting protein backbone turn motif." [VariO:mv] is_a: VariO:0079 ! effect on protein secondary structural element [Term] id: VariO:0090 name: effect on protein alpha beta motif def: "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] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0091 name: effect on protein beta turn def: "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] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0092 name: effect on protein st motif def: "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] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0093 name: effect on protein st staple def: "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] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0094 name: effect on protein gamma turn def: "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] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0095 name: effect on protein st turn def: "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] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0096 name: effect on protein schellman loop def: "Variation affecting protein motif of six or seven consecutive residues that contains two H-bonds." [VariO:mv] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0097 name: effect on protein nest motif def: "Variation affecting protein motif of two consecutive residues. Dihedral angles are used to sub-categorise the nests. Nest does not contain proline." [VariO:mv] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0098 name: effect on protein niche motif def: "Variation affecting a protein motif of three consecutive residues. Dihedral angles are used to sub-categorise the niche motifs." [VariO:mv] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0099 name: effect on protein asx motif def: "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] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0100 name: effect on protein beta bulge def: "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] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0101 name: effect on protein asx turn def: "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] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0102 name: effect on protein beta bulge loop def: "Variation affecting protein motif of three residues within a beta-sheet consisting of two H-bonds." [VariO:mv] is_a: VariO:0089 ! effect on protein turn motif [Term] id: VariO:0103 name: effect on protein coil def: "Variation affecting irregular, unstructured region of protein." [VariO:mv] is_a: VariO:0079 ! effect on protein secondary structural element [Term] id: VariO:0104 name: effect on transmembrane polypeptide def: "Variation altering membrane spanning protein." [VariO:mv] is_a: VariO:0070 ! effect on protein tertiary structure [Term] id: VariO:0105 name: effect on membrane protein extramembrane region def: "Variation affecting region not traversing the lipid bilayer in a membrane protein." [VariO:mv] is_a: VariO:0104 ! effect on transmembrane polypeptide [Term] id: VariO:0106 name: effect on membrane protein intramembrane region def: "Variation affecting region present in the lipid bilayer in a membrane protein." [VariO:mv] is_a: VariO:0104 ! effect on transmembrane polypeptide [Term] id: VariO:0107 name: effect on protein post translational modification def: "Variation affecting the covalent alteration of protein amino acid by post translational process." [VariO:mv] is_a: VariO:0070 ! effect on protein tertiary structure [Term] id: VariO:0108 name: deletion of a post translational modification site def: "Variation causing deletion of a post translational modification site." [VariO:mv] is_a: VariO:0107 ! effect on protein post translational modification [Term] id: VariO:0109 name: effect on protein processing def: "Variation affecting site of protein maturation by cleavage of peptide bond(s)." [VariO:mv] is_a: VariO:0107 ! effect on protein post translational modification [Term] id: VariO:0110 name: effect on protein splicing def: "Variation affecting post-translational removal of peptide sequences from within a protein sequence." [VariO:mv] is_a: VariO:0109 ! effect on protein processing [Term] id: VariO:0111 name: variation generating a novel protein processing site def: "Variation that generates a novel protein processing site." [VariO:mv] is_a: VariO:0109 ! effect on protein processing [Term] id: VariO:0112 name: variation preventing polypeptide processing def: "Variation causing prevention of polypeptide processing." [VariO:mv] is_a: VariO:0109 ! effect on protein processing [Term] id: VariO:0113 name: generation of a novel post translational modification site def: "Variation generating a novel post translational modification site." [VariO:mv] is_a: VariO:0107 ! effect on protein post translational modification [Term] id: VariO:0114 name: effect on amino acid size def: "Variation affecting amino acid side chain size." [VariO:mv] is_a: VariO:0070 ! effect on protein tertiary structure [Term] id: VariO:0115 name: effect on protein packing def: "Variation affecting amino acid packing in folded protein." [VariO:mv] is_a: VariO:0070 ! effect on protein tertiary structure [Term] id: VariO:0116 name: protein cavity formation def: "Variation causing formation of a cavity to protein core due to replacement of a side chain by a smaller one." [VariO:mv] is_a: VariO:0115 ! effect on protein packing [Term] id: VariO:0117 name: protein overpacking def: "Variation causing over packing of amino acids due to replacement by larger amino acid side chain." [VariO:mv] is_a: VariO:0115 ! effect on protein packing [Term] id: VariO:0118 name: effect on protein interaction site def: "Variation affecting ligand binding amino acid(s) in protein." [VariO:mv] is_a: VariO:0070 ! effect on protein tertiary structure [Term] id: VariO:0119 name: effect on protein binding site def: "Variation affecting region on the surface of a protein that interacts with another molecule." [VariO:mv] is_a: VariO:0118 ! effect on protein interaction site [Term] id: VariO:0120 name: effect on protein catalytic site def: "Variation affecting amino acid(s) in protein catalytic site." [VariO:mv] is_a: VariO:0118 ! effect on protein interaction site [Term] id: VariO:0121 name: effect on protein quaternary structure def: "Variation affecting three dimensional structure of a protein complex." [VariO:mv] is_a: VariO:0064 ! effect on protein 3D structure [Term] id: VariO:0122 name: effect on protein quaternary structure forming interaction def: "Variation affecting interaction between protein subunits in quaternary structure." [VariO:mv] is_a: VariO:0121 ! effect on protein quaternary structure [Term] id: VariO:0123 name: complex 3D structural change def: "Complex change of protein three dimensional structure." [VariO:mv] is_a: VariO:0064 ! effect on protein 3D structure [Term] id: VariO:0124 name: protein elongation def: "Variation prolonging protein chain at an end." [VariO:mv] is_a: VariO:0070 ! effect on protein tertiary structure [Term] id: VariO:0125 name: C-terminal protein elongation def: "Addition of one or more amino acids to protein C-terminus." [VariO:mv] is_a: VariO:0124 ! protein elongation [Term] id: VariO:0126 name: N-terminal protein elongation def: "Addition of one or more amino acids to protein N-terminus." [VariO:mv] is_a: VariO:0124 ! protein elongation [Term] id: VariO:0127 name: DNA variation origin def: "Origin of DNA variation." [VariO:mv] is_a: VariO:0129 ! DNA variation type created_by: Mauno Vihinen creation_date: 2013-10-11T08:46:32Z [Term] id: VariO:0128 name: variation affecting DNA def: "Effects of a variation on DNA level." [VariO:mv] is_a: VariO:0001 ! variation [Term] id: VariO:0129 name: DNA variation type def: "Type of DNA variation. Describes origin and classification of a variant." [VariO:mv] is_a: VariO:0128 ! variation affecting DNA [Term] id: VariO:0130 name: DNA variation of genetic origin def: "DNA variation that has genetic origin." [VariO:mv] is_a: VariO:0127 ! DNA variation origin [Term] id: VariO:0131 name: genomic variation def: "Variation of genomic level." [VariO:mv] is_a: VariO:0322 ! DNA variation classification [Term] id: VariO:0132 name: chromosomal variation def: "Variation at chromosomal level." [VariO:mv] is_a: VariO:0322 ! DNA variation classification [Term] id: VariO:0133 name: variation of chromosome number def: "Variation affecting chromosome number." [VariO:mv] synonym: "aneuploidy" RELATED [] is_a: VariO:0132 ! chromosomal variation [Term] id: VariO:0134 name: variation of chromosome structure def: "Variation affecting structure of chromosome." [VariO:mv] is_a: VariO:0132 ! chromosomal variation [Term] id: VariO:0135 name: DNA chain variation def: "Variation at DNA chain." [VariO:mv] is_a: VariO:0322 ! DNA variation classification [Term] id: VariO:0136 name: DNA substitution def: "Substitution of a DNA nucleotide." [VariO:mv] is_a: VariO:0135 ! DNA chain variation [Term] id: VariO:0137 name: effect on RNA tertiary structure def: "Variation affecting RNA tertiary structure." [VariO:mv] is_a: VariO:0338 ! variation affecting RNA structure created_by: med-mnv creation_date: 2018-04-26T12:45:52Z [Term] id: VariO:0138 name: variant def: "A genetic character, organism or individual with a difference to reference state." [VariO:mv] is_a: VariO:0232 ! variation attribute created_by: Mauno Vihinen creation_date: 2012-11-11T19:43:00Z [Term] id: VariO:0139 name: mutation def: "Any process generating variation." [VariO:mv] is_a: VariO:0232 ! variation attribute created_by: Mauno Vihinen creation_date: 2012-11-11T19:43:39Z [Term] id: VariO:0140 name: not changed def: "The observed feature is not changed in relation to the wild type form." [VariO:mv] is_a: VariO:0289 ! quantity change created_by: Mauno Vihinen creation_date: 2012-11-11T19:46:40Z [Term] id: VariO:0141 name: DNA deletion def: "Removal of one or more continuous nucleotides from DNA sequence." [VariO:mv] synonym: "nucleotide deletion" EXACT [] is_a: VariO:0135 ! DNA chain variation [Term] id: VariO:0142 name: DNA insertion def: "Addition of one or more nucleotides between two adjacent nucleotides in the DNA sequence." [VariO:mv] synonym: "nucleotide insertion" EXACT [] is_a: VariO:0135 ! DNA chain variation [Term] id: VariO:0143 name: DNA indel def: "A complex DNA variation consisting of both nucleotide insertion(s) and deletion(s)." [VariO:mv] is_a: VariO:0135 ! DNA chain variation [Term] id: VariO:0144 name: DNA translocation def: "A continuous stretch of DNA sequence moved to a new position within a chromosome." [VariO:mv] xref: MI:0593 xref: SO:0000199 is_a: VariO:0135 ! DNA chain variation [Term] id: VariO:0145 name: DNA inversion def: "A continuous stretch of DNA sequence inserted to the same position in reverse orientation." [VariO:mv] xref: SO:1000036 is_a: VariO:0144 ! DNA translocation [Term] id: VariO:0146 name: DNA variation of non-genetic origin def: "DNA variation that does not have genetic origin." [VariO:mv] is_a: VariO:0127 ! DNA variation origin [Term] id: VariO:0147 name: epigenetic DNA variation def: "Heritable DNA variation of non-genetic origin." [VariO:mv] is_a: VariO:0146 ! DNA variation of non-genetic origin [Term] id: VariO:0148 name: variation affecting DNA function def: "Variation having effect on DNA function and usage." [VariO:mv] is_a: VariO:0128 ! variation affecting DNA [Term] id: VariO:0149 name: effect on transcription def: "Variation affecting transcription, synthesis of either RNA on a template of DNA or DNA on a template of RNA." [VariO:mv] is_a: VariO:0148 ! variation affecting DNA function [Term] id: VariO:0150 name: effect on DNA information transfer def: "Variation affecting information transfer of DNA." [VariO:mv] is_a: VariO:0148 ! variation affecting DNA function [Term] id: VariO:0151 name: effect on DNA repair def: "Variation affecting the process of restoring DNA after damage." [VariO:mv] xref: GO:0006281 xref: Wikipedia:DNA_repair is_a: VariO:0148 ! variation affecting DNA function [Term] id: VariO:0152 name: effect on regulatory function of DNA def: "Variation affecting regulatory function of DNA." [VariO:mv] is_a: VariO:0148 ! variation affecting DNA function [Term] id: VariO:0153 name: chromatin variation def: "Variation affecting chromatin." [VariO:mv] is_a: VariO:0322 ! DNA variation classification created_by: med-mnv creation_date: 2018-03-05T16:05:29Z [Term] id: VariO:0154 name: effect on DNA replication def: "Variation originating from semi conservative DNA strand synthesis. The template for replication is either DNA or RNA molecule." [VariO:mv] is_a: VariO:0148 ! variation affecting DNA function [Term] id: VariO:0155 name: variation affecting DNA structure def: "Variation affecting structure of DNA." [VariO:mv] is_a: VariO:0128 ! variation affecting DNA [Term] id: VariO:0156 name: epigenetic DNA modification def: "Hereditary variation of DNA not affecting primary sequence." [VariO:mv] is_a: VariO:0155 ! variation affecting DNA structure [Term] id: VariO:0157 name: epigenetic DNA methylation def: "Inheritable cytosine or adenosine pyrimidine ring methylation regulating gene expression." [VariO:mv] is_a: VariO:0156 ! epigenetic DNA modification [Term] id: VariO:0158 name: nucleosome positioning def: "Positioning of nucleosomes to DNA strand." [VariO:mv] synonym: "chromatin modeling" EXACT [GO:0006338] synonym: "chromatin remodelling" EXACT [GO:0006338] is_a: VariO:0156 ! epigenetic DNA modification is_a: VariO:0226 ! chromatin structure variation relationship: part_of VariO:0156 ! epigenetic DNA modification relationship: part_of VariO:0226 ! chromatin structure variation [Term] id: VariO:0159 name: affected DNA level def: "Affected level of DNA." [VariO:mv] is_a: VariO:0155 ! variation affecting DNA structure [Term] id: VariO:0160 name: DNA chain affected def: "Variation effect on DNA level." [VariO:mv] is_a: VariO:0159 ! affected DNA level [Term] id: VariO:0161 name: variation in intron def: "Variation located in intron." [VariO:mv] xref: SO:0001627 is_a: VariO:0160 ! DNA chain affected [Term] id: VariO:0162 name: variation in exon def: "Variation located in exon." [VariO:mv] is_a: VariO:0160 ! DNA chain affected [Term] id: VariO:0163 name: variation at intergenic DNA def: "Variation located in intergenic DNA." [VariO:mv] xref: SO:0001628 is_a: VariO:0160 ! DNA chain affected [Term] id: VariO:0164 name: chromosome affected def: "Variation effect on chromosome level." [VariO:mv] is_a: VariO:0159 ! affected DNA level [Term] id: VariO:0165 name: genome affected def: "Variation effect on genome level." [VariO:mv] is_a: VariO:0159 ! affected DNA level [Term] id: VariO:0166 name: immunological receptor gene rearrangement def: "Somatic recombination combining gene segments in antibody, immunoglobulin B and T cell receptor and MCH coding genes." [VariO:mv] is_a: VariO:0447 ! immunological recognition molecule diversification created_by: med-mnv creation_date: 2015-09-22T19:10:52Z [Term] id: VariO:0167 name: effect on DNA form def: "Variation affecting DNA structural form." [VariO:mv] is_a: VariO:0171 ! effect on DNA tertiary structure created_by: med-mnv creation_date: 2017-01-16T12:52:26Z [Term] id: VariO:0168 name: somatic hypermutation def: "Immunoglobulin diversification mechanism by producing variations to antigen variable regions." [VariO:mv] is_a: VariO:0447 ! immunological recognition molecule diversification created_by: med-mnv creation_date: 2015-09-22T19:12:51Z [Term] id: VariO:0169 name: class switch recombination def: "Switching of immunoglobulin M to other isotype by changing a portion of a region coding for heavy chain." [VariO:mv] is_a: VariO:0447 ! immunological recognition molecule diversification created_by: med-mnv creation_date: 2015-09-22T19:12:51Z [Term] id: VariO:0170 name: immunological receptor gene conversion def: "Secondary immunological receptor diversification by replacing a DNA stretch by a homologous sequence." [VariO:mv] is_a: VariO:0447 ! immunological recognition molecule diversification created_by: med-mnv creation_date: 2015-09-22T19:12:51Z [Term] id: VariO:0171 name: effect on DNA tertiary structure def: "Variation affecting DNA tertiary structure." [VariO:mv] is_a: VariO:0155 ! variation affecting DNA structure [Term] id: VariO:0172 name: artificial DNA variation def: "Variation generated on purpose by e.g. chemical or physical treatment or artificial modification of DNA." [VariO:mv] is_a: VariO:0146 ! DNA variation of non-genetic origin created_by: Mauno Vihinen creation_date: 2012-11-16T08:44:55Z [Term] id: VariO:0173 name: effect on nucleic acid G-quadruplex def: "Variation affecting G-quadruplex of four stranded nucleic acid structure. The structure can be intramolecular, bimolecular or tetramolecular." [VariO:mv] is_a: VariO:0420 ! effect on four-stranded DNA is_a: VariO:0426 ! effect on four-stranded RNA relationship: part_of VariO:0420 ! effect on four-stranded DNA relationship: part_of VariO:0426 ! effect on four-stranded RNA [Term] id: VariO:0174 name: effect on i motif def: "Variation affecting cytosine rich DNA domain where strands associate both inter- and intramolecularly." [VariO:mv] is_a: VariO:0420 ! effect on four-stranded DNA [Term] id: VariO:0175 name: effect on DNA triple helix def: "Variation affecting DNA helix formed of three strands." [VariO:mv] is_a: VariO:0167 ! effect on DNA form [Term] id: VariO:0176 name: chromosome variation def: "Variation affecting chromosome." [VariO:mv] xref: SO:0000240 is_a: VariO:0155 ! variation affecting DNA structure [Term] id: VariO:0177 name: telomere length change def: "Variation affecting length of telomere sequence." [VariO:mv] is_a: VariO:0180 ! chromosome structure variation [Term] id: VariO:0178 name: telomere shortening def: "Variation shortening length of telomere sequence." [VariO:mv] is_a: VariO:0177 ! telomere length change [Term] id: VariO:0179 name: telomere extension def: "Variation extending length of telomere sequence." [VariO:mv] is_a: VariO:0177 ! telomere length change [Term] id: VariO:0180 name: chromosome structure variation def: "Variation affecting structure of chromosome." [VariO:mv] xref: SO:1000183 is_a: VariO:0176 ! chromosome variation [Term] id: VariO:0181 name: isochromosome def: "Chromosome lacking one arm with duplication of the other arm." [VariO:mv] is_a: VariO:0180 ! chromosome structure variation [Term] id: VariO:0182 name: ring chromosome def: "Circular chromosome with ends joined." [VariO:mv] xref: SO:1000045 is_a: VariO:0180 ! chromosome structure variation [Term] id: VariO:0183 name: chromosomal amplification def: "Increase in the frequency of a chromosomal region." [VariO:mv] is_a: VariO:0180 ! chromosome structure variation [Term] id: VariO:0184 name: interspersed repeat def: "Copies of a chromosomal region of length greater than one scattered to genome sequence." [VariO:mv] xref: SO:0000658 is_a: VariO:0427 ! type of chromosomal amplification [Term] id: VariO:0185 name: tandem repeat def: "Adjacent copies of a chromosomal region of length greater than 1." [VariO:mv] xref: SO:0000705 is_a: VariO:0427 ! type of chromosomal amplification [Term] id: VariO:0186 name: minisatellite def: "Tandem repetitive sequence consisting of units in length from seven to few tens of base pairs." [VariO:mv] is_a: VariO:0430 ! nucleotide expansion [Term] id: VariO:0187 name: copy number variation def: "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] xref: SO:0001019 is_a: VariO:0183 ! chromosomal amplification is_a: VariO:0193 ! chromosomal deletion relationship: part_of VariO:0183 ! chromosomal amplification relationship: part_of VariO:0193 ! chromosomal deletion [Term] id: VariO:0188 name: microsatellite def: "Tandem repetitive sequence consisting of units of two to six base pair." [VariO:mv] is_a: VariO:0430 ! nucleotide expansion [Term] id: VariO:0189 name: trinucleotide expansion def: "Tandem repetitive sequence consisting of three nucleotide units." [VariO:mv] is_a: VariO:0188 ! microsatellite [Term] id: VariO:0190 name: mononucleotide expansion def: "Tandem repetitive sequence consisting of one nucleotide type." [VariO:mv] is_a: VariO:0188 ! microsatellite [Term] id: VariO:0191 name: tetranucleotide expansion def: "Tandem repetitive sequence consisting of four nucleotide units." [VariO:mv] is_a: VariO:0188 ! microsatellite [Term] id: VariO:0192 name: DNA mobile genetic element insertion def: "Mobile genetic element incorporated into chromosome." [VariO:mv] is_a: VariO:0183 ! chromosomal amplification [Term] id: VariO:0193 name: chromosomal deletion def: "Deletion of chromosomal region." [VariO:mv] is_a: VariO:0180 ! chromosome structure variation [Term] id: VariO:0194 name: interstitial deletion def: "Deletion of chromosomal region not including terminus." [VariO:mv] is_a: VariO:0193 ! chromosomal deletion [Term] id: VariO:0195 name: terminal deletion def: "Deletion of chromosomal region from the end of chromosome arm." [VariO:mv] is_a: VariO:0193 ! chromosomal deletion [Term] id: VariO:0196 name: complex chromosomal variation def: "Chromosome structure variation with four or more breakpoints." [SO:ke, VariO:mv] xref: SO:1000146 is_a: VariO:0180 ! chromosome structure variation [Term] id: VariO:0197 name: chromosomal translocation def: "Translocation of chromosomal region." [VariO:mv] xref: SO:0000199 is_a: VariO:0180 ! chromosome structure variation [Term] id: VariO:0198 name: intrachromosomal translocation def: "Translocation of chromosomal region within a chromosome." [VariO:mv] is_a: VariO:0197 ! chromosomal translocation [Term] id: VariO:0199 name: chromosomal inversion def: "Intrachromosomal variation where a chromosomal region is inserted in reverse direction." [VariO:mv] is_a: VariO:0198 ! intrachromosomal translocation [Term] id: VariO:0200 name: paracentric inversion def: "Chromosomal inversion within a chromosome arm." [VariO:mv] xref: SO:1000047 is_a: VariO:0199 ! chromosomal inversion [Term] id: VariO:0201 name: pericentric inversion def: "Chromosomal inversion including centromere." [VariO:mv] xref: SO:1000046 is_a: VariO:0199 ! chromosomal inversion [Term] id: VariO:0202 name: interchromosomal translocation def: "Translocation of chromosomal region to another chromosome." [VariO:mv] is_a: VariO:0197 ! chromosomal translocation [Term] id: VariO:0203 name: reciprocal chromosomal translocation def: "Switching of chromosomal regions between nonhomologous chromosomes." [VariO:mv] xref: SO:1000048 is_a: VariO:0202 ! interchromosomal translocation [Term] id: VariO:0204 name: Robertsonian translocation def: "Fusion of long arms of two acrocentric chromosomes having very short p arms." [VariO:mv] xref: SO:1000043 is_a: VariO:0202 ! interchromosomal translocation [Term] id: VariO:0205 name: dinucleotide expansion def: "Tandem repetitive sequence consisting of two nucleotide units." [VariO:mv] is_a: VariO:0188 ! microsatellite created_by: med-mnv creation_date: 2015-09-17T10:53:06Z [Term] id: VariO:0206 name: chromosome number variation def: "Variation affecting the number of chromosomes." [VariO:mv] synonym: "aneuploidy" EXACT [] is_a: VariO:0176 ! chromosome variation [Term] id: VariO:0207 name: trisomy def: "Three copies of a chromosome in a cell or organism." [VariO:mv] is_a: VariO:0206 ! chromosome number variation [Term] id: VariO:0208 name: disomy def: "Two copies of a chromosome in a cell or organism ." [VariO:mv] is_a: VariO:0206 ! chromosome number variation [Term] id: VariO:0209 name: uniparental disomy def: "Both copies of a chromosome or a part of it in diploid cell or organism are from one parent." [VariO:mv] is_a: VariO:0208 ! disomy [Term] id: VariO:0210 name: isodisomy def: "Uniparental disomy with duplication of a single chromosome from one parent." [VariO:mv] is_a: VariO:0208 ! disomy [Term] id: VariO:0211 name: heterodisomy def: "Pair of non-identical chromosomes inherited from one parent." [VariO:mv] is_a: VariO:0208 ! disomy [Term] id: VariO:0212 name: nullisomy def: "No copies of a chromosome in a cell or organism." [VariO:mv] is_a: VariO:0206 ! chromosome number variation [Term] id: VariO:0213 name: tetrasomy def: "Four copies of a chromosome in a cell or organism." [VariO:mv] is_a: VariO:0206 ! chromosome number variation [Term] id: VariO:0214 name: monosomy def: "One copy of a chromosome in a cell or organism." [VariO:mv] is_a: VariO:0206 ! chromosome number variation [Term] id: VariO:0215 name: chromosome set number variation def: "Variation affecting number of entire chromosome sets." [VariO:mv] synonym: "euploidy" EXACT [] is_a: VariO:0428 ! genome variation [Term] id: VariO:0216 name: diploidy def: "Variation with two sets of chromosomes." [VariO:mv] is_a: VariO:0215 ! chromosome set number variation [Term] id: VariO:0217 name: tetraploidy def: "Variation with four sets of chromosomes." [VariO:mv] is_a: VariO:0215 ! chromosome set number variation created_by: Mauno creation_date: 2011-03-04T12:19:35Z [Term] id: VariO:0218 name: polyploidy def: "Variation with several sets of chromosomes." [VariO:mv] is_a: VariO:0215 ! chromosome set number variation [Term] id: VariO:0219 name: autopolyploidy def: "Variation with several sets of chromosomes originating from the same organism." [VariO:mv] is_a: VariO:0218 ! polyploidy [Term] id: VariO:0220 name: allopolyploidy def: "Variation with several sets of chromosomes originating from a different organism." [VariO:mv] is_a: VariO:0218 ! polyploidy [Term] id: VariO:0221 name: nulliploidy def: "Variation without chromosomes." [VariO:mv] is_a: VariO:0215 ! chromosome set number variation [Term] id: VariO:0222 name: triploidy def: "Variation with three sets of chromosomes." [VariO:mv] is_a: VariO:0215 ! chromosome set number variation [Term] id: VariO:0223 name: pentaploidy def: "Variation with five sets of chromosomes." [VariO:mv] is_a: VariO:0215 ! chromosome set number variation [Term] id: VariO:0224 name: hexaploidy def: "Variation with six sets of chromosomes." [VariO:mv] is_a: VariO:0215 ! chromosome set number variation [Term] id: VariO:0225 name: monoploidy def: "Variation with a single set of chromosomes." [VariO:mv] synonym: "haploidy" EXACT [] is_a: VariO:0215 ! chromosome set number variation [Term] id: VariO:0226 name: chromatin structure variation def: "Variation affecting structure of chromatin the complex of chromosomal DNA and histone proteins." [VariO:mv] is_a: VariO:0155 ! variation affecting DNA structure [Term] id: VariO:0227 name: variation affecting DNA property def: "Variation affecting characteristic property of DNA." [VariO:mv] is_a: VariO:0128 ! variation affecting DNA [Term] id: VariO:0228 name: protein fusion def: "Fusion of two protein chains. Produced from fusion gene of two joined genes." [VariO:mv] is_a: VariO:0124 ! protein elongation created_by: Mauno Vihinen creation_date: 2012-12-11T08:59:44Z [Term] id: VariO:0229 name: association of DNA variation to pathogenicity def: "Implication of a DNA variant to pathogenicity." [VariO:mv] is_a: VariO:0227 ! variation affecting DNA property [Term] id: VariO:0230 name: effect on DNA interaction def: "Variation affecting interaction of DNA with its partner." [VariO:mv] is_a: VariO:0227 ! variation affecting DNA property [Term] id: VariO:0231 name: conservation of DNA variation site def: "Conservation of the variation site in related DNA sequences." [VariO:mv] is_a: VariO:0227 ! variation affecting DNA property [Term] id: VariO:0232 name: variation attribute def: "Attributes define and modulate terms at other levels." [VariO:mv] is_a: VariO:0001 ! variation [Term] id: VariO:0233 name: conservation def: "Sequence conservation attribute." [VariO:mv] is_a: VariO:0232 ! variation attribute [Term] id: VariO:0234 name: conserved region def: "Variation at a region of sequence similarity in multiple sequence alignment of related sequences." [VariO:mv] is_a: VariO:0233 ! conservation [Term] id: VariO:0235 name: invariant region def: "Variation at invariant sequence region in multiple sequence alignment of related sequences." [VariO:mv] is_a: VariO:0233 ! conservation [Term] id: VariO:0236 name: interaction def: "Mutual or reciprocal action or influence that happens at a given place and time between participating molecules." [src_code:NR, VariO:mv] is_a: VariO:0232 ! variation attribute [Term] id: VariO:0237 name: genetic interaction def: "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] xref: MI:0208 is_a: VariO:0236 ! interaction [Term] id: VariO:0238 name: genetic interaction defined by inequality def: "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] synonym: "genetic inequality" EXACT [MI:0931] xref: MI:0931 is_a: VariO:0237 ! genetic interaction [Term] id: VariO:0239 name: single nonmonotonic genetic interaction defined by inequality def: "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] synonym: "single nonmonotonic" EXACT [MI:0800] synonym: "single nonmonotonic genetic interaction (sensu inequality)" EXACT [MI:0800] xref: MI:0800 is_a: VariO:0238 ! genetic interaction defined by inequality [Term] id: VariO:0240 name: missing protein def: "Variation preventing protein translation because of e. g. initiation codon variation or mRNA surveillance mechanism." [VariO:mv] is_a: VariO:0325 ! protein variation classification created_by: Mauno Vihinen creation_date: 2012-12-11T13:07:02Z [Term] id: VariO:0241 name: RNA translocation def: "A continuous stretch of RNA sequence moved to a new position." [VariO:mv] is_a: VariO:0328 ! RNA variation classification created_by: Mauno Vihinen creation_date: 2012-12-18T16:17:33Z [Term] id: VariO:0242 name: conditional genetic interaction defined by inequality def: "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] synonym: "conditional" EXACT [MI:0798] synonym: "conditional genetic interaction (sensu inequality)" EXACT [MI:0798] xref: MI:0798 is_a: VariO:0238 ! genetic interaction defined by inequality [Term] id: VariO:0243 name: additive genetic interaction defined by inequality def: "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] synonym: "additive" EXACT [MI:0799] synonym: "additive genetic interaction (sensu inequality)" EXACT [MI:0799] xref: MI:0799 is_a: VariO:0238 ! genetic interaction defined by inequality [Term] id: VariO:0244 name: RNA inversion def: "A continuous stretch of RNA sequence inserted to the same position in reverse orientation." [VriO:mv] is_a: VariO:0241 ! RNA translocation created_by: Mauno Vihinen creation_date: 2012-12-18T16:17:33Z [Term] id: VariO:0245 name: missing RNA def: "Variation preventing transcription e. g. because of impaired transcription machinery or variation in the transcription regulation or start site." [VariO:mv] is_a: VariO:0328 ! RNA variation classification created_by: Mauno Vihinen creation_date: 2013-01-04T09:23:09Z [Term] id: VariO:0246 name: artificial protein variation def: "Protein variation generated on purpose." [VariO:mv] is_a: VariO:0024 ! variation emerging at protein level created_by: gerard creation_date: 2013-02-01T11:24:30Z [Term] id: VariO:0247 name: artificial RNA variation def: "RNA variation generated on purpose." [VariO:mv] is_a: VariO:0333 ! RNA variation of non-genetic origin created_by: gerard creation_date: 2013-02-01T11:27:07Z [Term] id: VariO:0248 name: positive genetic interaction def: "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] synonym: "positive gent int" EXACT [MI:0935] xref: MI:0935 is_a: VariO:0237 ! genetic interaction [Term] id: VariO:0249 name: double nonmonotonic genetic interaction defined by inequality def: "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] synonym: "double nonmonotonic" EXACT [MI:0801] synonym: "double nonmonotonic genetic interaction (sensu inequality)" EXACT [MI:0801] xref: MI:0801 is_a: VariO:0238 ! genetic interaction defined by inequality is_a: VariO:0248 ! positive genetic interaction [Term] id: VariO:0250 name: epistatic genetic interaction def: "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] synonym: "epistatis" EXACT [MI:0930] xref: MI:0930 is_a: VariO:0248 ! positive genetic interaction [Term] id: VariO:0251 name: epistatic genetic interaction defined by inequality def: "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] synonym: "epistatic" EXACT [MI:0797] synonym: "epistatic genetic interaction (sensu inequality)" EXACT [MI:0797] xref: MI:0797 is_a: VariO:0238 ! genetic interaction defined by inequality is_a: VariO:0250 ! epistatic genetic interaction [Term] id: VariO:0252 name: asynthetic genetic interaction defined by inequality def: "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] synonym: "asynthetic" EXACT [MI:0795] synonym: "asynthetic genetic interaction (sensu inequality)" EXACT [MI:0795] xref: MI:0795 is_a: VariO:0238 ! genetic interaction defined by inequality is_a: VariO:0250 ! epistatic genetic interaction [Term] id: VariO:0253 name: suppressive genetic interaction defined by inequality def: "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] synonym: "suppression" EXACT [MI:0796] synonym: "suppressive genetic interaction (sensu inequality)" EXACT [MI:0796] xref: MI:0796 is_a: VariO:0238 ! genetic interaction defined by inequality is_a: VariO:0250 ! epistatic genetic interaction [Term] id: VariO:0254 name: neutral genetic interaction def: "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] synonym: "neutral gent int" EXACT [MI:0934] xref: MI:0934 is_a: VariO:0237 ! genetic interaction [Term] id: VariO:0255 name: noninteractive genetic interaction defined by inequality def: "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] synonym: "noninteractive" EXACT [MI:0932] synonym: "noninteractive genetic interaction (sensu inequality)" EXACT [MI:0932] xref: MI:0932 is_a: VariO:0238 ! genetic interaction defined by inequality is_a: VariO:0254 ! neutral genetic interaction [Term] id: VariO:0256 name: negative genetic interaction def: "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] synonym: "negative gen int" EXACT [MI:0933] xref: MI:0933 is_a: VariO:0237 ! genetic interaction [Term] id: VariO:0257 name: synthetic genetic interaction defined by inequality def: "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] synonym: "synthetic" EXACT [MI:0794] synonym: "synthetic genetic interaction (sensu inequality)" EXACT [MI:0794] xref: MI:0794 is_a: VariO:0238 ! genetic interaction defined by inequality is_a: VariO:0256 ! negative genetic interaction [Term] id: VariO:0258 name: structural level of interaction def: "Molecular structural level of interaction." [VariO:mv] is_a: VariO:0236 ! interaction [Term] id: VariO:0259 name: intermolecular interaction def: "Interaction between molecules." [VariO:mv] is_a: VariO:0258 ! structural level of interaction [Term] id: VariO:0260 name: intramolecular interaction def: "Interaction within a molecule." [VariO:mv] is_a: VariO:0258 ! structural level of interaction [Term] id: VariO:0261 name: colocalization def: "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] xref: MI:0403 is_a: VariO:0236 ! interaction [Term] id: VariO:0262 name: interactor def: "Entity participating in a physical or functional interaction." [SBO:0000336] xref: SBO:0000336 is_a: VariO:0236 ! interaction [Term] id: VariO:0263 name: small molecule def: "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] xref: MI:0328 is_a: VariO:0262 ! interactor [Term] id: VariO:0264 name: metal def: "Metal atom." [CHEBI:33521] xref: CHEBI:33521 is_a: VariO:0263 ! small molecule [Term] id: VariO:0265 name: solvent def: "A liquid that can dissolve other substances (solutes) without any change in their chemical composition." [CHEBI:46787] xref: CHEBI:46787 is_a: VariO:0263 ! small molecule [Term] id: VariO:0266 name: water def: "An inorganic hydroxy compound that has formula H2O." [CHEBI:15377] xref: CHEBI:15377 is_a: VariO:0265 ! solvent [Term] id: VariO:0267 name: complex def: "Set of interacting molecules that can be copurified." [PMID:14755292] xref: MI:0314 is_a: VariO:0262 ! interactor [Term] id: VariO:0268 name: ribonucleoprotein complex def: "A macromolecular complex containing both protein and RNA molecules." [PMID:14755292] synonym: "ribonucleoprot compl" EXACT [MI:0316] xref: MI:0316 is_a: VariO:0267 ! complex [Term] id: VariO:0269 name: protein complex def: "A stable set of interacting proteins that can be copurified and operate as a functional unit." [PMID:14755292] synonym: "protein-protein complex" EXACT [GO:0043234] xref: GO:0043234 xref: MI:0315 is_a: VariO:0267 ! complex [Term] id: VariO:0270 name: protein dna complex def: "A stable set of interacting protein and DNA that can be copurified and operate as a functional unit." [PMID:14755292] xref: MI:0233 is_a: VariO:0267 ! complex [Term] id: VariO:0271 name: unknown participant def: "Any type of molecule, including complexes, that may be observed but not identified." [PMID:14755292] xref: MI:0329 is_a: VariO:0262 ! interactor [Term] id: VariO:0272 name: gene def: "Interactor of genetic interaction." [MI:0000704] xref: MI:0250 is_a: VariO:0262 ! interactor [Term] id: VariO:0273 name: biopolymer def: "Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds." [PMID:14577292] xref: MI:0383 is_a: VariO:0262 ! interactor [Term] id: VariO:0274 name: nucleic acid def: "Linear polymer of nucleotides, linked by 3',5' phosphodiester linkages." [PMID:14755292] xref: GO:0005561 xref: MI:0318 is_a: VariO:0273 ! biopolymer [Term] id: VariO:0275 name: peptide def: "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] synonym: "oligopeptide" EXACT [MI:0327] synonym: "polypeptide" EXACT [MI:0327] xref: MI:0327 is_a: VariO:0273 ! biopolymer [Term] id: VariO:0276 name: polysaccharide def: "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] xref: MI:0904 is_a: VariO:0273 ! biopolymer [Term] id: VariO:0277 name: protein def: "A linear polymer of amino acids joined by peptide bonds in a specific sequence." [PMID:14755292] xref: GO:0003675 xref: MI:0326 is_a: VariO:0273 ! biopolymer [Term] id: VariO:0278 name: association def: "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] xref: MI:0914 is_a: VariO:0236 ! interaction [Term] id: VariO:0279 name: interaction physical force def: "Interaction physical force." [VariO:mv] is_a: VariO:0236 ! interaction [Term] id: VariO:0280 name: covalent bond def: "A chemical link between two atoms in which electrons are shared between them." [http://chemistry.about.com/od/chemistryglossary/a/covalentbonddef.htm] is_a: VariO:0279 ! interaction physical force [Term] id: VariO:0281 name: disulphide bridge def: "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] xref: SO:0001088 is_a: VariO:0280 ! covalent bond [Term] id: VariO:0282 name: non covalent bond def: "Interaction between biochemical entities that results in the formation of a non-covalent bond." [VariO:mv] xref: SBO:0000177 is_a: VariO:0279 ! interaction physical force [Term] id: VariO:0283 name: hydrogen bond def: "Attractive interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom." [VariO:mv] synonym: "H-bond" RELATED [FIX:0000503] xref: FIX:0000503 xref: http://chemistry.about.com/od/chemistryglossary/g/hbond.htm is_a: VariO:0282 ! non covalent bond [Term] id: VariO:0284 name: hydrogen bond network def: "Network of interactions formed by several hydrogen bonds." [VariO:mv] is_a: VariO:0283 ! hydrogen bond [Term] id: VariO:0285 name: hydrophobic interaction def: "Interaction of nonpolar (un-ionizable) hydrocarbon molecules forced together because of stronger water-water interaction." [http://medical-dictionary.thefreedictionary.com/Hydrophobic+Interaction] is_a: VariO:0282 ! non covalent bond [Term] id: VariO:0286 name: salt bridge def: "Interaction between charged groups." [VariO:mv] is_a: VariO:0282 ! non covalent bond [Term] id: VariO:0287 name: van der Waals interaction def: "Weak attractive electrical force between neutral groups or molecules." [VariO:mv] xref: FIX:0000506 is_a: VariO:0282 ! non covalent bond [Term] id: VariO:0288 name: electrostatic interaction def: "Attraction between two electrically charged groups or molecules." [VariO:mv] is_a: VariO:0282 ! non covalent bond [Term] id: VariO:0289 name: quantity change def: "Quantity attribute." [VariO:mv] is_a: VariO:0232 ! variation attribute [Term] id: VariO:0290 name: decreased def: "The observed feature is decreased compared to that in the wild type (slower, weaker, lower, smaller, etc.)." [SGD:curators] xref: APO:0000003 is_a: VariO:0289 ! quantity change [Term] id: VariO:0291 name: increased def: "The observed feature is increased compared to that in the wild type (faster, stronger, higher, larger, etc.)." [SGD:curators] xref: APO:0000004 is_a: VariO:0289 ! quantity change [Term] id: VariO:0292 name: missing def: "The observed feature is missing compared to that in the wild type." [VariO:mv] is_a: VariO:0289 ! quantity change [Term] id: VariO:0293 name: pathogenicity association def: "Pathogenicity attribute." [VariO:mv] is_a: VariO:0232 ! variation attribute [Term] id: VariO:0294 name: disease causing def: "Variation is causative of disease." [VariO:mv] is_a: VariO:0293 ! pathogenicity association [Term] id: VariO:0295 name: not related to clinical phenotype def: "Variation is not related to clinical phenotype." [VariO:mv] is_a: VariO:0293 ! pathogenicity association [Term] id: VariO:0296 name: disease associated def: "Variation is disease related." [VariO:mv] is_a: VariO:0293 ! pathogenicity association [Term] id: VariO:0297 name: variation affecting RNA def: "Effects of a variation on RNA level." [VariO:mv] is_a: VariO:0001 ! variation [Term] id: VariO:0298 name: variation affecting RNA property def: "Variation affecting characteristic property of RNA." [VariO:mv] is_a: VariO:0297 ! variation affecting RNA [Term] id: VariO:0299 name: effect on RNA degradation def: "Variation affecting degradation of RNA." [VariO:mv] is_a: VariO:0298 ! variation affecting RNA property [Term] id: VariO:0300 name: effect on RNA folding def: "Variation affecting folding of RNA." [VariO:mv] is_a: VariO:0298 ! variation affecting RNA property [Term] id: VariO:0301 name: effect on RNA stability def: "Variation affecting stability of transcript." [VariO:mv] xref: SO:0001546 is_a: VariO:0298 ! variation affecting RNA property [Term] id: VariO:0302 name: conservation of RNA variation site def: "Conservation of the variation site in related RNA sequences." [VariO:mv] is_a: VariO:0298 ! variation affecting RNA property [Term] id: VariO:0303 name: polysomy def: "An excess of a particular chromosome in a cell or organism." [VariO:mv] is_a: VariO:0206 ! chromosome number variation created_by: gerard creation_date: 2013-02-01T11:30:39Z [Term] id: VariO:0304 name: association of RNA variation to pathogenicity def: "Implication of an RNA variant to pathogenicity." [VariO:mv] is_a: VariO:0298 ! variation affecting RNA property [Term] id: VariO:0305 name: effect on RNA interaction def: "Variation affecting interaction of RNA with its partner." [VariO:mv] is_a: VariO:0298 ! variation affecting RNA property [Term] id: VariO:0306 name: RNA variation type def: "Type of RNA variation. Describes origin and classification of a variant." [VariO:mv] is_a: VariO:0297 ! variation affecting RNA [Term] id: VariO:0307 name: RNA variation of genetic origin def: "RNA variation that has genetic origin." [VariO:mv] is_a: VariO:0324 ! RNA variation origin [Term] id: VariO:0308 name: missense variation def: "Nucleotide change in the mRNA triplet codon codes for another amino acid." [VariO:mv] is_a: VariO:0312 ! RNA substitution [Term] id: VariO:0309 name: termination codon change def: "RNA nucleotide change in termination codon." [VariO:mv] xref: SO:0001590 is_a: VariO:0328 ! RNA variation classification [Term] id: VariO:0310 name: nonsense variation def: "Nucleotide change in the mRNA codon triplet creates a terminator codon." [VariO:mv] is_a: VariO:0312 ! RNA substitution [Term] id: VariO:0311 name: RNA indel def: "A complex RNA variation consisting of both nucleotide insertion(s) and deletion(s)." [VariO:mv] is_a: VariO:0328 ! RNA variation classification [Term] id: VariO:0312 name: RNA substitution def: "Substitution of RNA nucleotide." [VariO:mv] is_a: VariO:0328 ! RNA variation classification [Term] id: VariO:0313 name: transition def: "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] is_a: VariO:0136 ! DNA substitution is_a: VariO:0312 ! RNA substitution relationship: owl:topObjectProperty VariO:0312 ! RNA substitution relationship: part_of VariO:0136 ! DNA substitution [Term] id: VariO:0314 name: pyrimidine transition def: "A substitution of a pyrimidine, C or T (or U), for another pyrimidine." [VariO:mv] is_a: VariO:0313 ! transition [Term] id: VariO:0315 name: purine transition def: "A substitution of a purine, A or G, for another purine." [VariO:mv] is_a: VariO:0313 ! transition [Term] id: VariO:0316 name: transversion def: "Change of a pyrimidine nucleotide, C or T (or U), into a purine nucleotide, A or G, or vice versa." [VariO:mv] xref: http://en.wikipedia.org/wiki/Transversion "wiki" is_a: VariO:0136 ! DNA substitution is_a: VariO:0312 ! RNA substitution relationship: part_of VariO:0136 ! DNA substitution relationship: part_of VariO:0312 ! RNA substitution [Term] id: VariO:0317 name: initiation codon change def: "RNA nucleotide change in the initiation codon." [VariO:mv] xref: SO:0001582 is_a: VariO:0328 ! RNA variation classification [Term] id: VariO:0318 name: silent variation def: "RNA variation that does not change the encoded amino acid." [VariO:mv] is_a: VariO:0312 ! RNA substitution [Term] id: VariO:0319 name: RNA deletion def: "One or more continuous nucleotides are missing from RNA sequence." [VariO:mv] is_a: VariO:0328 ! RNA variation classification [Term] id: VariO:0320 name: in-frame deletion def: "Deletion of nucleotides in multiples of three so that the mRNA coding sequence frame is retained." [VariO:mv] is_a: VariO:0319 ! RNA deletion [Term] id: VariO:0321 name: out-of-frame deletion def: "Deletion of nucleotide(s) causing alteration of mRNA coding sequence frame." [VariO:mv] is_a: VariO:0319 ! RNA deletion [Term] id: VariO:0322 name: DNA variation classification def: "Classification of DNA variation." [VariO:mv] is_a: VariO:0129 ! DNA variation type created_by: Mauno Vihinen creation_date: 2013-10-11T08:46:32Z [Term] id: VariO:0323 name: protein variation origin def: "Origin of protein variation." [VariO:mv] is_a: VariO:0012 ! protein variation type created_by: Mauno Vihinen creation_date: 2013-10-11T08:53:23Z [Term] id: VariO:0324 name: RNA variation origin def: "Origin of RNA variation." [VariO:mv] is_a: VariO:0306 ! RNA variation type creation_date: 2013-10-11T09:04:23Z [Term] id: VariO:0325 name: protein variation classification def: "Classification of protein variation." [VariO:mv] is_a: VariO:0012 ! protein variation type created_by: Mauno Vihinen creation_date: 2013-10-11T08:59:04Z [Term] id: VariO:0326 name: RNA insertion def: "Addition of one or more nucleotides between adjacent nucleotides in RNA sequence." [VariO:mv] is_a: VariO:0328 ! RNA variation classification [Term] id: VariO:0327 name: out-of-frame insertion def: "Insertion of nucleotide(s) causing alteration of mRNA reading frame." [VariO:mv] is_a: VariO:0326 ! RNA insertion [Term] id: VariO:0328 name: RNA variation classification def: "Classification of RNA variation." [VariO:mv] is_a: VariO:0306 ! RNA variation type created_by: Mauno Vihinen creation_date: 2013-10-11T09:05:02Z [Term] id: VariO:0329 name: alternative RNA form def: "RNA variation due to defective fidelity of transcription." [VariO:mv] is_a: VariO:0333 ! RNA variation of non-genetic origin creation_date: 2014-10-23T00:29:53Z [Term] id: VariO:0330 name: mistranslated protein def: "Protein variation due to defective fidelity of translation." [VariO:mv] is_a: VariO:0024 ! variation emerging at protein level created_by: Mauno Vihinen creation_date: 2014-10-23T00:31:56Z [Term] id: VariO:0331 name: alternative form of mRNA def: "Alternative form of mRNA molecule." [VariO:mv] is_a: VariO:0351 ! protein coding RNA created_by: med-mnv creation_date: 2018-04-26T14:47:12Z [Term] id: VariO:0332 name: in-frame insertion def: "Insertion of nucleotides in multiples of three so that the reading frame is retained." [VariO:mv] is_a: VariO:0326 ! RNA insertion [Term] id: VariO:0333 name: RNA variation of non-genetic origin def: "RNA variation that does not have genetic origin being modified at RNA level." [VariO:mv] is_a: VariO:0324 ! RNA variation origin [Term] id: VariO:0334 name: RNA splicing change def: "Change to RNA splicing." [VariO:mv] is_a: VariO:0328 ! RNA variation classification [Term] id: VariO:0335 name: decayed RNA def: "RNA molecule destroyed due to appearance of a premature termination codon." [VariO:mv] is_a: VariO:0333 ! RNA variation of non-genetic origin [Term] id: VariO:0336 name: modified RNA def: "Post transcriptionally modified RNA." [VariO:mv] is_a: VariO:0333 ! RNA variation of non-genetic origin [Term] id: VariO:0337 name: modified DNA def: "DNA variation due to biological, chemical, physical or other modification." [VariO:mv] is_a: VariO:0146 ! DNA variation of non-genetic origin created_by: Mauno Vihinen creation_date: 2014-10-23T00:42:47Z [Term] id: VariO:0338 name: variation affecting RNA structure def: "Variation affecting structure of RNA." [VariO:mv] is_a: VariO:0297 ! variation affecting RNA [Term] id: VariO:0343 name: synonymous variation def: "mRNA variation not affecting the sequence of the translated protein." [VariO:mv] is_a: VariO:0232 ! variation attribute created_by: med-mnv creation_date: 2015-06-04T13:23:24Z [Term] id: VariO:0349 name: affected RNA type def: "Affected type of RNA." [VariO:mv] is_a: VariO:0338 ! variation affecting RNA structure [Term] id: VariO:0350 name: non-protein coding RNA def: "Variation affecting RNA not coding for protein." [VariO:mv] synonym: "ncRNA" EXACT [] synonym: "non-coding RNA\nncRNA" EXACT [] is_a: VariO:0349 ! affected RNA type [Term] id: VariO:0351 name: protein coding RNA def: "RNA coding for protein." [VariO:mv] is_a: VariO:0349 ! affected RNA type [Term] id: VariO:0352 name: coding region of mRNA def: "Variation affecting region coding for protein in protein coding RNA." [VariO:mv] is_a: VariO:0351 ! protein coding RNA [Term] id: VariO:0353 name: non-coding region of mRNA def: "Variation affecting region not coding for protein in protein coding mRNA." [VariO:mv] is_a: VariO:0350 ! non-protein coding RNA [Term] id: VariO:0354 name: effect on post transcriptional RNA modification def: "Variation affecting post transcriptional RNA modification." [VariO:mv] is_a: VariO:0338 ! variation affecting RNA structure [Term] id: VariO:0356 name: alternatively polyadenylated mRNA def: "Polyadenylation of mRNA molecule at alternative site." [VariO:mv] is_a: VariO:0331 ! alternative form of mRNA [Term] id: VariO:0361 name: RNA sugar variation def: "Post transcriptional modification of RNA nucleoside sugar." [VariO:mv] is_a: VariO:0338 ! variation affecting RNA structure [Term] id: VariO:0362 name: effect on RNA splicing def: "Effect to process where introns in mRNA are cut away from exons." [VariO:mv] xref: SO:0001568 is_a: VariO:0354 ! effect on post transcriptional RNA modification [Term] id: VariO:0363 name: effect on RNA localization def: "Variation affecting cellular localization of RNA." [VariO:mv] is_a: VariO:0298 ! variation affecting RNA property created_by: med-mnv creation_date: 2018-05-07T11:20:14Z [Term] id: VariO:0364 name: effect on RNA aggregation def: "Variation affecting aggregation tendency of RNA." [VariO:mv] is_a: VariO:0298 ! variation affecting RNA property created_by: med-mnv creation_date: 2018-05-07T11:20:14Z [Term] id: VariO:0365 name: effect on cis splicing def: "Intronic splicing within an RNA molecule." [VariO:mv] is_a: VariO:0362 ! effect on RNA splicing [Term] id: VariO:0366 name: variation at recursive splice site def: "Variation affecting splicing at recursive splice site which subdivides a large intron." [VariO:mv] is_a: VariO:0508 ! affected splice site [Term] id: VariO:0367 name: variation at five prime splice site def: "Variation affecting intronic region bordering exon or retained RNA region, at the five prime end of the intron." [VariO:mv] is_a: VariO:0508 ! affected splice site [Term] id: VariO:0368 name: variation at canonical five prime splice site def: "Variation affecting canonical prime splice site at five prime end." [VariO:mv] is_a: VariO:0367 ! variation at five prime splice site [Term] id: VariO:0369 name: variation at non canonical five prime splice site def: "Variation affecting non canonical splice site at five prime end." [VariO:mv] is_a: VariO:0367 ! variation at five prime splice site [Term] id: VariO:0370 name: variation at three prime splice site def: "Variation affecting intronic region bordering the exon or retained RNA region, at the 3' edge of the intron." [VariO:mv] is_a: VariO:0508 ! affected splice site [Term] id: VariO:0371 name: variation at non canonical three prime splice site def: "Variation affecting non canonical splice site at three prime end." [VariO:mv] is_a: VariO:0370 ! variation at three prime splice site [Term] id: VariO:0372 name: variation at canonical three prime splice site def: "Variation affecting canonical splice site at three prime end." [VariO:mv] is_a: VariO:0370 ! variation at three prime splice site [Term] id: VariO:0373 name: cryptic splice site activation def: "Activation of new splice site." [VariO:mv] xref: SO:0001569 is_a: VariO:0504 ! inclusion of cryptic exon [Term] id: VariO:0374 name: cryptic splice donor activation def: "Activation of new splice donor site." [VariO:mv] xref: SO:0001571 is_a: VariO:0373 ! cryptic splice site activation [Term] id: VariO:0375 name: cryptic splice acceptor activation def: "Activation of new splice acceptor site." [VariO:mv] xref: SO:0001570 is_a: VariO:0373 ! cryptic splice site activation [Term] id: VariO:0376 name: effect on trans splicing def: "Variation affecting splicing and ligation different RNA molecules." [VariO:mv] is_a: VariO:0362 ! effect on RNA splicing [Term] id: VariO:0377 name: retrotransposon insertion def: "Insertion of retrotransposon into chromosome. Retrotransposon is transcribed from DNA to RNA, and then reverse transcribed to DNA." [VariO:mv] is_a: VariO:0192 ! DNA mobile genetic element insertion created_by: med-mnv creation_date: 2015-08-26T12:50:29Z [Term] id: VariO:0378 name: DNA transposon def: "Insertion of a DNA transposable element into chromosome." [VariO:mv] is_a: VariO:0192 ! DNA mobile genetic element insertion created_by: med-mnv creation_date: 2015-08-26T12:50:29Z [Term] id: VariO:0379 name: LINE def: "Long interspersed nuclear element generated by retrotransposition." [VariO:mv] is_a: VariO:0377 ! retrotransposon insertion created_by: med-mnv creation_date: 2015-08-26T12:51:03Z [Term] id: VariO:0380 name: SINE def: "Short interspersed nuclear element generated by retrotransposition. Length below 500 bp." [VariO:mv] is_a: VariO:0377 ! retrotransposon insertion created_by: med-mnv creation_date: 2015-08-26T12:51:03Z [Term] id: VariO:0381 name: effect on RNA double helix def: "Variation affecting RNA double helix." [VariO:mv] is_a: VariO:0137 ! effect on RNA tertiary structure created_by: med-mnv creation_date: 2018-05-07T11:22:31Z [Term] id: VariO:0382 name: effect on RNA secondary structure def: "Variation affecting RNA secondary structure." [VariO:mv] is_a: VariO:0338 ! variation affecting RNA structure [Term] id: VariO:0383 name: effect on RNA multiloop def: "Variation affecting closed RNA structure in which at least two double stranded regions meet." [VariO:mv] is_a: VariO:0382 ! effect on RNA secondary structure [Term] id: VariO:0384 name: effect on RNA bulge def: "Variation affecting RNA structure in which nucleotides in one strand do not form base pairs." [VariO:mv] is_a: VariO:0382 ! effect on RNA secondary structure [Term] id: VariO:0385 name: effect on RNA interior loop def: "Variation affecting RNA structure in which both the strands do not form base pairs." [VariO:mv] is_a: VariO:0382 ! effect on RNA secondary structure [Term] id: VariO:0386 name: effect on RNA stem def: "Variation effecting hydrogen bonding in contiguous nested base pairs in RNA." [VariO:mv] is_a: VariO:0382 ! effect on RNA secondary structure [Term] id: VariO:0387 name: effect on RNA hairpin loop def: "Variation affecting loop connecting adjacent regions forming helix in RNA." [VariO:mv] is_a: VariO:0382 ! effect on RNA secondary structure [Term] id: VariO:0388 name: LTR def: "Retrotransposon that has long terminal repeat sequences. Sizes from about 100 bp to over 5 kb." [VariO:mv] is_a: VariO:0377 ! retrotransposon insertion created_by: med-mnv creation_date: 2015-08-26T12:51:03Z [Term] id: VariO:0389 name: pentanucleotide expansion def: "Tandem repetitive sequence consisting of five nucleotide units." [VariO:mv] is_a: VariO:0188 ! microsatellite created_by: med-mnv creation_date: 2015-09-17T10:55:04Z [Term] id: VariO:0390 name: effect on DNA double helix def: "Variation affecting DNA double helical structure." [VariO:mv] is_a: VariO:0167 ! effect on DNA form created_by: med-mnv creation_date: 2017-01-16T12:53:57Z [Term] id: VariO:0391 name: plasmid affected def: "Variation effect on independently replicating small DNA molecule." [VariO:mv] is_a: VariO:0072 ! extrachromosomal DNA affected created_by: med-mnv creation_date: 2015-09-18T20:15:22Z [Term] id: VariO:0392 name: insertion sequence def: "Simple, relatively short transposable element. IS elements contain only transposition related genes." [VariO:mv] is_a: VariO:0192 ! DNA mobile genetic element insertion created_by: med-mnv creation_date: 2015-09-18T20:28:19Z [Term] id: VariO:0393 name: epigenetic RNA variation def: "RNA variation of epigenetic origin." [VariO:mv] is_a: VariO:0333 ! RNA variation of non-genetic origin created_by: med-mnv creation_date: 2018-05-07T11:43:50Z [Term] id: VariO:0394 name: effect on DNA cruciform def: "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] is_a: VariO:0420 ! effect on four-stranded DNA created_by: med-mnv creation_date: 2015-09-18T20:44:08Z [Term] id: VariO:0396 name: variation affecting RNA function def: "Variation having effect on RNA function and usage." [VariO:mv] is_a: VariO:0297 ! variation affecting RNA [Term] id: VariO:0397 name: effect on RNA splicing function def: "Variation affecting splicing function of RNA." [VariO:mv] is_a: VariO:0396 ! variation affecting RNA function [Term] id: VariO:0398 name: effect on catalytic RNA activity def: "Variation affecting catalytic function of RNA." [VariO:mv] is_a: VariO:0396 ! variation affecting RNA function [Term] id: VariO:0399 name: effect on translation def: "Variation affecting translation of protein." [VariO:mv] is_a: VariO:0396 ! variation affecting RNA function [Term] id: VariO:0400 name: effect on regulatory function of RNA def: "Variation affecting regulatory function of RNA." [VariO:mv] is_a: VariO:0396 ! variation affecting RNA function [Term] id: VariO:0401 name: effect on amino acid transfer of RNA def: "Variation affecting RNA function in amino acid transfer." [VariO:mv] is_a: VariO:0396 ! variation affecting RNA function [Term] id: VariO:0402 name: effect on RNA information transfer def: "Variation affecting information transfer by RNA." [VariO:mv] is_a: VariO:0396 ! variation affecting RNA function [Term] id: VariO:0403 name: group I intron def: "Transposable element coding for self-splicing ribozyme when transcribed. Splicing is initiated by nucleophilic attack of an exogenous GTP or guanosine." [VariO:mv] is_a: VariO:0472 ! self-splicing intron created_by: med-mnv creation_date: 2015-09-21T10:06:37Z [Term] id: VariO:0404 name: group II intron def: "Transposable element coding for a self-splicing ribozyme when transcribed. Intron excision does not require GTP." [VariO:mv] is_a: VariO:0472 ! self-splicing intron created_by: med-mnv creation_date: 2015-09-21T10:06:37Z [Term] id: VariO:0405 name: dicentric translocation def: "Fusion of two chromosome segments both containing a centromere." [VariO:mv] is_a: VariO:0202 ! interchromosomal translocation created_by: med-mnv creation_date: 2015-09-22T19:15:03Z [Term] id: VariO:0407 name: edited DNA def: "Variation generated by chromosome editing." [VariO:mv] is_a: VariO:0146 ! DNA variation of non-genetic origin created_by: med-mnv creation_date: 2015-09-22T19:20:45Z [Term] id: VariO:0408 name: RNA chimera def: "Fusion transcript of exons from two or more genes." [VariO:mv] is_a: VariO:0333 ! RNA variation of non-genetic origin created_by: med-mnv creation_date: 2015-09-24T13:21:02Z [Term] id: VariO:0409 name: frameshifted RNA def: "Transcript with -1 or +1 frameshift due to slipping back or skipping a nucleotide on a ribosome." [VariO:mv] is_a: VariO:0333 ! RNA variation of non-genetic origin created_by: med-mnv creation_date: 2015-09-24T13:21:02Z [Term] id: VariO:0410 name: effect on single stranded DNA structure def: "Variation affecting single stranded DNA structure." [VariO:mv] is_a: VariO:0167 ! effect on DNA form created_by: med-mnv creation_date: 2018-11-08T10:04:23Z [Term] id: VariO:0411 name: alternatively spliced RNA def: "mRNA molecule matured by splicing at an alternative site." [VariO:mv] is_a: VariO:0331 ! alternative form of mRNA created_by: med-mnv creation_date: 2015-10-13T19:36:23Z [Term] id: VariO:0412 name: effect on catalytic DNA activity def: "Variation affecting catalytic function of DNA." [VariO:mv] is_a: VariO:0148 ! variation affecting DNA function created_by: med-mnv creation_date: 2016-11-29T11:11:11Z [Term] id: VariO:0413 name: effect on A DNA def: "Variation affecting A form of right-handed DNA." [VariO:mv] is_a: VariO:0390 ! effect on DNA double helix created_by: med-mnv creation_date: 2017-01-16T12:55:40Z [Term] id: VariO:0414 name: effect on B DNA def: "Variation affecting B form of right-handed DNA." [VariO:mv] is_a: VariO:0390 ! effect on DNA double helix created_by: med-mnv creation_date: 2017-01-16T12:55:40Z [Term] id: VariO:0415 name: effect on C DNA def: "Variation affecting C form of right-handed DNA." [VariO:mv] is_a: VariO:0390 ! effect on DNA double helix created_by: med-mnv creation_date: 2017-01-16T12:55:40Z [Term] id: VariO:0416 name: effect on L DNA def: "Variation affecting L form of right-handed DNA." [VariO:mv] is_a: VariO:0390 ! effect on DNA double helix created_by: med-mnv creation_date: 2017-01-16T12:55:40Z [Term] id: VariO:0417 name: effect on S DNA def: "Variation affecting S form of right-handed DNA." [VariO:mv] is_a: VariO:0390 ! effect on DNA double helix created_by: med-mnv creation_date: 2017-01-16T12:55:40Z [Term] id: VariO:0418 name: effect on D DNA def: "Variation affecting D form of right-handed DNA." [VariO:mv] is_a: VariO:0390 ! effect on DNA double helix created_by: med-mnv creation_date: 2017-01-16T13:10:01Z [Term] id: VariO:0419 name: effect on H DNA def: "Variation affecting H form of intramolecular triple helical DNA." [VariO:mv] is_a: VariO:0422 ! effect on intramolecular DNA triple helix created_by: med-mnv creation_date: 2017-01-16T13:14:56Z [Term] id: VariO:0420 name: effect on four-stranded DNA def: "Variation affecting four-stranded DNA." [VariO:mv] is_a: VariO:0167 ! effect on DNA form created_by: med-mnv creation_date: 2017-01-16T13:17:51Z [Term] id: VariO:0421 name: effect on Z DNA def: "Variation affecting Z form of left-handed DNA." [VariO:mv] is_a: VariO:0390 ! effect on DNA double helix created_by: med-mnv creation_date: 2017-01-16T13:20:36Z [Term] id: VariO:0422 name: effect on intramolecular DNA triple helix def: "Variation affecting triple helical DNA structure where the third strand is provided by one of the strands forming the duplex." [VariO:mv] is_a: VariO:0175 ! effect on DNA triple helix created_by: med-mnv creation_date: 2017-01-16T13:22:35Z [Term] id: VariO:0423 name: effect on intermolecular DNA triple helix def: "Variation affecting triple helical DNA structure where the third strand is from a second DNA molecule." [VariO:mv] is_a: VariO:0175 ! effect on DNA triple helix created_by: med-mnv creation_date: 2017-01-16T13:24:18Z [Term] id: VariO:0424 name: effect on DNA-RNA hybrid def: "Variation affecting DNA-RNA hybrid." [VariO:mv] is_a: VariO:0137 ! effect on RNA tertiary structure is_a: VariO:0167 ! effect on DNA form created_by: med-mnv creation_date: 2017-01-16T13:29:46Z [Term] id: VariO:0425 name: effect on RNA triple helix def: "Variation affecting RNA helix formed of three strands." [VariO:mv] is_a: VariO:0137 ! effect on RNA tertiary structure created_by: med-mnv creation_date: 2017-01-16T13:48:49Z [Term] id: VariO:0426 name: effect on four-stranded RNA def: "Variation affecting four-stranded RNA." [VariO:mv] is_a: VariO:0137 ! effect on RNA tertiary structure created_by: med-mnv creation_date: 2017-01-16T13:48:49Z [Term] id: VariO:0427 name: type of chromosomal amplification def: "Classification of chromosomal amplification type." [VariO:mv] is_a: VariO:0183 ! chromosomal amplification created_by: med-mnv creation_date: 2017-01-17T09:34:30Z [Term] id: VariO:0428 name: genome variation def: "Variation affecting genome." [VariO:mv] is_a: VariO:0155 ! variation affecting DNA structure created_by: med-mnv creation_date: 2017-01-23T09:01:36Z [Term] id: VariO:0429 name: complex genomic variation def: "Chromosome structure variation due to several breakpoints." [VariO:mv] is_a: VariO:0428 ! genome variation created_by: med-mnv creation_date: 2017-01-23T09:03:57Z [Term] id: VariO:0430 name: nucleotide expansion def: "Repetitive sequence consisting of one more nucleotide units." [VariO:mv] is_a: VariO:0183 ! chromosomal amplification created_by: med-mnv creation_date: 2017-01-23T09:09:22Z [Term] id: VariO:0431 name: effect on R loop def: "Effect on DNA-RNA R loop structure of short RNA-DNA hybrid and the displaced single stranded DNA." [VariO:mv] is_a: VariO:0424 ! effect on DNA-RNA hybrid created_by: med-mnv creation_date: 2017-01-23T09:32:22Z [Term] id: VariO:0432 name: effect on T loop def: "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] is_a: VariO:0390 ! effect on DNA double helix created_by: med-mnv creation_date: 2017-01-23T09:34:30Z [Term] id: VariO:0433 name: effect on D loop def: "Effect on DNA displacement loop where two double-stranded DNA molecules are separated locally by a third strand of DNA or RNA." [VariO:mv] is_a: VariO:0423 ! effect on intermolecular DNA triple helix relationship: part_of VariO:0423 ! effect on intermolecular DNA triple helix relationship: part_of VariO:0424 ! effect on DNA-RNA hybrid created_by: med-mnv creation_date: 2017-01-23T09:45:49Z [Term] id: VariO:0434 name: DNA sugar variation def: "Replacement of the deoxyribonucleoside monophosphate by ribonucleoside monophosphate in the DNA backbone." [VariO:mv] is_a: VariO:0155 ! variation affecting DNA structure created_by: med-mnv creation_date: 2017-03-23T10:54:09Z [Term] id: VariO:0435 name: effect on protein reaction kinetics def: "Effect of variation to protein reaction kinetics." [VariO:mv] is_a: VariO:0053 ! effect on protein activity created_by: med-mnv creation_date: 2017-04-28T14:52:51Z [Term] id: VariO:0436 name: mature RNA def: "Completely processed RNA molecule." [VariO:mv] is_a: VariO:0336 ! modified RNA created_by: med-mnv creation_date: 2017-04-28T14:58:30Z [Term] id: VariO:0437 name: alternatively initiated mRNA def: "RNA variation causing alternative translation initiation." [VariO:mv] is_a: VariO:0331 ! alternative form of mRNA created_by: med-mnv creation_date: 2017-04-28T16:01:26Z [Term] id: VariO:0438 name: epigenetic RNA modification def: "Epigenetic modification of RNA." [VariO:mv] is_a: VariO:0338 ! variation affecting RNA structure created_by: med-mnv creation_date: 2018-05-07T14:40:53Z [Term] id: VariO:0439 name: effect on RNA activity def: "Effect of variation on RNA activity." [VariO:mv] is_a: VariO:0298 ! variation affecting RNA property created_by: med-mnv creation_date: 2017-04-28T16:23:47Z [Term] id: VariO:0440 name: effect on RNA reaction kinetics def: "Effect of variation on RNA reaction kinetics." [VariO:mv] is_a: VariO:0439 ! effect on RNA activity created_by: med-mnv creation_date: 2017-04-28T16:26:01Z [Term] id: VariO:0441 name: effect on RNA affinity def: "Effect of variation on RNA affinity to binding molecule(s)." [VariO:mv] is_a: VariO:0439 ! effect on RNA activity created_by: med-mnv creation_date: 2017-04-28T16:26:01Z [Term] id: VariO:0442 name: effect on RNA specificity def: "Effect of variation on substrate binding specificity of RNA." [VariO:mv] is_a: VariO:0439 ! effect on RNA activity created_by: med-mnv creation_date: 2017-04-28T16:26:01Z [Term] id: VariO:0443 name: alternatively initiated protein def: "Protein variant originating from alternative translation initiation." [VariO:mv] is_a: VariO:0024 ! variation emerging at protein level created_by: med-mnv creation_date: 2017-05-03T09:09:05Z [Term] id: VariO:0444 name: de novo variation def: "Variation that has emerged in a germ cell on one of the parents or in the fertilized egg during early embryogenesis." [VariO:mv] is_a: VariO:0130 ! DNA variation of genetic origin created_by: med-mnv creation_date: 2018-01-08T11:31:50Z [Term] id: VariO:0445 name: germinal variation def: "Variation that has been inherited from a germline cell." [VariO:mv] synonym: "germline variation" RELATED [] is_a: VariO:0130 ! DNA variation of genetic origin created_by: med-mnv creation_date: 2017-12-15T09:58:57Z [Term] id: VariO:0446 name: somatic variation def: "Variation that has its origin in a cell in soma." [VariO:mv] is_a: VariO:0130 ! DNA variation of genetic origin created_by: med-mnv creation_date: 2017-12-15T09:58:57Z [Term] id: VariO:0447 name: immunological recognition molecule diversification def: "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] is_a: VariO:0180 ! chromosome structure variation created_by: med-mnv creation_date: 2017-12-15T10:47:27Z [Term] id: VariO:0448 name: organellar DNA affected def: "Variation effect on DNA within cellular compartment." [VariO:mv] is_a: VariO:0072 ! extrachromosomal DNA affected created_by: med-mnv creation_date: 2018-02-01T12:42:12Z [Term] id: VariO:0449 name: extrachromosomal circular DNA def: "Circular DNA molecule not part of the chromosomes." [VariO:mv] is_a: VariO:0072 ! extrachromosomal DNA affected created_by: med-mnv creation_date: 2018-02-01T12:47:35Z [Term] id: VariO:0450 name: mitochondrial DNA affected def: "Variation affecting DNA within mitochondria." [VariO:mv] is_a: VariO:0448 ! organellar DNA affected created_by: med-mnv creation_date: 2018-02-01T12:52:27Z [Term] id: VariO:0451 name: plastid DNA affected def: "Variation affecting DNA within plastids e.g. chloroplasts." [VariO:mv] is_a: VariO:0448 ! organellar DNA affected created_by: med-mnv creation_date: 2018-02-01T12:53:15Z [Term] id: VariO:0452 name: heptanucleotide expansion def: "Tandem repetitive sequence consisting of six nucleotide units." [VariO:mv] is_a: VariO:0188 ! microsatellite created_by: med-mnv creation_date: 2018-02-01T14:49:25Z [Term] id: VariO:0453 name: histone modification def: "Epigenetic modification of histone." [VariO:mv] is_a: VariO:0156 ! epigenetic DNA modification created_by: med-mnv creation_date: 2018-02-06T09:08:59Z [Term] id: VariO:0454 name: variation at topology associating domain def: "Variation affecting topology associating domain (TAD)." [VariO:mv] is_a: VariO:0226 ! chromatin structure variation created_by: med-mnv creation_date: 2018-03-05T16:55:07Z [Term] id: VariO:0455 name: effect on A motif is_a: VariO:0410 ! effect on single stranded DNA structure created_by: med-mnv creation_date: 2018-11-08T10:05:56Z [Term] id: VariO:0456 name: RNA genome def: "Genome composed of RNA molecule." [] is_a: VariO:0351 ! protein coding RNA [Term] id: VariO:0457 name: RNA virus genome def: "Genome for a RNA virus." [] is_a: VariO:0456 ! RNA genome [Term] id: VariO:0458 name: viroid genome def: "Genome for an infectious particle." [] is_a: VariO:0456 ! RNA genome [Term] id: VariO:0459 name: satelletite genome def: "Genome for a subviral agent." [] is_a: VariO:0456 ! RNA genome [Term] id: VariO:0460 name: pre-mRNA def: "Unprocessed mRNA." [] is_a: VariO:0351 ! protein coding RNA [Term] id: VariO:0461 name: mRNA def: "Mature mRNA." [] is_a: VariO:0460 ! pre-mRNA [Term] id: VariO:0462 name: circular RNA def: "Covalently closed single-stranded RNA chain." [] synonym: "circRNA" EXACT [] is_a: VariO:0351 ! protein coding RNA [Term] id: VariO:0463 name: antisense RNA def: "Single-stranded non-coding RNA compelementary to a mRNA or part of it." [] is_a: VariO:0477 ! regulatory RNA [Term] id: VariO:0464 name: non-coding sense RNA def: "Single-stranded noncoding RNA overlapping with mRNA but not coding for a protein." [] is_a: VariO:0477 ! regulatory RNA [Term] id: VariO:0465 name: functional non-coding RNA def: "Non-coding RNA with a function." [] is_a: VariO:0350 ! non-protein coding RNA [Term] id: VariO:0466 name: retrotransposon RNA intermediate def: "RNA intermediate of a retrotransposon." [] synonym: "class I transposable element\ntransposon via RNA intermediate" EXACT [] is_a: VariO:0465 ! functional non-coding RNA [Term] id: VariO:0467 name: translation related non-coding RNA def: "RNA involved in protein synthesis." [] is_a: VariO:0465 ! functional non-coding RNA [Term] id: VariO:0468 name: transfer RNA def: "Transfer RNA involved in protein synthesis. Modiefied tRNA contains amino acid and carries it to ribosome." [] synonym: "tRNA" EXACT [] is_a: VariO:0467 ! translation related non-coding RNA [Term] id: VariO:0469 name: large subunit ribosomal RNA def: "Non-coding RNA that is a constituent of the large ribosomal subunit." [] synonym: "LSU RNA" EXACT [] is_a: VariO:0493 ! ribosomal RNA [Term] id: VariO:0470 name: small subunit ribosomal RNA def: "Non-coding RNA that is a constituent of the small ribosomal unit." [] synonym: "SSU RNA" EXACT [] is_a: VariO:0493 ! ribosomal RNA [Term] id: VariO:0471 name: intron synonym: "Intervening region ithat is spliced off during RNA maturation." EXACT [] is_a: VariO:0467 ! translation related non-coding RNA [Term] id: VariO:0472 name: self-splicing intron def: "Intron with an intrinsic splicing activity." [] is_a: VariO:0471 ! intron [Term] id: VariO:0473 name: spliceosomal intron def: "Intron removed by spliceosome." [] is_a: VariO:0471 ! intron [Term] id: VariO:0474 name: intron retention def: "Inclusion intron sequence to mRNA." [] is_a: VariO:0365 ! effect on cis splicing property_value: owl:backwardCompatibleWith "targeting RNA" xsd:string [Term] id: VariO:0475 name: telomerase RNA def: "Non-coding RNA component of telomerase." [] is_a: VariO:0465 ! functional non-coding RNA [Term] id: VariO:0476 name: catalytic RNA def: "RNA with catalytic activity." [] is_a: VariO:0465 ! functional non-coding RNA [Term] id: VariO:0477 name: regulatory RNA def: "RNA with regulatory activity." [] is_a: VariO:0465 ! functional non-coding RNA [Term] id: VariO:0478 name: microRNA def: "Short non-coding RNA that binds to complementary region in mRNA and silences and regulates gene expression." [] synonym: "miRNA" EXACT [] is_a: VariO:0477 ! regulatory RNA [Term] id: VariO:0479 name: small intervening RNA def: "Short double-stranded non-coding RNA regulating gene expresion by causing degration of mRNA with complementary sequence." [] synonym: "siRNA" EXACT [] is_a: VariO:0477 ! regulatory RNA [Term] id: VariO:0480 name: piwi-interacting RNA def: "Non-coding RNA binding to piwi-superfamily Argonaute proteins to silence transposons, repeat-derived transcripts and genetic elements." [] synonym: "piRNA" EXACT [] is_a: VariO:0477 ! regulatory RNA [Term] id: VariO:0481 name: signal recognition particle RNA def: "Non-coding RNA component of signal recognition particle." [] is_a: VariO:0465 ! functional non-coding RNA [Term] id: VariO:0482 name: X-chromosome inactivation center RNA def: "Non-coding RNA component of X-inactivation center." [] is_a: VariO:0465 ! functional non-coding RNA [Term] id: VariO:0483 name: RNA editing related RNA def: "Non-coding RNA component of editosome complex." [] is_a: VariO:0465 ! functional non-coding RNA [Term] id: VariO:0484 name: DNA editing related RNA def: "Non-coding RNA component of DNA editing complex." [] is_a: VariO:0465 ! functional non-coding RNA [Term] id: VariO:0485 name: spliceosomal RNA synonym: "Non-coding RNA component of spliceosome." EXACT [] is_a: VariO:0465 ! functional non-coding RNA [Term] id: VariO:0486 name: location or origin of non-coding RNA is_a: VariO:0350 ! non-protein coding RNA [Term] id: VariO:0487 name: nuclear non-coding RNA def: "Non-coding RNA in nucleus." [] is_a: VariO:0486 ! location or origin of non-coding RNA [Term] id: VariO:0488 name: mitochondrial non-coding RNA def: "Non-coding RNA in mitochondrion." [] is_a: VariO:0486 ! location or origin of non-coding RNA [Term] id: VariO:0489 name: chromatin related non-coding RNA def: "Non-coding RNA related to chromatin." [] is_a: VariO:0486 ! location or origin of non-coding RNA [Term] id: VariO:0490 name: centromeric non-coding RNA def: "Non-coding RNA related to centromere." [] is_a: VariO:0486 ! location or origin of non-coding RNA [Term] id: VariO:0491 name: size of non-coding RNA def: "Classification of non-coding RNA based on the length." [] is_a: VariO:0350 ! non-protein coding RNA [Term] id: VariO:0492 name: short non-coding RNA def: "Non-coding RNA shorter than 200 nucleotides or base pairs." [] synonym: "small non-coding RNA\nsRNA" EXACT [] is_a: VariO:0491 ! size of non-coding RNA [Term] id: VariO:0493 name: ribosomal RNA def: "Non-coding RNA constituent of ribosome." [] synonym: "rRNA" EXACT [] is_a: VariO:0467 ! translation related non-coding RNA [Term] id: VariO:0494 name: long non-coding RNA def: "Non-coding RNA longer than 200 nucleotides or base pairs." [] synonym: "large non-coding RNA\nlncRNA" EXACT [] is_a: VariO:0491 ! size of non-coding RNA [Term] id: VariO:0495 name: very long non-coding RNA def: "Non-coding RNA longer than 10 kb." [] synonym: "vlnicRNA" EXACT [] is_a: VariO:0491 ! size of non-coding RNA [Term] id: VariO:0496 name: exon def: "Transcript region that is part in mature mRNA." [] is_a: VariO:0461 ! mRNA [Term] id: VariO:0497 name: alternatively terminated mRNA def: "Variation causing alternative mRNA termination." [] is_a: VariO:0331 ! alternative form of mRNA [Term] id: VariO:0498 name: effect on RNA modification def: "Variation affecting post transcriptional RNA modification." [] is_a: VariO:0354 ! effect on post transcriptional RNA modification [Term] id: VariO:0499 name: modified mRNA nucleotide def: "Post transcriptionally modified nucleotide in mRNA." [] is_a: VariO:0331 ! alternative form of mRNA [Term] id: VariO:0500 name: effect on RNA pseudoknot def: "Variation affecting RNA stucture containing at teast two stem loops where part of one stem is intercalated to the other stem." [] is_a: VariO:0382 ! effect on RNA secondary structure [Term] id: VariO:0501 name: RNA fragment def: "RNA produced by degradation of processing of an RNA molecule." [] is_a: VariO:0486 ! location or origin of non-coding RNA [Term] id: VariO:0502 name: exon skipping def: "Variation where an exon is completele cleaved out from a mature transcript." [] is_a: VariO:0365 ! effect on cis splicing [Term] id: VariO:0503 name: loss of exon fragment def: "Transcript from which part of an exon is missing." [] is_a: VariO:0365 ! effect on cis splicing [Term] id: VariO:0504 name: inclusion of cryptic exon def: "Transcript that includes a cryptic exon from the middle of intron." [] is_a: VariO:0365 ! effect on cis splicing [Term] id: VariO:0505 name: inclusion of intron fragment def: "Transcript that contains and additional stretch from intron." [] is_a: VariO:0365 ! effect on cis splicing [Term] id: VariO:0508 name: affected splice site def: "Type of variation affecting splice site." [] is_a: VariO:0365 ! effect on cis splicing [Term] id: VariO:0509 name: effect on mode of splicing def: "Variation affecting the type of RNA splicing." [] is_a: VariO:0362 ! effect on RNA splicing [Term] id: VariO:0510 name: effect on co-transcriptional splicing def: "Variation affecting splicing occurring simultnaeously with transcription." [] is_a: VariO:0509 ! effect on mode of splicing [Term] id: VariO:0511 name: effect on non-sequential splicing def: "Variation affecting splicing that does not occur in sequential order." [] is_a: VariO:0509 ! effect on mode of splicing [Term] id: VariO:0512 name: effect on recursive splicing def: "Variation affecting intron splicing that occurs in several splicing events." [] is_a: VariO:0509 ! effect on mode of splicing [Term] id: VariO:0513 name: mutually exclusive exon def: "Only one of two exons is incluided into mRNA." [] synonym: "snoRNA" EXACT [] is_a: VariO:0365 ! effect on cis splicing [Typedef] id: adjacent_to name: adjacent_to def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence." [SO:ke] [Typedef] id: associated_with name: associated_with comment: This relationship is vague and up for discussion. [Typedef] id: complete_evidence_for_feature name: complete_evidence_for_feature def: "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] comment: 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. is_transitive: true [Typedef] id: contains name: contains def: "'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'." [PSI-MOD:ref] comment: The inverse relationship to "part of". is_transitive: true [Typedef] id: derives_from name: derives_from is_transitive: true [Typedef] id: evidence_for_feature name: evidence_for_feature def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke] comment: 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. is_transitive: true [Typedef] id: genome_of name: genome_of [Typedef] id: has_functional_parent name: has functional parent def: "'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] comment: This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent. is_transitive: true [Typedef] id: has_origin name: has_origin [Typedef] id: has_part name: has_part [Typedef] id: has_quality name: has_quality comment: The relationship between a feature and an attribute. [Typedef] id: member_of name: member_of comment: 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. is_transitive: true [Typedef] id: negatively_regulates name: negatively_regulates [Typedef] id: non_functional_homolog_of name: non_functional_homolog_of def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke] [Typedef] id: part_of name: part_of is_transitive: true [Typedef] id: partial_evidence_for_feature name: partial_evidence_for_feature def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke] [Typedef] id: position_of name: position_of [Typedef] id: positively_regulates name: positively_regulates [Typedef] id: regulates name: regulates transitive_over: part_of ! part_of [Typedef] id: sequence_of name: sequence_of [Typedef] id: variant_of name: variant_of def: "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] comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.