A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence.
This relationship is vague and up for discussion.
B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.
If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'.
B is evidence_for_feature A, if an instance of B supports the existence of A.
This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
'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.
This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent.
The relationship between a feature and an attribute.
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.
A relationship between a pseudogenic feature and its functional ancestor.
B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.
A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.
Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.
Effects of a variation on protein level.
Effect of variation on protein function.
Effect of variation on the movement of a protein along filament of a polymeric molecule.
Effect of variation on storage protein. Storage proteins are cellular sources of amino acids and metal ions.
Effect of variation on structural role of protein. Structural proteins are fibrous and involved in increasing rigidity and stiffness of biological systems.
Effect of variation on selective non-covalent interaction of protein.
Effect of variation on catalytic function of protein.
Effect of variation on transport function of protein in facilitating passage of an atom or molecule through membrane.
Variation affecting abundance of produced RNA molecules.
Effect of variation on information transfer by protein to control activity of specific processes in cells, tissues or organs.
Type of protein variation. Describes origin and classification of a variant.
Protein variation that has genetic origin.
Removal of one or more continuous amino acids from protein.
Shortening of protein sequence from terminus.
Deletion of one or more amino acids from a protein, without affecting the sequence after deletion.
mRNA variation leading to amino acid change in translated protein. The variant alters the codon so that it encodes another amino acid.
Addition of one or more amino acids to protein sequence.
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.
Insertion of one or more amino acids to the protein without affecting the sequence after insertion.
Substitution of an amino acid in protein.
A complex protein variation consisting of both amino acid insertion(s) and deletion(s).
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.
Protein variation that does not have genetic origin being modified at protein level.
Heritable protein variation of non-genetic origin.
Inheritance of protein or protein complex structure without involvement of genetic information.
Protein conformation change induced by structurally modified protein.
Protein molecule chemically modified after translation.
Amino acid indel without affecting the sequence after the indel position.
RNA indel not affecting reading frame after indel position.
RNA indel containing a number of nucleotides not divisible by three and therefore causing change to reading frame.
Variation affecting characteristic property of protein.
Effect of variation on the targeting of a protein within a cell or cellular compartment.
effect on protein subcellular localization
Effect of variation on stability of protein.
Effect of variation on the potential of protein to dissolve in a liquid.
Variation affecting the formation of particles of aggregated proteins.
effect on protein inclusion body formation
Variation at a covarying sequence position.
Variation affecting protein aggregation tendency.
Type of protein function affecting variation.
Effect of variation causing new or enhanced protein activity.
Variation generates new protein function.
Dominant variation that acts to opposite direction than the normal protein.
Effect of variation reducing or abolishing protein activity.
Effect of variation to the accessibility of protein region to solvent.
Variation leading to burying of exposed region.
Implication of a protein variant to pathogenicity.
association of protein variation to pathogenicity
Effect of variation on charge in protein.
Variation affecting electrostatics of the protein surface.
Variation changing protein isoelectric point.
Effect of variation on degradation of protein.
Variation affecting abundance of produced protein molecules.
Effect of variation on activity of protein.
Effect of variation on protein affinity to binding molecule(s).
Effect of variation on substrate binding specificity of protein.
Effect of variation to enzyme reaction kinetics.
Conservation of the variant site in related protein sequences.
Effect of variation on the interaction of protein with its partner.
Effect of variation on contact energy between interacting molecules.
Variation affecting structure of protein.
Hereditary protein structure modification of non-genetic origin.
Variation affecting the formation of infectious protein having misfolded structure.
Variation affecting heritable protein complex structure.
Variation affecting protein three dimensional structure.
Variation affecting dynamics in protein structure.
Variation affecting protein structural flexibility.
Variation affecting induced fit of protein binding to its partner.
Variation affecting protein structural disorder.
Variation in affecting protein allosteric site.
Variation affecting rate of protein folding.
Variation affecting protein tertiary structure.
Variation changing protein conformation.
Variation causing large overall protein conformational change.
Variation causing local and minor conformational change.
Variation affecting protein structure due to alteration to domain orientation.
Variation affecting formation of intramolecular disulphide bonds.
Variation affecting protein secondary structural element of local ordered structure.
effect on protein secondary structural element
Variation affecting secondary structure conformation where the peptide backbone forms a coil.
Variation affecting protein left handed helix turning anticlockwise.
Variation affecting protein right handed helix where the coiled conformation turns in a clockwise, right handed screw.
Variation affecting protein helix having 4.1 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.
Variation affecting protein helix having 3 residues per turn. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.
Variation affecting protein helix having 3.6 residues per turn. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.
Variation affecting extended protein backbone structure.
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).
effect on protein antiparallel beta strand
Variation affecting beta strand forming part of parallel beta sheet. Hydrogen bonds are formed with another region of protein running in the same direction. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees).
Variation affecting protein backbone turn motif.
Variation affecting protein motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative.
Variation affecting protein motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which is used to sub-categorize the turns.
Variation affecting protein motif of five consecutive residues and two H-bonds, where residue(i) is either serine or threonine. Side chain O of residue(i) is H-bonded to the main chain NH of residue(i+2) or (i+3), and main chain CO or residue(i) is H-bonded to the main chain NH or residue(i+3) or (i+4).
Variation affecting protein motif of four or five consecutive residues and one H-bond in which residue(i) is serine or threonine, the side chain OH of residue(i) is H-bonded to the main chain CO or residue(i-3) or (i-4), and phi angles of residues(i-1), (i-2) and (i-3) are negative.
Variation affecting protein turn defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.
Variation affecting protein motif of three consecutive residues and one H-bond in which: residue(i) is serine or threonine, the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
Variation affecting protein motif of six or seven consecutive residues that contains two H-bonds.
Variation affecting protein motif of two consecutive residues. Dihedral angles are used to sub-categorise the nests. Nest does not contain proline.
Variation affecting a protein motif of three consecutive residues. Dihedral angles are used to sub-categorise the niche motifs.
Variation affecting protein motif of five consecutive residues and two H-bonds in which: Residue(i) is aspartate or asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).
Variation affecting protein motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.
Variation affecting protein motif of three consecutive residues and one H-bond in which: residue(i) is aspartate or asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).
Variation affecting protein motif of three residues within a beta-sheet consisting of two H-bonds.
Variation affecting irregular, unstructured region of protein.
Variation altering membrane spanning protein.
Variation affecting region not traversing the lipid bilayer in a membrane protein.
effect on membrane protein extramembrane region
Variation affecting region present in the lipid bilayer in a membrane protein.
effect on membrane protein intramembrane region
Variation affecting the covalent alteration of protein amino acid by post translational process.
effect on protein post translational modification
Variation causing deletion of a post translational modification site.
deletion of a post translational modification site
Variation affecting site of protein maturation by cleavage of peptide bond(s).
Variation affecting post-translational removal of peptide sequences from within a protein sequence.
Variation that generates a novel protein processing site.
variation generating a novel protein processing site
Variation causing prevention of polypeptide processing.
variation preventing polypeptide processing
Variation generating a novel post translational modification site.
generation of a novel post translational modification site
Variation affecting amino acid side chain size.
Variation affecting amino acid packing in folded protein.
Variation causing formation of a cavity to protein core due to replacement of a side chain by a smaller one.
Variation causing over packing of amino acids due to replacement by larger amino acid side chain.
Variation affecting ligand binding amino acid(s) in protein.
Variation affecting region on the surface of a protein that interacts with another molecule.
Variation affecting amino acid(s) in protein catalytic site.
Variation affecting three dimensional structure of a protein complex.
Variation affecting interaction between protein subunits in quaternary structure.
effect on protein quaternary structure forming interaction
Complex change of protein three dimensional structure.
Variation prolonging protein chain at an end.
Addition of one or more amino acids to protein C-terminus.
Addition of one or more amino acids to protein N-terminus.
Type of DNA variation. Describes origin and classification of a variant.
Variation affecting structure of chromosome.
Variation affecting RNA tertiary structure.
A genetic character, organism or individual with a difference to reference state.
The observed feature is not changed in relation to the wild type form.
Removal of one or more continuous nucleotides from DNA sequence.
Addition of one or more nucleotides between two adjacent nucleotides in the DNA sequence.
A complex DNA variation consisting of both nucleotide insertion(s) and deletion(s).
A continuous stretch of DNA sequence moved to a new position within a chromosome.
A continuous stretch of DNA sequence inserted to the same position in reverse orientation.
DNA variation that does not have genetic origin.
Heritable DNA variation of non-genetic origin.
Variation having effect on DNA function and usage.
Variation affecting transcription, synthesis of either RNA on a template of DNA or DNA on a template of RNA.
Variation affecting information transfer of DNA.
Variation affecting the process of restoring DNA after damage.
Variation affecting regulatory function of DNA.
Variation originating from semi conservative DNA strand synthesis. The template for replication is either DNA or RNA molecule.
Hereditary variation of DNA not affecting primary sequence.
Inheritable cytosine or adenosine pyrimidine ring methylation regulating gene expression.
Positioning of nucleosomes to DNA strand.
Somatic recombination combining gene segments in antibody, immunoglobulin B and T cell receptor and MCH coding genes.
immunological receptor gene rearrangement
Variation affecting DNA structural form.
Immunoglobulin diversification mechanism by producing variations to antigen variable regions.
Switching of immunoglobulin M to other isotype by changing a portion of a region coding for heavy chain.
Secondary immunological receptor diversification by replacing a DNA stretch by a homologous sequence.
Variation affecting DNA tertiary structure.
Variation generated on purpose by e.g. chemical or physical treatment or artificial modification of DNA.
Variation affecting G-quadruplex of four stranded nucleic acid structure. The structure can be intramolecular, bimolecular or tetramolecular.
Variation affecting cytosine rich DNA domain where strands associate both inter- and intramolecularly.
Variation affecting DNA helix formed of three strands.
Variation affecting length of telomere sequence.
Variation shortening length of telomere sequence.
Variation extending length of telomere sequence.
Chromosome lacking one arm with duplication of the other arm.
Increase in the frequency of a chromosomal region.
Copies of a chromosomal region of length greater than one scattered to genome sequence.
Adjacent copies of a chromosomal region of length greater than 1.
Tandem repetitive sequence consisting of units in length from seven to few tens of base pairs.
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.
Tandem repetitive sequence consisting of units of two to six base pair.
Tandem repetitive sequence consisting of three nucleotide units.
Tandem repetitive sequence consisting of one nucleotide type.
Tandem repetitive sequence consisting of four nucleotide units.
Mobile genetic element incorporated into chromosome.
Deletion of chromosomal region not including terminus.
Deletion of chromosomal region from the end of chromosome arm.
Chromosome structure variation with four or more breakpoints.
Translocation of chromosomal region within a chromosome.
Intrachromosomal variation where a chromosomal region is inserted in reverse direction.
Chromosomal inversion within a chromosome arm.
Chromosomal inversion including centromere.
Translocation of chromosomal region to another chromosome.
Switching of chromosomal regions between nonhomologous chromosomes.
Fusion of long arms of two acrocentric chromosomes having very short p arms.
Tandem repetitive sequence consisting of two nucleotide units.
Variation affecting the number of chromosomes.
Three copies of a chromosome in a cell or organism.
Two copies of a chromosome in a cell or organism .
Both copies of a chromosome or a part of it in diploid cell or organism are from one parent.
Uniparental disomy with duplication of a single chromosome from one parent.
Uniparental disomy with both homologous chromosomes from one parent.
No copies of a chromosome in a cell or organism.
Four copies of a chromosome in a cell or organism.
One copy of a chromosome in a cell or organism.
Variation affecting number of entire chromosome sets.
Variation with four sets of chromosomes.
Variation with several sets of chromosomes.
Variation with several sets of chromosomes originating from the same organism.
Variation with several sets of chromosomes originating from a different organism.
Variation with three sets of chromosomes.
Variation with five sets of chromosomes.
Variation with a single set of chromosomes.
Variation affecting structure of chromatin the complex of chromosomal DNA and histone proteins.
Variation affecting characteristic property of DNA.
Fusion of two protein chains. Produced from fusion gene of two joined genes.
Implication of a DNA variant to pathogenicity.
association of DNA variation to pathogenicity
Variation affecting interaction of DNA with its partner.
Conservation of the variation site in related DNA sequences.
Attributes define and modulate terms at other levels.
Variation at a region of sequence similarity in multiple sequence alignment of related sequences.
Variation at invariant sequence region in multiple sequence alignment of related sequences.
Mutual or reciprocal action or influence that happens at a given place and time between participating molecules.
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.
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.
genetic interaction defined by inequality
The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g. WT > a > ab > b.
single nonmonotonic genetic interaction (sensu inequality)
single nonmonotonic genetic interaction defined by inequality
Variation preventing protein translation because of e. g. initiation codon variation or mRNA surveillance mechanism.
A continuous stretch of RNA sequence moved to a new position.
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.
conditional genetic interaction (sensu inequality)
conditional genetic interaction defined by inequality
Single-variant phenotype effects combine to give a double-variant effect different from the wild type and different from single variant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b.
additive genetic interaction (sensu inequality)
additive genetic interaction defined by inequality
A continuous stretch of RNA sequence inserted to the same position in reverse orientation.
Variation preventing transcription e. g. because of impaired transcription machinery or variation in the transcription regulation or start site.
The phenotype of the double variant ab is weaker than expected from the combination of the individual effects of a and b.
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.
double nonmonotonic genetic interaction (sensu inequality)
double nonmonotonic genetic interaction defined by inequality
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.
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).
epistatic genetic interaction (sensu inequality)
epistatic genetic interaction defined by inequality
The phenotype resulting from genetic perturbation of A alone, B alone and AB combined have the same effect on the WT background. E. g., WT > a = b = ab.
asynthetic genetic interaction (sensu inequality)
asynthetic genetic interaction defined by inequality
The phenotype resulting from genetic perturbation of A has an effect on WT, but that effect is abolished by adding the suppressor b, which itself shows no single-variant effect. E. g., WT = b = ab > a.
suppressive genetic interaction (sensu inequality)
suppressive genetic interaction defined by inequality
The phenotype of the double variant ab is equal to the phenotype expected from the combination of the individual effects of a and b.
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.
noninteractive genetic interaction (sensu inequality)
noninteractive genetic interaction defined by inequality
The phenotype of the double variant ab is stronger than expected from the combination of the individual effects of a and b.
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.
synthetic genetic interaction (sensu inequality)
synthetic genetic interaction defined by inequality
Molecular structural level of interaction.
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.
Entity participating in a physical or functional interaction.
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.
A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
An inorganic hydroxy compound that has formula H2O.
Set of interacting molecules that can be copurified.
A macromolecular complex containing both protein and RNA molecules.
A stable set of interacting proteins that can be copurified and operate as a functional unit.
A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
Any type of molecule, including complexes, that may be observed but not identified.
Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
Linear polymer of nucleotides, linked by 3',5' phosphodiester linkages.
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.
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.
A linear polymer of amino acids joined by peptide bonds in a specific sequence.
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.
A chemical link between two atoms in which electrons are shared between them.
The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain.
Interaction between biochemical entities that results in the formation of a non-covalent bond.
Attractive interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom.
Network of interactions formed by several hydrogen bonds.
Interaction of nonpolar (un-ionizable) hydrocarbon molecules forced together because of stronger water-water interaction.
Weak attractive electrical force between neutral groups or molecules.
Attraction between two electrically charged groups or molecules.
The observed feature is decreased compared to that in the wild type (slower, weaker, lower, smaller, etc.).
The observed feature is increased compared to that in the wild type (faster, stronger, higher, larger, etc.).
The observed feature is missing compared to that in the wild type.
Variation is not related to clinical phenotype.
Variation affecting characteristic property of RNA.
Variation affecting stability of transcript.
Conservation of the variation site in related RNA sequences.
An excess of a particular chromosome in a cell or organism.
Implication of an RNA variant to pathogenicity.
association of RNA variation to pathogenicity
Variation affecting interaction of RNA with its partner.
Type of RNA variation. Describes origin and classification of a variant.
Nucleotide change in the mRNA triplet codon codes for another amino acid.
RNA nucleotide change in termination codon.
Nucleotide change in the mRNA codon triplet creates a terminator codon.
A complex RNA variation consisting of both nucleotide insertion(s) and deletion(s).
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.
A substitution of a pyrimidine, C or T (or U), for another pyrimidine.
A substitution of a purine, A or G, for another purine.
Change of a pyrimidine nucleotide, C or T (or U), into a purine nucleotide, A or G, or vice versa.
RNA nucleotide change in the initiation codon.
RNA variation that does not change the encoded amino acid.
One or more continuous nucleotides are missing from RNA sequence.
Deletion of nucleotides in multiples of three so that the mRNA coding sequence frame is retained.
Deletion of nucleotide(s) causing alteration of mRNA coding sequence frame.
Addition of one or more nucleotides between adjacent nucleotides in RNA sequence.
Insertion of nucleotide(s) causing alteration of mRNA reading frame.
RNA variation due to defective fidelity of transcription.
Protein variation due to defective fidelity of translation.
Insertion of nucleotides in multiples of three so that the reading frame is retained.
RNA variation that does not have genetic origin being modified at RNA level.
Post transcriptionally chemically modified RNA.
RNA molecule destroyed due to appearance of a premature termination codon.
DNA variation due to biological, chemical, physical or other modification.
Chemical modification of RNA transcript by RNA editing mechanism.
RNA editing process of chemical modification of a nucleotide in RNA.
Insertion of one or more nucleotides to RNA by RNA editing process.
Deletion of one or more nucleotides from RNA by RNA editing process.
mRNA variation not affecting the sequence of the translated protein.
Variation causing nonsense-mediated decay of RNA due to premature translation termination codon.
RNA degradation by nonsense-mediated decay
Nonsense-associated altered RNA splicing.
RNA modification by nonsense-associated altered splicing
Variation affecting RNA not coding for protein.
Variation affecting RNA coding for protein.
Variation affecting region coding for protein in protein coding RNA.
Variation affecting region not coding for protein in protein coding mRNA.
non-coding region of protein coding mRNA
Enzymatic addition of adenylyl residues to the 3' end of RNA molecule.
Polyadenylation of mRNA molecule at alternative site.
Modification of five prime nucleotide in RNA by adding guanine nucleotide with five prime to five prime linkage.
Covalent modification of RNA during maturation.
Post transcriptional modification of RNA base.
Post transcriptional modification of RNA nucleoside sugar.
Process where introns in mRNA are cut away from exons.
Variation affecting cellular localization of RNA.
Variation affecting aggregation tendency of RNA.
Intronic splicing within a mRNA molecule.
Splicing at recursive splice site which subdivides a large intron.
Intronic two base pair region bordering exon, at the five prime end of the intron.
Canonical prime splice site at five prime end.
Non canonical splice site at five prime end.
Intronic two base pair region bordering the exon, at the 3' edge of the intron.
Non canonical splice site at three prime end.
Canonical splice site at three prime end.
Splicing and ligation of two different mRNA molecules.
Insertion of retrotransposon into chromosome. Retrotransposon is transcribed from DNA to RNA, and then reverse transcribed to DNA.
Insertion of a DNA transposable element into chromosome.
Long interspersed nuclear element generated by retrotransposition.
Short interspersed nuclear element generated by retrotransposition. Length below 500 bp.
Variation affecting RNA secondary structure.
Variation affecting closed RNA structure in which at least two double stranded regions meet.
Variation affecting RNA structure in which nucleotides in one strand do not form base pairs.
Variation affecting RNA structure in which both the strands do not form base pairs.
Variation affecting hydrogen bonding in contiguous nested base pairs in RNA.
Variation affecting loop connecting adjacent regions forming helix in RNA.
Retrotransposon that has long terminal repeat sequences. Sizes from about 100 bp to over 5 kb.
Tandem repetitive sequence consisting of five nucleotide units.
Variation affecting DNA double helical structure.
Variation effect on independently replicating small DNA molecule.
Simple, relatively short transposable element. IS elements contain only transposition related genes.
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.
RNA splicing by inherent ribozyme activity of the mRNA molecule.
Variation having effect on RNA function and usage.
Variation affecting splicing function of RNA.
Variation affecting catalytic function of RNA.
Variation affecting translation of protein.
Variation affecting regulatory function of RNA.
Variation affecting RNA function in amino acid transfer.
Variation affecting information transfer by RNA.
Transposable element coding for self-splicing ribozyme when transcribed. Splicing is initiated by nucleophilic attack of an exogenous GTP or guanosine.
Transposable element coding for a self-splicing ribozyme when transcribed. Intron excision does not require GTP.
Fusion of two chromosome segments both containing a centromere.
Variation causing Staufen-mediated RNA decay.
RNA degradation by Staufen-mediated decay
Variation generated by chromosome editing.
Fusion transcript of exons from two or more genes.
Transcript with -1 or +1 frameshift due to slipping back or skipping a nucleotide on a ribosome.
Variation affecting single stranded DNA structure.
RNA molecule matured by splicing at an alternative site.
Variation affecting catalytic function of DNA.
Variation affecting A form of right-handed DNA.
Variation affecting B form of right-handed DNA.
Variation affecting C form of right-handed DNA.
Variation affecting L form of right-handed DNA.
Variation affecting S form of right-handed DNA.
Variation affecting D form of right-handed DNA.
Variation affecting H form of intramolecular triple helical DNA.
Variation affecting Z form of left-handed DNA.
Variation affecting triple helical DNA structure where the third strand is provided by one of the strands forming the duplex.
effect on intramolecular DNA triple helix
Variation affecting triple helical DNA structure where the third strand is from a second DNA molecule.
effect on intermolecular DNA triple helix
Variation affecting RNA helix formed of three strands.
Classification of chromosomal amplification type.
Chromosome structure variation due to several breakpoints.
Repetitive sequence consisting of one more nucleotide units.
Effect on DNA-RNA R loop structure of short RNA-DNA hybrid and the displaced single stranded DNA.
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.
Effect on DNA displacement loop where two double-stranded DNA molecules are separated locally by a third strand of DNA or RNA.
Replacement of the deoxyribonucleoside monophosphate by ribonucleoside monophosphate in the DNA backbone.
Effect of variation to protein reaction kinetics.
RNA molecule that has matured by processing.
RNA variation causing alternative translation initiation.
Effect of variation on RNA reaction kinetics.
Effect of variation on RNA affinity to binding molecule(s).
Effect of variation on substrate binding specificity of RNA.
Protein variant originating from alternative translation initiation.
Variation that has emerged in a germ cell on one of the parents or in the fertilized egg during early embryogenesis.
Variation that has been inherited from a germline cell.
Variation that has its origin in a cell in soma.
Processes that recombine and modify genes coding for immunological recognition molecules (antigens, B- and T-cell receptors, MCH type I and II molecules).
immunological recognition molecule diversification
Variation effect on DNA within cellular compartment.
Circular DNA molecule not part of the chromosomes.
Variation affecting DNA within mitochondria.
Variation affecting DNA within plastids e.g. chloroplasts.
Tandem repetitive sequence consisting of six nucleotide units.
Variation affecting topology associating domain (TAD).
variation at topology associating domain