04:04:2013 16:48 1.2 OBO-Edit 2.3-beta5 eco mchibucos definition has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym used_in 2010-12-09T05:00:20Z eco mchibucos used_in evidence A type of information that is used to support an assertion. ECO:0000000 eco evidence code evidence_code A type of information that is used to support an assertion. ECO:MCC inference from background scientific knowledge A curator inference that links the current annotation to a different evidence-based annotation via background knowledge of the curator. ECO:0000001 IC eco inferred by curator A curator inference that links the current annotation to a different evidence-based annotation via background knowledge of the curator. ECO:MCC ECO:go GO:IC IC GO:IC inferred by curator direct assay evidence ECO:0000002 Experimental evidence that is based on direct measurement of some aspect of a biological feature. eco ECO:MCC Experimental evidence that is based on direct measurement of some aspect of a biological feature. GO:IDA reconstitution assay evidence ECO:0000003 eco cell fractionation evidence ECO:0000004 IDA: cell fractionation Used when an annotation is made based on separation of subcellular components based on their physical properties, such as density in sucrose density gradients. This evidence is used mostly for annotations to the cellular component ontology. eco TAIR:TED Used when an annotation is made based on separation of subcellular components based on their physical properties, such as density in sucrose density gradients. This evidence is used mostly for annotations to the cellular component ontology. enzyme assay evidence ECO:0000005 IDA: enzyme assays PSI-MI:MI:0415 Used when an annotation is made based on assays that determine the catalytic activity of enzymes. eco enzymatic study PSI-MI:MI:0415 TAIR:TED Used when an annotation is made based on assays that determine the catalytic activity of enzymes. experimental evidence An evidence type that is based on the results of a laboratory assay. ECO:0000006 EXP eco inferred from experiment An evidence type that is based on the results of a laboratory assay. ECO:MCC GOC:ecd EXP GO:EXP GO:EXP inferred from experiment immunofluorescence evidence A type of protein assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell. ECO:0000007 IDA: immunofluorescence eco A type of protein assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell. ECO:MCC TAIR:TED expression pattern evidence ECO:0000008 Experimental evidence that is based on characterization of gene expression. IEP Use this evidence type when the annotation is inferred from the timing or location of expression of a gene. It may be difficult to determine whether the expression pattern truly indicates that a gene plays a role in a given process. eco inferred from expression pattern GO:IEP inferred from expression pattern ECO:MCC Experimental evidence that is based on characterization of gene expression. GO:IEP GO:IEP IEP transcript expression evidence ECO:0000009 eco protein expression evidence ECO:0000010 eco genetic interaction evidence ECO:0000011 TAIR:TED:0000006 eco functional complementation evidence ECO:0000012 IGI: functional complementation Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a mutant background in the organism of the gene's origin or a heterologous organism with a mutation in the homologous gene. eco TAIR:TED Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a mutant background in the organism of the gene's origin or a heterologous organism with a mutation in the homologous gene. transgenic rescue experiment evidence ECO:0000013 eco mutant phenotype evidence ECO:0000015 The IMP evidence code covers those cases when the function, process or cellular localization of a gene product is inferred based on differences in the function, process, or cellular localization between two different alleles of the corresponding gene. The IMP code is used for cases where one allele may be designated 'wild-type' and another as 'mutant'. It is also used in cases where allelic variation occurs naturally and no specific allele is designated as wild-type or mutant. Caution should be used when making annotations from gain-of-function mutations as it may be difficult to infer a gene's normal function from a gain of function mutation, although it is sometimes possible. eco GO:IMP The IMP evidence code covers those cases when the function, process or cellular localization of a gene product is inferred based on differences in the function, process, or cellular localization between two different alleles of the corresponding gene. The IMP code is used for cases where one allele may be designated 'wild-type' and another as 'mutant'. It is also used in cases where allelic variation occurs naturally and no specific allele is designated as wild-type or mutant. Caution should be used when making annotations from gain-of-function mutations as it may be difficult to infer a gene's normal function from a gain of function mutation, although it is sometimes possible. loss-of-function mutant phenotype evidence ECO:0000016 eco ectopic expression evidence ECO:0000017 IMP: analysis of overexpression/ectopic expression phenotype Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress or ectopically express the gene product in question. eco TAIR:TED Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress or ectopically express the gene product in question. anti-sense experiment evidence ECO:0000018 IMP: anti-sense experiments Used when an annotation is based on a phenotype observed when expressing an anti-sense version of a gene product in a wild-type (for that gene product) background. eco TAIR:TED Used when an annotation is based on a phenotype observed when expressing an anti-sense version of a gene product in a wild-type (for that gene product) background. RNAi evidence ECO:0000019 IMP: RNAi experiment Inference based on a phenotype observed when expressing an RNAi construct that includes a fragment of the gene product in a wild-type (for that gene product) background. A double-stranded RNA specifically suppresses the expression of the gene bearing its complementary sequence. eco Inference based on a phenotype observed when expressing an RNAi construct that includes a fragment of the gene product in a wild-type (for that gene product) background. A double-stranded RNA specifically suppresses the expression of the gene bearing its complementary sequence. TAIR:TED specific protein inhibition evidence A type of protein assay evidence based on the inhibition of the molecular function of a protein. ECO:0000020 eco A type of protein assay evidence based on the inhibition of the molecular function of a protein. ECO:MCC physical interaction evidence ECO:0000021 Experimental evidence that is based on characterization of an interaction between a gene product and another molecule. GOECO:IPI IPI Molecules interacted with might include protein, nucleic acid, ion, or complex. PSI-MI:MI:0045 eco inferred from physical interaction GOECO:IPI inferred from physical interaction inferred from physical interaction GOECO:IPI GOECO:IPI IPI ECO:MCC Experimental evidence that is based on characterization of an interaction between a gene product and another molecule. experimental interaction detection PSI-MI:MI:0045 co-purification evidence A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex. ECO:0000022 IPI: co-purification PSI-MI:MI:0025 eco A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex. TAIR:TED copurification PSI-MI:MI:0025 affinity evidence A type of physical interaction evidence that depends on the strength of the interaction between two entities. ECO:0000023 PSI-MI:MI:0400 eco ligand binding evidence A type of physical interaction evidence that depends on the strength of the interaction between two entities. ECO:MCC PSI-MI:MI:0400 affinity technology PSI-MI:MI:0400 protein binding evidence ECO:0000024 eco hybrid interaction evidence A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein. ECO:0000025 PSI-MI:MI:0090 Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode. eco A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein. ECO:MCC PSI-MI:MI:0090 protein complementation assay PSI-MI:MI:0090 nucleic acid hybridization evidence ECO:0000026 eco structural similarity evidence A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes. ECO:0000027 For GO annotation, in the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field. eco A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes. ECO:MCC TAIR:TED motif similarity evidence ECO:0000028 ISS: recognized domains Used when an annotation is made based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence. eco TAIR:TED Used when an annotation is made based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence. match to InterPro signature evidence ECO:0000029 eco BLAST evidence used in manual assertion A type of BLAST evidence that is used in a manual assertion. ECO:0000030 curated BLAST analysis eco A type of BLAST evidence that is used in a manual assertion. ECO:MCC protein BLAST evidence used in manual assertion ECO:0000031 GO_REF:0000012 GO_REF:0000018 GO_REF:0000027 Protein BLAST evidence that is used in a manual assertion. curated protein BLAST analysis eco ECO:MCC Protein BLAST evidence that is used in a manual assertion. Pairwise alignment (TIGR) GO_REF:0000012 dictyBase 'Inferred from Electronic Annotation (BLAST method)' GO_REF:0000018 BLAST search criteria for ISS assignment in PAMGO_GAT GO_REF:0000027 nucleotide BLAST evidence used in manual assertion ECO:0000032 Nucleotide BLAST evidence that is used in a manual assertion. curated nucleic acid BLAST analysis eco ECO:MCC Nucleotide BLAST evidence that is used in a manual assertion. traceable author statement An author statement that is based on a cited reference. ECO:0000033 The traceable author statement (TAS) evidence code covers author statements that are attributed to a cited source. Typically this type of information comes from review articles. Material from the introductions and discussion sections of non-review papers may also be suitable if another reference is cited as the source of experimental work or analysis. When annotating with this code the curator should use caution and be aware that authors often cite papers dealing with experiments that were performed in organisms different from the one being discussed in the paper at hand. Thus a problem with the TAS code is that it may turn out from following up the references in the paper that no experiments were performed on the gene in the organism actually being characterized in the primary paper. For this reason we recommend (when time and resources allow) that curators track down the cited paper and annotate directly from the experimental paper using the appropriate experimental evidence code. When this is not possible and it is necessary to annotate from reviews, the TAS code is the appropriate code to use for statements that are associated with a cited reference. Once an annotation has been made to a given term using an experimental evidence code, we recommend removing any annotations made to the same term using the TAS evidence code. eco An author statement that is based on a cited reference. ECO:MCC GO:TAS non-traceable author statement An author statement that is not associated with results presented or a cited reference. ECO:0000034 The non-traceable author statement evidence code should be used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation. The source of the information may be peer reviewed papers, textbooks, database records or vouchered specimens. eco An author statement that is not associated with results presented or a cited reference. ECO:MCC no biological data found A curator inference that states that a search found no information about a biological feature. ECO:0000035 ND eco no biological data available GO:ND ND GO:ND no biological data available A curator inference that states that a search found no information about a biological feature. ECO:MCC GO:ND not_recorded An evidence that reflects an annotation was made before curators began tracking evidence types. ECO:0000037 NR The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations. eco not recorded true GO:NR not recorded GO:NR NR An evidence that reflects an annotation was made before curators began tracking evidence types. ECO:MCC GO:NR transient rescue experiment evidence ECO:0000038 eco protein assay evidence ECO:0000039 eco immunological assay evidence ECO:0000040 eco similarity evidence An evidence type that is based on comparing likeness of distinct biological entities. ECO:0000041 IS eco inferred from similarity An evidence type that is based on comparing likeness of distinct biological entities. ECO:MCC PhenoScape:IS gain-of-function mutant phenotype evidence ECO:0000042 eco sequence similarity evidence A sequence similarity analysis may involve a gene or a gene product, and it could be based on similarity to a single other gene or to a group of other genes. A type of similarity based on biomolecular sequence. ECO:0000044 ISS eco inferred from sequence or structural similarity inferred from sequence similarity GO:ISS inferred from sequence or structural similarity GO:ISS ISS A type of similarity based on biomolecular sequence. ECO:MCC TAIR:TED spatial pattern of protein expression evidence ECO:0000045 eco protein expression level evidence ECO:0000046 eco spatial pattern of transcript expression evidence ECO:0000047 eco transcript expression level evidence ECO:0000048 eco reporter gene assay evidence ECO:0000049 IEP: expression of a reporter gene Used when an annotation is made on the basis of the expression pattern of a reporter gene. The reporter gene may consist of the native promoter of the gene in question that drives the expression of a readily assayable gene product such as GUS or GFP. The reporter gene may also be a marker of a particular type of physiological response. eco TAIR:TED Used when an annotation is made on the basis of the expression pattern of a reporter gene. The reporter gene may consist of the native promoter of the gene in question that drives the expression of a readily assayable gene product such as GUS or GFP. The reporter gene may also be a marker of a particular type of physiological response. voucher specimen analysis evidence ECO:0000050 IVS Used when an annotation is made on the basis of for a phenotype description for a species or higher level group that given by an author who explicitly references an observation of a voucher specimen(s). Voucher specimens are defined as those specimens with permanent museum catalog numbers. Thus it would be possible for a person to examine this particular specimen and observe the annotated phenotype. eco PhenoScape:DOA Used when an annotation is made on the basis of for a phenotype description for a species or higher level group that given by an author who explicitly references an observation of a voucher specimen(s). Voucher specimens are defined as those specimens with permanent museum catalog numbers. Thus it would be possible for a person to examine this particular specimen and observe the annotated phenotype. genetic similarity evidence A genetic similarity analysis might consider genetic markers, polymorphisms, alleles, or other characteristics sometimes considered as part of the field of traditional genetics. Although an attempt has been made to treat as distinct the concepts of "genetic", "genotypic", "genomic", and "sequence", there is considerable overlap in usage throughout the field of biology. A type of similarity based on genotype without respect to expression. ECO:0000051 IGTS eco inferred from genetic similarity A type of similarity based on genotype without respect to expression. ECO:MCC PhenoScape:IGTS suppressor/enhancer interaction evidence ECO:0000052 IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals) TAIR:TED:0000063 eco computational combinatorial evidence A type of combinatorial analysis where data are combined and evaluated by an algorithm. Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. ECO:0000053 TAIR:TED:0000004 eco A type of combinatorial analysis where data are combined and evaluated by an algorithm. ECO:MCC ECO:go double mutant phenotype evidence ECO:0000054 IGI: double mutant analysis Used when an annotation is made based on the phenotype of double mutant organism that contains a mutation in the gene product of interest in addition to a second mutation at an unrelated locus. eco TAIT:TED Used when an annotation is made based on the phenotype of double mutant organism that contains a mutation in the gene product of interest in addition to a second mutation at an unrelated locus. array experiment evidence ECO:0000055 eco epistatic interaction evidence ECO:0000056 IGI: epistatic interactions Used when an annotation is based on results of epistatis analysis of an allele of the gene in question and a mutant allele at another locus. eco TAIR:TED Used when an annotation is based on results of epistatis analysis of an allele of the gene in question and a mutant allele at another locus. phenotypic similarity evidence A type of similarity based on the expression of a genotype in an environment. ECO:0000057 IPTS Phenotype is defined as the outcome of the expression of a genotype in a given environment. A comparison might involve whole organisms or sub-parts of organisms. eco inferred from phenotypic similarity A type of similarity based on the expression of a genotype in an environment. ECO:MCC PhenoScape:IPTS expression microarray evidence ECO:0000058 eco experimental phenotypic evidence ECO:0000014 ECO:0000059 Experimental evidence that is based on the expression of a genotype in an environment. eco inferred from phenotype ECO:MCC Experimental evidence that is based on the expression of a genotype in an environment. positional similarity evidence ECO:0000060 IPS Used when an annotation is made based on the similarity of the location and or arrangement of structures. eco PhenoScape:IPS Used when an annotation is made based on the similarity of the location and or arrangement of structures. quantitative trait analysis evidence ECO:0000061 IGI: quantitative trait analysis Used when an annotation is made for a gene product that has not been cloned but is associated with a quantitative trait locus. eco TAIR:tn Used when an annotation is made for a gene product that has not been cloned but is associated with a quantitative trait locus. genomic microarray evidence ECO:0000062 eco compositional similarity evidence ECO:0000063 ICS Used when an annotation is made based on the similarity of the histological makeup of structures. eco PhenoScape:ICS Used when an annotation is made based on the similarity of the histological makeup of structures. functional complementation in heterologous system evidence ECO:0000064 IGI: functional complementation in heterologous system Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a heterologous organism with a mutation in the homologous gene. eco TAIR:TED Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a heterologous organism with a mutation in the homologous gene. CpG island microarray evidence ECO:0000065 eco yeast one-hybrid evidence A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors. ECO:0000066 IPI: yeast one-hybrid assay PSI-MI:MI:0432 The assay involves screening a library of candidate proteins for the ability bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to a yeast reporter gene (TAIR:TED). eco one hybrid PSI-MI:MI:0432 A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors. ECO:MCC PSI-MI:MI:0432 TAIR:TED developmental similarity evidence ECO:0000067 IDS Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures. eco PhenoScape:IDS Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures. yeast 2-hybrid evidence ECO:0000068 IPI: yeast two-hybrid assay Used when an annotation is based on the interaction between two proteins in a yeast two-hybrid assay. The assay involves screening a trap-tagged library with a bait-tagged vector. The library is tagged with a DNA-binding domain (trap) and the bait is tagged with a transcriptional activation domain. Interaction between a library-trap protein and the bait results in activation of a yeast reporter gene whose transcription can be experimentally assayed. eco TAIR:TED Used when an annotation is based on the interaction between two proteins in a yeast two-hybrid assay. The assay involves screening a trap-tagged library with a bait-tagged vector. The library is tagged with a DNA-binding domain (trap) and the bait is tagged with a transcriptional activation domain. Interaction between a library-trap protein and the bait results in activation of a yeast reporter gene whose transcription can be experimentally assayed. differential methylation hybridization evidence ECO:0000069 eco co-immunoprecipitation evidence A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification. ECO:0000070 IPI: co-immunoprecipitation If performing GO annotation, the interacting protein is referenced in the evidence_with column. PSI-MI:MI:0019 eco A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification. ECO:MCC coimmunoprecipitation PSI-MI:MI:0019 morphological similarity evidence ECO:0000071 IMS Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures. eco PhenoScape:IMS Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures. Sos-recruitment assay evidence A type of physical interaction evidence that is based on a genetic screening system that detects protein-protein interactions and is not based on a transcriptional readout. ECO:0000072 IPI: Sos-recruitment assay eco true A type of physical interaction evidence that is based on a genetic screening system that detects protein-protein interactions and is not based on a transcriptional readout. TAIR:TED experimental genomic evidence ECO:0000073 Experimental evidence that characterizes an attribute of the genome underlying a gene product. eco inferred from genomic analysis ECO:MCC Experimental evidence that characterizes an attribute of the genome underlying a gene product. split-ubiquitin assay evidence ECO:0000074 IPI: split-ubiquitin assay PSI-MI:MI:0112 Used when an annotation is based on the interaction of two proteins in a split-ubiquitin assay. The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquiting (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough together to reconstitute split-ubiquitin, resulting in the release of the reporter protein by the action of the UBPs. eco ubiquitin reconstruction PSI-MI:MI:0112 TAIR:TED Used when an annotation is based on the interaction of two proteins in a split-ubiquitin assay. The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquiting (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough together to reconstitute split-ubiquitin, resulting in the release of the reporter protein by the action of the UBPs. gene expression similarity evidence ECO:0000075 IGES Used when an annotation is made based on the similarity of expression of genes in structures. eco PhenoScape:IGES Used when an annotation is made based on the similarity of expression of genes in structures. far-Western blotting evidence ECO:0000076 IPI: far-Western analysis PSI-MI:MI:0047 Used when an annotation is based on the interaction of protein with another in a far-Western assay. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody. The interacting protein is referenced in the evidence_with column. eco TAIR:TED Used when an annotation is based on the interaction of protein with another in a far-Western assay. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody. The interacting protein is referenced in the evidence_with column. methylation-specific polymerase chain reaction evidence ECO:0000077 eco methylation-specific PCR evidence Southern hybridization evidence ECO:0000078 ISS: Southern blotting Used when an annotation is based on the hybridization of a probe derived from the gene in question with a gene of known function/process/component. Can also be used when a probe derived from a gene of known function/process/component hybridizes with the gene in question. eco TAIR:TED Used when an annotation is based on the hybridization of a probe derived from the gene in question with a gene of known function/process/component. Can also be used when a probe derived from a gene of known function/process/component hybridizes with the gene in question. affinity chromatography evidence "Used when an annotation is made based on affinity chromatography, which is a selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent" (from original definition by TAIR:TED). Types of highly specific interaction might include those of antigen and antibody, enzyme and substrate, or receptor and ligand. A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound. ECO:0000079 IDA: affinity chromatography PSI-MI:MI:0004 eco affinity chromatography technology PSI-MI:MI:0004 A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound. ECO:MCC TAIR:TED phylogenetic evidence A type of similarity that indicates common ancestry. ECO:0000080 IP eco A type of similarity that indicates common ancestry. ECO:MCC PhenoScape:IP IP PhenoScape:IP targeting sequence prediction evidence ECO:0000081 ISS: targeting sequence prediction Used when a component annotation is made based on the presence of a targeting sequence in a protein's primary sequence. The presence of the targeting sequence may be detected by computational prediction and/or the author's manual examination of the sequence. eco TAIR:TED Used when a component annotation is made based on the presence of a targeting sequence in a protein's primary sequence. The presence of the targeting sequence may be detected by computational prediction and/or the author's manual examination of the sequence. polymerase chain reaction evidence ECO:0000082 PCR evidence eco transmembrane domain prediction evidence ECO:0000083 ISS: transmembrane domain prediction Used when a component annotation is made based on the presence of one or more transmembrane domains in a protein's primary sequence. The presence of the transmembrane domains may be detected by computational prediction and/or the author's manual examination of the sequence. eco TAIR:TED Used when a component annotation is made based on the presence of one or more transmembrane domains in a protein's primary sequence. The presence of the transmembrane domains may be detected by computational prediction and/or the author's manual examination of the sequence. gene neighbors evidence 2009-03-20T11:55:18Z ECO:0000084 Evidence that supports the identity of a gene product on the basis of the identity of neighboring genes. GO_REF:0000025 Genomic cluster analyses include synteny and operon structure. ICL eco inferred from genome cluster mgiglio ECO:MCC Evidence that supports the identity of a gene product on the basis of the identity of neighboring genes. GOC:mg Operon structure as IGC evidence GO_REF:0000025 immunoprecipitation evidence A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody. ECO:0000085 IDA: immunoprecipitation eco A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody. ECO:MCC TAIR:TED intermethylated site amplification evidence ECO:0000086 eco immunolocalization evidence A type of protein assay evidence that involves the use of antibodies to detect biomolecules. ECO:0000087 IDA: immunolocalization eco A type of protein assay evidence that involves the use of antibodies to detect biomolecules. ECO:MCC biological system reconstruction 2009-03-20T12:00:17Z ECO:0000088 Evidence based on reconstruction of a biological system that is based on an existing experimentally supported model of that biological system. ISR The biological system in question might be a multi-step process or a physical complex comprising several components. A common basis for system reconstruction is orthology, where all of the components of an experimentally characterized complex exist in one organism; if a second organism contains orthologs of all components, then the existence of the complex is inferred. In the case of a genome-wide analysis, a gene product is said to fulfill a necessary function for a pathway or complex when, with all of the other necessary functions or components also present, the pathway or complex is reconstructed. eco inferred from system reconstruction mgiglio ECO:MCC Evidence based on reconstruction of a biological system that is based on an existing experimentally supported model of that biological system. GOC:mg restriction landmark genomic scanning evidence ECO:0000089 RLGS evidence eco immunogold labelling evidence A type of protein assay evidence that involves attaching colloidal gold particles to a secondary antibody, which is attached to a primary antibody that binds a specific protein or cell part, followed by visualization with electron microscopy. ECO:0000090 IDA: immunogold labelling eco A type of protein assay evidence that involves attaching colloidal gold particles to a secondary antibody, which is attached to a primary antibody that binds a specific protein or cell part, followed by visualization with electron microscopy. ECO:MCC epitope-tagged protein immunolocalization evidence ECO:0000092 IDA: immunolocalization of epitope-tagged protein Used when an annotation is made based on immunolocalization of recombinant proteins fused with epitopes that are recognized by antibodies. eco TAIR:TED Used when an annotation is made based on immunolocalization of recombinant proteins fused with epitopes that are recognized by antibodies. oligonucleotide microarray evidence ECO:0000093 eco biological assay evidence Direct assay evidence that is derived by using a living organism to measure the effect of a substance, factor, or condition. ECO:0000094 IDA: bioassay eco Direct assay evidence that is derived by using a living organism to measure the effect of a substance, factor, or condition. ECO:MCC TAIR:TED electrophoretic mobility shift assay evidence ECO:0000096 IDA: electrophoretic mobility shift assay PSI-MI:MI:0413 Used when an annotation is made based on electrophoretic mobility shift of macromolecules, compounds, and proteins. Most commonly used for detecting the binding of protein to DNA. eco electrophoretic mobility shift assay PSI-MI:MI:0413 TAIR:TED Used when an annotation is made based on electrophoretic mobility shift of macromolecules, compounds, and proteins. Most commonly used for detecting the binding of protein to DNA. cDNA microarray evidence ECO:0000097 eco in situ hybridization evidence ECO:0000098 IDA: in situ hybridization Used when an annotation is made based on a method that hybridizes a labeled nucleic acid probe to a tissue or cell specimen in which the cellular structures are still intact. Depending on the label and protocol used, the probe may detect complementary DNA or RNA by hybridizing specifically to that gene or sequence. eco TAIR:TED Used when an annotation is made based on a method that hybridizes a labeled nucleic acid probe to a tissue or cell specimen in which the cellular structures are still intact. Depending on the label and protocol used, the probe may detect complementary DNA or RNA by hybridizing specifically to that gene or sequence. fractionation evidence ECO:0000100 eco Affymetrix array experiment evidence ECO:0000101 eco co-fractionation evidence ECO:0000102 IDA: co-fractionation Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules. eco TAIR:TED Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules. microarray RNA expression level evidence ECO:0000104 IEP: transcript levels (e.g. microarray data) Used when an annotation is made based on levels of RNA expression determined by microarray experiment. eco TAIR:TED Used when an annotation is made based on levels of RNA expression determined by microarray experiment. Nimblegen array evidence ECO:0000105 eco Northern assay evidence ECO:0000106 IEP: transcript levels (e.g. Northerns) Used when an annotation is made based on levels of RNA expression determined by a Northern blot experiment. eco TAIR:TED Used when an annotation is made based on levels of RNA expression determined by a Northern blot experiment. reverse transcription polymerase chain reaction transcription evidence ECO:0000108 IEP: transcript levels (e.g. RT-PCR) RT-PCR transcription evidence Used when an annotation is made based on levels of RNA expression determined by an RT-PCR experiment (quantitative or otherwise). eco TAIR:TED Used when an annotation is made based on levels of RNA expression determined by an RT-PCR experiment (quantitative or otherwise). reverse transcription polymerase chain reaction evidence ECO:0000109 RT-PCR evidence eco RNA protection assay evidence ECO:0000110 IEP: RNA protection assay Used when an annotation is made based on levels of RNA expression determined by an RNA protection assay. eco TAIR:TED Used when an annotation is made based on levels of RNA expression determined by an RNA protection assay. Western blot evidence ECO:0000112 IEP: protein levels (e.g. Western blots) Used when an annotation is made based on levels of protein expression determined by a Western blot assay. eco TAIR:TED Used when an annotation is made based on levels of protein expression determined by a Western blot assay. expression library screen evidence A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein. ECO:0000114 IEP: expression library screening eco A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein. ECO:MCC TAIR:TED differential hybridization evidence ECO:0000116 IEP: differential hybridization Used when an annotation is made based on results of a differential hybridization experiment that demonstrates expression of an RNA under one condition and not another. eco TAIR:TED Used when an annotation is made based on results of a differential hybridization experiment that demonstrates expression of an RNA under one condition and not another. subtractive hybridization evidence ECO:0000118 IEP: subtractive hybridization Used when an annotation is made based on results of a subtractive hybridization experiment that demonstrates expression of an RNA under one condition and not another. eco TAIR:TED Used when an annotation is made based on results of a subtractive hybridization experiment that demonstrates expression of an RNA under one condition and not another. over expression analysis evidence ECO:0000120 IMP: analysis of overexpression/ectopic expression phenotype Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress the gene product in question. eco TAIR:TED Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress the gene product in question. protein localization evidence ECO:0000122 eco fusion protein localization evidence ECO:0000124 eco green fluorescent protein fusion protein localization evidence ECO:0000126 GFP fusion protein localization evidence IDA: localization of GFP/YFP fusion protein eco yellow fluorescent protein fusion protein localization evidence ECO:0000128 IDA: localization of GFP/YFP fusion protein YFP fusion protein localization evidence eco beta-glucuronidase fusion protein localization evidence ECO:0000130 GUS fusion protein localization evidence GUS staining evidence IDA: localization of GUS fusion protein eco beta-galactosidase fusion protein localization evidence ECO:0000132 LacZ fusion protein localization evidence eco transport assay evidence ECO:0000134 IDA: transport assay eco nucleic acid binding evidence ECO:0000136 eco ribohomopolymer binding assay evidence ECO:0000138 IDA: ribohomopolymer binding assay eco thin layer chromatography evidence A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate. ECO:0000140 IDA: thin layer chromatography TLC evidence eco A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate. ECO:MCC protein:ion binding evidence ECO:0000142 eco Southwestern blot evidence ECO:0000144 IDA: Southwestern analysis Used when an annotation is made based on a Southwestern blot analysis, which detects DNA binding of proteins using labeled DNA as probe hybridizing to electrophoretically separated proteins. eco TAIR:TED Used when an annotation is made based on a Southwestern blot analysis, which detects DNA binding of proteins using labeled DNA as probe hybridizing to electrophoretically separated proteins. Northwestern blot evidence ECO:0000146 IDA: Northwestern analysis Used when an annotation is made based on a Northwestern blot analysis, which detects RNA binding of proteins using labeled RNA as probe hybridizing to electrophoretically separated proteins. eco TAIR:TED Used when an annotation is made based on a Northwestern blot analysis, which detects RNA binding of proteins using labeled RNA as probe hybridizing to electrophoretically separated proteins. in vitro binding evidence ECO:0000148 IDA: in vitro binding assay eco true in vitro transcription reconstitution assay evidence ECO:0000150 IDA: in vitro reconstitution assay with recombinant protein eco in vitro recombinant protein transcription reconstitution assay evidence ECO:0000152 IDA: in vitro reconstitution assay with recombinant protein eco heterologous protein expression evidence ECO:0000154 IDA: protein expression in heterologous system eco protein separation evidence ECO:0000156 eco protein separation followed by direct sequencing evidence ECO:0000158 IDA: protein separation and direct sequencing eco protein separation followed by fragment identification evidence ECO:0000160 IDA: protein separation and fragment identification eco heterologous system uptake evidence ECO:0000162 IDA: uptake assay in heterologous system Used when an annotation is made based on small molecule update assays carried out in a heterologous system that contains a recombinant protein. eco TAIR:TED Used when an annotation is made based on small molecule update assays carried out in a heterologous system that contains a recombinant protein. electrophysiology assay evidence ECO:0000164 eco two-electrode voltage clamp experiment evidence ECO:0000166 IDA: two-electrode voltage clamp technique eco transcription assay ECO:0000168 eco transcriptional activation assay ECO:0000170 IDA: transcriptional activation assay Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene. eco TAIR:TED Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene. biochemical trait analysis evidence ECO:0000172 IMP: analysis of biochemical trait Used when an annotation is made based on the analysis of a biochemical aspect of a mutant phenotype; for example, the accumulation of a biosynthetic intermediate. eco TAIR:TED Used when an annotation is made based on the analysis of a biochemical aspect of a mutant phenotype; for example, the accumulation of a biosynthetic intermediate. mutant physiological response evidence ECO:0000174 IMP: analysis of physiological response Used when an annotation is made based on the physiological response of a mutant to an external stimulus; for example, abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions. eco TAIR:TED Used when an annotation is made based on the physiological response of a mutant to an external stimulus; for example, abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions. mutant visible phenotype evidence ECO:0000176 IMP: analysis of visible trait Used when an annotation is made based on the visual examination of a mutant phenotype; for example, abnormalities in organism morphology. eco TAIR:TED Used when an annotation is made based on the visual examination of a mutant phenotype; for example, abnormalities in organism morphology. genomic context evidence An evidence type that is based on the location of a gene, which gives rise to a gene product, within the genome. ECO:0000177 This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis. eco An evidence type that is based on the location of a gene, which gives rise to a gene product, within the genome. ECO:MCC ECO:go in vivo assay evidence ECO:0000178 eco animal model system study evidence A type of experimental evidence arising from the investigation of an animal model system. ECO:0000179 eco A type of experimental evidence arising from the investigation of an animal model system. ECO:MCC clinical study evidence A type of experimental evidence arising from a controlled investigation that uses human subjects. ECO:0000180 eco A type of experimental evidence arising from a controlled investigation that uses human subjects. ECO:MCC in vitro assay evidence ECO:0000181 eco in vitro culture assay evidence ECO:0000182 eco ex vivo assay cell-free assay evidence ECO:0000183 eco in vitro assay enzyme inhibition evidence A type of specific protein inhibition evidence where the protein under study is an enzyme. ECO:0000184 eco A type of specific protein inhibition evidence where the protein under study is an enzyme. ECO:MCC sequence alignment evidence 2010-03-18T12:21:31Z ECO:00000057 ECO:0000200 ISA Used when a sequence alignment is the basis for making an annotation, but only when the alignment has been manually reviewed; or if the information is in a published paper, the authors have manually reviewed the evidence. Such alignments may be pairwise alignments or multiple alignments. BLAST produces pairwise alignments and any annotations based solely on the evaluation of BLAST results should use this code. eco inferred from sequence alignment mchibucos GO:ISA inferred from sequence alignment GO:ISA ISA Used when a sequence alignment is the basis for making an annotation, but only when the alignment has been manually reviewed; or if the information is in a published paper, the authors have manually reviewed the evidence. Such alignments may be pairwise alignments or multiple alignments. BLAST produces pairwise alignments and any annotations based solely on the evaluation of BLAST results should use this code. url:http://www.geneontology.org/GO.evidence.shtml sequence orthology evidence 2010-03-18T12:30:06Z ECO:00000060 ECO:0000201 ISO Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. Orthology is established by multiple criteria generally including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors. eco inferred from sequence orthology mchibucos ortholog evidence Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. Orthology is established by multiple criteria generally including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors. url:http://www.geneontology.org/GO.evidence.shtml GO:ISO inferred from sequence orthology GO:ISO ISO match to sequence model evidence 2010-03-18T12:32:30Z ECO:00000063 ECO:0000202 ISM Sequence similarity evidence that is based on a sequence-based statistical model that predicts the function of a gene product. Used when evidence from any kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Examples of relevant evidence are: Hidden Markov Models, PROSITE motifs, and tools such as tRNASCAN. eco inferred from sequence model mchibucos GO:ISM ISM ECO:MCC Sequence similarity evidence that is based on a sequence-based statistical model that predicts the function of a gene product. url:http://www.geneontology.org/GO.evidence.shtml GO:ISM inferred from sequence model automatic assertion 2010-03-18T12:36:04Z An assertion method that does not involve human review. An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically. ECO:00000067 ECO:0000203 eco mchibucos An assertion method that does not involve human review. ECO:MCC author statement 2010-06-21T11:17:21Z An evidence type that is based on an assertion by the author of a paper, which is read by a curator. ECO:0000204 eco mchibucos An evidence type that is based on an assertion by the author of a paper, which is read by a curator. ECO:MCC curator inference 2010-08-18T05:55:12Z An evidence type that is based on conclusions drawn by a curator. ECO:0000205 eco mchibucos An evidence type that is based on conclusions drawn by a curator. ECO:MCC BLAST evidence 2010-08-06T04:48:24Z A type of sequence alignment evidence obtained with basic local alignment search tool (BLAST). ECO:0000206 eco mchibucos A type of sequence alignment evidence obtained with basic local alignment search tool (BLAST). ECO:MCC nucleotide BLAST evidence 2010-08-06T04:49:58Z BLAST evidence from aligning nucleotide sequence with nucleotide sequence. ECO:0000207 eco mchibucos BLAST evidence from aligning nucleotide sequence with nucleotide sequence. ECO:MCC protein BLAST evidence 2010-08-06T04:50:45Z BLAST evidence from aligning amino acid or translated nucleotide sequence with amino acid or translated nucleotide sequence. ECO:0000208 eco mchibucos BLAST evidence from aligning amino acid or translated nucleotide sequence with amino acid or translated nucleotide sequence. ECO:MCC BLAST evidence used in automatic assertion 2010-08-06T04:55:21Z A type of BLAST evidence that is used in an automatic assertion. ECO:0000209 eco mchibucos A type of BLAST evidence that is used in an automatic assertion. ECO:MCC nucleotide BLAST evidence used in automatic assertion 2010-08-06T05:09:51Z ECO:0000210 Nucleotide BLAST evidence that is used in an automatic assertion. eco mchibucos ECO:MCC Nucleotide BLAST evidence that is used in an automatic assertion. protein BLAST evidence used in automatic assertion 2010-08-06T05:11:04Z ECO:0000211 Protein BLAST evidence that is used in an automatic assertion. eco mchibucos ECO:MCC Protein BLAST evidence that is used in an automatic assertion. combinatorial evidence 2010-08-06T05:24:57Z A key aspect of this type of evidence is that two or more pieces of information are combined to generate an emergent type of evidence not possible with the constituent pieces of evidence alone. A combinatorial analysis typically involves incorporation of different types of evidence. A type of evidence that arises out of the integration of more than one line of evidence. ECO:0000036 ECO:0000043 ECO:0000212 eco inferred from in-silico analysis mchibucos A type of evidence that arises out of the integration of more than one line of evidence. ECO:MCC combinatorial evidence used in automatic assertion 2010-08-06T05:28:33Z A type of combinatorial analysis that is used in an automatic assertion. Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. ECO:0000213 eco mchibucos A type of combinatorial analysis that is used in an automatic assertion. ECO:MCC biological aspect of descendant evidence 2010-10-05T11:16:50Z A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene. ECO:0000214 This type of evidence can be used in support of both positive and "not" GO annotations. It should be used to annotate ancestral genes but not extant ones. eco mchibucos A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene. ECO:MCC rapid divergence from ancestral sequence evidence 2010-10-05T03:41:34Z A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event. ECO:0000215 Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence. eco mchibucos A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event. ECO:MCC phylogenetic determination of loss of key residues evidence 2010-10-05T03:43:17Z A type of phylogenetic evidence characterized by the absence of key sequence residues. ECO:0000216 The loss of certain residues important for function can indicate that a sequence lacks a particular function. eco mchibucos A type of phylogenetic evidence characterized by the absence of key sequence residues. ECO:MCC assertion method 2010-11-12T04:17:37Z A means by which a statement is made about an entity. ECO:0000217 eco mchibucos A means by which a statement is made about an entity. ECO:MCC manual assertion 2010-11-12T04:20:02Z A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information. An assertion method that involves human review. ECO:0000218 eco mchibucos An assertion method that involves human review. ECO:MCC nucleotide sequencing assay evidence 2010-11-15T12:22:40Z A sequencing assay result for a biopolymer that comprises nucleotides. DNA sequencing ECO:0000219 eco mchibucos A sequencing assay result for a biopolymer that comprises nucleotides. ECO:MCC DNA sequencing OBI:0000626 sequencing assay evidence 2010-11-15T01:44:45Z A type of experimental evidence where the order of molecules that constitute a biopolymer is determined. ECO:0000220 eco mchibucos A type of experimental evidence where the order of molecules that constitute a biopolymer is determined. ECO:MCC OBI:0600047 high throughput nucleotide sequencing assay evidence 2010-11-15T02:19:34Z A nucleotide sequencing assay result that is derived from a parallelized sequencing technique. ECO:0000221 Typically thousands to millions of reads are produced in parallel. eco mchibucos A nucleotide sequencing assay result that is derived from a parallelized sequencing technique. ECO:MCC Illumina sequencing evidence 2010-11-15T02:38:03Z A high throughput nucleotide sequencing result derived by Illumina (Solexa) sequencing technology. ECO:0000222 In Illumina sequencing technology, adapters are ligated onto the ends of randomly fragmented DNA. After single-stranded fragments are bound to the inside surface of a flow cell channel, they undergo in-place bridge PCR amplification. To begin the sequencing cycle, labeled reversible terminators, primers and DNA polymerase are added, followed by laser excitation of the fluorescent label and high resolution scanning. After non-incorporated nucleotides are washed away and the dye is chemically removed, the next cycle repeats with four labeled reversible terminators, primers and DNA polymerase, again followed by imaging. Solexa sequencing result eco mchibucos A high throughput nucleotide sequencing result derived by Illumina (Solexa) sequencing technology. ECO:MCC OBI:0000724 Solexa sequencing result 454 pyrosequencing evidence 2010-11-15T03:50:14Z 454 pyrosequencing technology amplifies individual DNA fragments inside water droplets within an oil solution (emulsion PCR). Within each droplet, a single DNA template is attached to a single primer-coated bead. Each bead is subsequently captured in a picolitre well within the sequencing machine. A luciferase-based readout system is used to identify individual nucleotides added to the nascent DNA. A high throughput nucleotide sequencing result derived by 454 pyrosequencing technology. ECO:0000223 eco mchibucos pyrosequencing A high throughput nucleotide sequencing result derived by 454 pyrosequencing technology. ECO:MCC OBI:0000730 pyrosequencing SOLiD sequencing evidence 2010-11-15T04:17:41Z A high throughput nucleotide sequencing result derived by SOLiD sequencing technology. ECO:0000224 SOLiD sequencing technology is based on sequencing by ligation. After library preparation, emulsion PCR and bead enrichment are performed, including 3' modification of templates on selected beads to allow covalent bonding to a slide. 3' modified beads are attached to a glass slide and primers are added. Four fluorescently labeled di-base probes are added and multiple cycles of ligation, detection and cleavage are performed. The number of cycles determines read length. After a number of ligation cycles, the extension product is removed and another round of ligation cycles is performed with a new primer complimentary to the n-1 position of the template. Five rounds of primer reset are performed for each sequence tag. eco mchibucos A high throughput nucleotide sequencing result derived by SOLiD sequencing technology. ECO:MCC OBI:0000706 chain termination sequencing evidence 2010-11-15T04:46:31Z A nucleotide sequencing assay result derived by the chain termination sequencing method. Chain termination sequencing, also called Sanger sequencing after its developer, uses dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. Single-stranded DNA template, DNA primer, DNA polymerase, fluorescently or radioactively labeled nucleotides, and one of four ddNTPs are added together in each of four separate sequencing reactions. The synthesized and labeled DNA fragments from each of the four reactions are denatured, separated by size by gel electrophoresis, and visualized by autoradiography or UV light. ECO:0000225 Sanger sequencing dye terminator sequencing eco mchibucos A nucleotide sequencing assay result derived by the chain termination sequencing method. ECO:MCC OBI:0000695 chromatin immunoprecipitation evidence 2010-11-16T01:29:08Z A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence. ChIP evidence Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq). ECO:0000226 PSI-MI:MI:0402 eco mchibucos chromatin immunoprecipitation assay PSI-MI:MI:0402 A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence. ECO:MCC chromatin immunoprecipitation-PCR evidence 2010-11-16T05:02:00Z A chromatin immunoprecipitation (ChIP) evidence that uses polymerase chain reaction (PCR) for DNA detection. ChIP-PCR evidence ECO:0000227 eco mchibucos A chromatin immunoprecipitation (ChIP) evidence that uses polymerase chain reaction (PCR) for DNA detection. ECO:MCC chromatin immunoprecipitation-qPCR evidence 2010-11-16T05:26:47Z A chromatin immunoprecipitation (ChIP) evidence that uses quantitative polymerase chain reaction (qPCR) for DNA detection. ChIP-qPCR evidence ECO:0000228 eco mchibucos A chromatin immunoprecipitation (ChIP) evidence that uses quantitative polymerase chain reaction (qPCR) for DNA detection. ECO:MCC chromatin immunoprecipitation-seq evidence 2010-11-16T05:30:41Z A chromatin immunoprecipitation (ChIP) evidence that uses high-throughput sequencing for DNA detection. ChIP-SEQ evidence ChIP-seq evidence ECO:0000229 eco mchibucos A chromatin immunoprecipitation (ChIP) evidence that uses high-throughput sequencing for DNA detection. ECO:MCC OBI:0000716 ChIP-SEQ evidence OBI:0000716 chromatin immunoprecipitation-chip evidence 2010-11-16T05:43:55Z A chromatin immunoprecipitation (ChIP) evidence that uses a tiling microarray for DNA detection. ChIP-chip evidence ChIP-on-chip evidence ECO:0000230 PSI-MI:MI:0225 eco mchibucos A chromatin immunoprecipitation (ChIP) evidence that uses a tiling microarray for DNA detection. ECO:MCC chromatin immunoprecipitation array PSI-MI:MI:0225 quantitative polymerase chain reaction evidence 2010-11-16T05:57:20Z A polymerase chain reaction experiment where the reaction product is quantified in real-time across cycles by means of fluorescent dyes. ECO:0000231 Q-PCR evidence Quantitative PCR enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. eco mchibucos qRT-PCR evidence quantitative PCR evidence real-time PCR evidence real-time polymerase chain reaction evidence A polymerase chain reaction experiment where the reaction product is quantified in real-time across cycles by means of fluorescent dyes. ECO:MCC chromosome conformation capture-based evidence 2010-11-17T12:27:14Z 3C A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, and DNA processing and quantitation. Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C. ECO:0000232 chromosome conformation capture eco mchibucos A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, and DNA processing and quantitation. ECO:MCC chromosome conformation capture evidence 2010-11-17T12:46:15Z 3C 3C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C differs only in the fifth step, which involves performing either standard polymerase chain reaction (PCR) or quantitative PCR (qPCR) for product quantitation. A type of chromosome conformation capture-based evidence that is derived by performing a type of polymerase chain reaction (PCR) in the final product quantitation step. ECO:0000233 eco mchibucos A type of chromosome conformation capture-based evidence that is derived by performing a type of polymerase chain reaction (PCR) in the final product quantitation step. ECO:MCC circularized chromosome conformation capture evidence 2010-11-19T01:20:28Z 4C 4C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 4C differs only in the fifth step, which involves inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation. A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray. ECO:0000234 chromosome conformation capture on chip circularized 3C eco mchibucos A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray. ECO:MCC carbon-copy chromosome conformation capture evidence 2010-11-19T01:22:20Z 5C 5C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 5C differs only in the fifth step, which involves ligation-mediated amplification (LMA) followed by product quantitation. A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation. ECO:0000235 carbon-copy 3C eco mchibucos A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation. ECO:MCC chromosome conformation capture-PCR evidence 2010-11-19T03:00:47Z 3C 3C-PCR A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step. ECO:0000236 eco mchibucos A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step. ECO:MCC chromosome conformation capture-qPCR evidence 2010-11-19T03:06:47Z 3C-qPCR 3C-quantitative PCR 3C-real-time PCR A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step. ECO:0000237 eco mchibucos A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step. ECO:MCC Hi-C evidence 2010-11-19T04:24:03Z A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation. ECO:0000238 Hi-C is used to study the structural properties and spatial organization of chromosomes inside cells. Hi-C is similar to other types of chromosome conformation capture technology, but involves the addition of biotinylated nucleotides during the second or fourth step and enrichment for ligated fragments using immunoprecipitation after the fourth step. eco mchibucos A type of chromosome conformation capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation. ECO:MCC chromosome conformation capture sequencing evidence 2010-11-30T03:22:25Z 3C sequencing 3C-seq 3C-seq is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C-seq differs only in the fifth step, which involves inverse polymerase chain reaction (PCR) on a circularized 3C library prior to product quantitation. 4C sequencing 4C-seq A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with high-throughput (HT) sequencing. ECO:0000239 circularized 3C sequencing circularized 3C-seq eco mchibucos A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with high-throughput (HT) sequencing. ECO:MCC anatomical perturbation evidence 2010-12-06T12:24:16Z ECO:0000240 Experimental phenotypic evidence where a structural feature of an organism is disrupted. eco mchibucos ECO:MCC Experimental phenotypic evidence where a structural feature of an organism is disrupted. environmental perturbation evidence 2010-12-06T12:33:58Z ECO:0000241 Experimental phenotypic evidence where the extra-organismal context of an organism is modified. Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth. eco mchibucos mechanical constraint evidence ECO:MCC Experimental phenotypic evidence where the extra-organismal context of an organism is modified. tissue ablation evidence 2010-12-06T12:33:58Z A tissue ablation experiment involves observing the phenotype of an entity whose tissues have been disrupted through genetic or biochemical manipulation, physical destruction, or some other means. A type of anatomical perturbation that is based on disruption of tissue. ECO:0000242 ablated tissue evidence eco mchibucos A type of anatomical perturbation that is based on disruption of tissue. ECO:MCC tissue grafting evidence 2010-12-06T12:33:58Z A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure. ECO:0000243 eco mchibucos A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure. ECO:MCC combinatorial evidence used in manual assertion 2010-12-09T02:02:12Z A type of combinatorial analysis that is used in a manual assertion. Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. ECO:0000244 eco mchibucos A type of combinatorial analysis that is used in a manual assertion. ECO:MCC computational combinatorial evidence used in manual assertion 2010-12-09T02:37:54Z A type of computational combinatorial analysis that is used in a manual assertion. ECO:0000245 GOECO:RCA RCA eco inferred from reviewed computational analysis mchibucos A type of computational combinatorial analysis that is used in a manual assertion. ECO:MCC GOECO:RCA inferred from reviewed computational analysis inferred from reviewed computational analysis GOECO:RCA GOECO:RCA RCA computational combinatorial evidence used in automatic assertion 2010-12-09T02:37:54Z A type of computational combinatorial analysis that is used in an automatic assertion. ECO:0000246 eco mchibucos A type of computational combinatorial analysis that is used in an automatic assertion. ECO:MCC sequence alignment evidence used in manual assertion 2010-12-09T05:12:27Z ECO:0000247 GOECO:ISA ISA Sequence alignment evidence that is used in a manual assertion. eco inferred from sequence alignment mchibucos inferred from sequence alignment GOECO:ISA ECO:MCC Sequence alignment evidence that is used in a manual assertion. GOECO:ISA inferred from sequence alignment GOECO:ISA ISA sequence alignment evidence used in automatic assertion 2010-12-09T05:12:27Z ECO:0000248 Sequence alignment evidence that is used in an automatic assertion. eco mchibucos ECO:MCC Sequence alignment evidence that is used in an automatic assertion. sequence similarity evidence used in automatic assertion 2010-12-09T05:22:30Z ECO:0000249 Sequence similarity evidence that is used in an automatic assertion. eco mchibucos ECO:MCC Sequence similarity evidence that is used in an automatic assertion. sequence similarity evidence used in manual assertion 2010-12-09T05:22:30Z ECO:0000250 GOECO:ISS Sequence similarity evidence that is used in a manual assertion. eco mchibucos inferred from sequence or structural similarity GOECO:ISS ECO:MCC Sequence similarity evidence that is used in a manual assertion. similarity evidence used in automatic assertion 2010-12-09T05:28:12Z ECO:0000251 Similarity evidence that is used in an automatic assertion. eco mchibucos ECO:MCC Similarity evidence that is used in an automatic assertion. similarity evidence used in manual assertion 2010-12-09T05:28:12Z ECO:0000252 Similarity evidence that is used in a manual assertion. eco mchibucos ECO:MCC Similarity evidence that is used in a manual assertion. genetic similarity evidence used in manual assertion 2010-12-10T01:42:44Z ECO:0000253 Genetic similarity evidence that is used in a manual assertion. eco mchibucos ECO:MCC Genetic similarity evidence that is used in a manual assertion. genetic similarity evidence used in automatic assertion 2010-12-10T01:42:44Z ECO:0000254 Genetic similarity evidence that is used in an automatic assertion. eco mchibucos ECO:MCC Genetic similarity evidence that is used in an automatic assertion. match to sequence model evidence used in manual assertion 2010-12-10T02:26:35Z A match to sequence model evidence that is employed in a manual assertion. ECO:0000255 GOECO:ISM GO_REF:0000011 eco mchibucos inferred from sequence model GOECO:ISM Hidden Markov Models (TIGR) GO_REF:0000011 A match to sequence model evidence that is employed in a manual assertion. ECO:MCC match to sequence model evidence used in automatic assertion 2010-12-10T02:26:35Z A match to sequence model evidence that is employed in an automatic assertion. ECO:0000256 GO_REF:0000002 GO_REF:0000019 eco mchibucos Gene Ontology annotation through association of InterPro records with GO terms. GO_REF:0000002 A match to sequence model evidence that is employed in an automatic assertion. ECO:MCC Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara GO_REF:0000019 motif similarity evidence used in manual assertion 2010-12-10T02:44:34Z ECO:0000257 Motif similarity evidence that is employed in a manual assertion. eco mchibucos ECO:MCC Motif similarity evidence that is employed in a manual assertion. motif similarity evidence used in automatic assertion 2010-12-10T02:44:34Z ECO:0000258 Motif similarity evidence that is employed in an automatic assertion. eco mchibucos ECO:MCC Motif similarity evidence that is employed in an automatic assertion. match to InterPro signature evidence used in automatic assertion 2010-12-10T02:54:51Z A match to InterPro signature evidence that is employed in an automatic assertion. ECO:0000259 eco mchibucos A match to InterPro signature evidence that is employed in an automatic assertion. ECO:MCC match to InterPro signature evidence used in manual assertion 2010-12-10T02:54:51Z A match to InterPro signature evidence that is employed in a manual assertion. ECO:0000260 eco mchibucos A match to InterPro signature evidence that is employed in a manual assertion. ECO:MCC targeting sequence prediction evidence used in automatic assertion 2010-12-10T03:02:49Z A targeting sequence prediction that is employed in an automatic assertion. ECO:0000261 eco mchibucos A targeting sequence prediction that is employed in an automatic assertion. ECO:MCC targeting sequence prediction evidence used in manual assertion 2010-12-10T03:02:49Z A targeting sequence prediction that is employed in a manual assertion. ECO:0000262 eco mchibucos A targeting sequence prediction that is employed in a manual assertion. ECO:MCC transmembrane domain prediction evidence used in automatic assertion 2010-12-10T03:28:35Z ECO:0000263 Transmembrane domain prediction that is employed in an automatic assertion. eco mchibucos ECO:MCC Transmembrane domain prediction that is employed in an automatic assertion. transmembrane domain prediction evidence used in manual assertion 2010-12-10T03:28:35Z ECO:0000264 Transmembrane domain prediction that is employed in a manual assertion. eco mchibucos ECO:MCC Transmembrane domain prediction that is employed in a manual assertion. sequence orthology evidence used in automatic assertion 2010-12-10T03:39:41Z ECO:0000265 GO_REF:0000003 GO_REF:0000019 GO_REF:0000035 Ortholog evidence Sequence orthology evidence that is employed in an automatic assertion. eco mchibucos Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara GO_REF:0000035 Gene Ontology annotation based on Enzyme Commission mapping. GO_REF:0000003 Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara GO_REF:0000019 ECO:MCC Sequence orthology evidence that is employed in an automatic assertion. sequence orthology evidence used in manual assertion 2010-12-10T03:39:41Z ECO:0000266 GOECO:ISO Ortholog evidence Sequence orthology evidence that is employed in a manual assertion. eco mchibucos ECO:MCC Sequence orthology evidence that is employed in a manual assertion. inferred from sequence orthology GOECO:ISO enzyme-linked immunoabsorbent assay evidence 2010-12-14T01:57:13Z A type of protein assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen. ECO:0000267 ELISA evidence PSI-MI:MI:0411 eco enzyme-linked immunosorbent assay mchibucos A type of protein assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen. ECO:MCC enzyme linked immunosorbent assay PSI-MI:MI:0411 flow cytometry evidence 2010-12-14T02:07:08Z A direct assay that passes a stream of cells or particles past a light source, followed by using a detector to monitor light scatter or fluorochrome excitation to characterize the cells or particles. ECO:0000268 FCM eco mchibucos A direct assay that passes a stream of cells or particles past a light source, followed by using a detector to monitor light scatter or fluorochrome excitation to characterize the cells or particles. ECO:MCC experimental evidence used in manual assertion 2010-12-20T05:36:49Z A type of experimental evidence that is used in a manual assertion. ECO:0000269 GOECO:EXP eco mchibucos A type of experimental evidence that is used in a manual assertion. ECO:MCC inferred from experiment GOECO:EXP expression evidence used in manual assertion 2010-12-20T05:46:39Z A type of expression pattern evidence that is used in a manual assertion. ECO:0000270 GOECO:IEP eco mchibucos A type of expression pattern evidence that is used in a manual assertion. ECO:MCC inferred from expression pattern GOECO:IEP array experiment evidence used in manual assertion 2010-12-20T05:51:58Z A type of array experiment evidence that is used in a manual assertion. ECO:0000271 eco mchibucos A type of array experiment evidence that is used in a manual assertion. ECO:MCC Affymetrix array experiment evidence used in manual assertion 2010-12-20T05:53:36Z A type of Affymetrix array experiment evidence that is used in a manual assertion. ECO:0000272 eco mchibucos A type of Affymetrix array experiment evidence that is used in a manual assertion. ECO:MCC cDNA microarray evidence used in manual assertion 2010-12-20T05:55:49Z A type of evidence arising from a cDNA microarray experiment that is used in a manual assertion. ECO:0000273 eco mchibucos A type of evidence arising from a cDNA microarray experiment that is used in a manual assertion. ECO:MCC CpG island microarray evidence used in manual assertion 2010-12-20T05:58:44Z A type of evidence arising from a CpG island microarray experiment that is used in a manual assertion. ECO:0000274 eco mchibucos A type of evidence arising from a CpG island microarray experiment that is used in a manual assertion. ECO:MCC expression microarray evidence used in manual assertion 2010-12-20T06:01:26Z A type of expression microarray evidence that is used in a manual assertion. ECO:0000275 eco mchibucos A type of expression microarray evidence that is used in a manual assertion. ECO:MCC genomic microarray evidence used in manual assertion 2010-12-20T06:03:28Z A type of evidence arising from a genomic microarray experiment that is used in a manual assertion. ECO:0000276 eco mchibucos A type of evidence arising from a genomic microarray experiment that is used in a manual assertion. ECO:MCC Nimblegen array evidence used in manual assertion 2010-12-20T06:05:20Z A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion. ECO:0000277 eco mchibucos A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion. ECO:MCC oligonucleotide microarray evidence used in manual assertion 2010-12-20T06:09:45Z A type of evidence arising from an oligonucleotide microarray experiment that is used in a manual assertion. ECO:0000278 eco mchibucos A type of evidence arising from an oligonucleotide microarray experiment that is used in a manual assertion. ECO:MCC Western blot evidence used in manual assertion 2010-12-20T06:20:01Z A type of Western blot assay that is used in a manual assertion. ECO:0000279 eco mchibucos A type of Western blot assay that is used in a manual assertion. ECO:MCC protein expression level evidence used in manual assertion 2010-12-20T06:21:54Z A type of protein expression level analysis that is used in a manual assertion. ECO:0000280 eco mchibucos A type of protein expression level analysis that is used in a manual assertion. ECO:MCC expression library screen evidence used in manual assertion 2010-12-20T06:24:05Z A type of expression library screen evidence that is used in a manual assertion. ECO:0000281 eco mchibucos A type of expression library screen evidence that is used in a manual assertion. ECO:MCC heterologous protein expression evidence used in manual assertion 2010-12-20T06:27:04Z A type of heterologous protein expression analysis that is used in a manual assertion. ECO:0000282 eco mchibucos A type of heterologous protein expression analysis that is used in a manual assertion. ECO:MCC spatial pattern of protein expression evidence used in manual assertion 2010-12-20T06:31:44Z A type of protein expression spatial pattern analysis that is used in a manual assertion. ECO:0000283 eco mchibucos A type of protein expression spatial pattern analysis that is used in a manual assertion. ECO:MCC protein expression evidence used in manual assertion 2010-12-20T06:33:46Z A type of protein expression analysis that is used in a manual assertion. ECO:0000284 eco mchibucos A type of protein expression analysis that is used in a manual assertion. ECO:MCC microarray RNA expression level evidence used in manual assertion 2010-12-20T06:41:33Z A type of microarray RNA expression level data that is used in manual assertion. ECO:0000285 eco mchibucos A type of microarray RNA expression level data that is used in manual assertion. ECO:MCC transcript expression level used in manual assertion 2010-12-20T06:52:03Z A type of transcript expression level data that is used in manual assertion. ECO:0000286 eco mchibucos A type of transcript expression level data that is used in manual assertion. ECO:MCC differential hybridization evidence used in manual assertion 2010-12-20T06:55:14Z A type of differential hybridization experiment that is used in a manual assertion. ECO:0000287 eco mchibucos A type of differential hybridization experiment that is used in a manual assertion. ECO:MCC RNA protection assay evidence used in manual assertion 2010-12-20T06:57:33Z A type of RNA protection assay that is used in a manual assertion. ECO:0000288 eco mchibucos A type of RNA protection assay that is used in a manual assertion. ECO:MCC spatial pattern of transcript expression evidence used in manual assertion 2010-12-20T06:59:18Z A type of spatial pattern of transcript expression analysis that is used in a manual assertion. ECO:0000289 eco mchibucos A type of spatial pattern of transcript expression analysis that is used in a manual assertion. ECO:MCC subtractive hybridization evidence used in manual assertion 2010-12-20T07:00:48Z A type of subtractive hybridization experiment that is used in a manual assertion. ECO:0000290 eco mchibucos A type of subtractive hybridization experiment that is used in a manual assertion. ECO:MCC transcript expression evidence used in manual assertion 2010-12-20T07:02:08Z A type of transcript expression evidence that is used in a manual assertion. ECO:0000291 eco mchibucos A type of transcript expression evidence that is used in a manual assertion. ECO:MCC morpholino experiment evidence 2011-01-10T03:36:25Z A type of experimental phenotypic evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell. ECO:0000292 Morpholino oligonucleotides modify gene expression by blocking access of other molecules to specific, approximately 25-base-long regions of the base-pairing surfaces of ribonucleic acid (RNA). To achieve this anti-sense knockdown technique, delivery of the morpholino can be achieved via microinjection, electroporation, or another method. anti-sense eco mchibucos A type of experimental phenotypic evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell. ECO:MCC systematic evolution of ligands by exponential amplification evidence 2011-01-10T04:23:50Z A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand. ECO:0000293 PSI-MI:MI:0657 SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein. SELEX evidence eco in vitro evolution evidence in vitro selection evidence mchibucos A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand. ECO:MCC url:http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment systematic evolution of ligands by exponential enrichment PSI-MI:MI:0657 bacterial one-hybrid evidence 2011-01-10T06:16:20Z A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey). B1H evidence Bacterial one-hybrid assay is a method for screening a library of candidate proteins (prey plasmid) for the ability to bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to reporter genes (bait plasmid). Transformation of a bacterial host with two different plasmids is required: One is designed to express the "bait". The other plasmid contains a "prey" which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes. ECO:0000294 eco mchibucos A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey). ECO:MCC RNA-seq evidence 2011-01-11T12:54:50Z A type of transcript expression evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules. ECO:0000295 RNA sequencing Total RNA is isolated from cells and mRNA is purified by targeting the 3' polyadenylated (poly(A)) tail with poly(T) oligos covalently attached to a substrate. Next, cDNA fragments are generated either by hydrolysis of RNA into 200-300 base oligonucleotides, preceded by reverse transcription, or by reverse transcription initiated by random primers. The cDNA second strand is synthesized, fragments are adapter ligated and high-throughput sequencing is performed by Roche 454, Illumina, ABI-SOLiD, or another HT sequencing technology. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed. WTSS eco mchibucos whole transcriptome shotgun sequencing PMID:18611170 whole transcriptome shotgun sequencing A type of transcript expression evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules. ECO:MCC green fluorescent protein transcript localization evidence 2011-01-11T02:31:19Z A transcriptional activation assay that uses a green fluorescent protein (GFP) reporter gene. ECO:0000296 This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of green fluorescent protein". eco localization of GFP transcript mchibucos A transcriptional activation assay that uses a green fluorescent protein (GFP) reporter gene. ECO:MCC LacZ transcript localization evidence 2011-01-11T02:53:19Z A transcriptional activation assay that uses a LacZ reporter gene. ECO:0000297 This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of LacZ protein". eco mchibucos A transcriptional activation assay that uses a LacZ reporter gene. ECO:MCC cleavage arrested development evidence 2011-01-11T03:28:49Z A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked. ECO:0000298 In the embryos of some organisms, inhibition of cytokinesis blocks neither the cell cycle nor the unfolding of the developmental program. As such, embryonic morphology can be frozen, allowing analysis of the developmental fate of each cell present at the time of cleavage arrest. eco mchibucos A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked. ECO:MCC cytochalasin experiment evidence 2011-01-11T03:30:29Z A type of cleavage arrested development that arises after treatment with cytochalasin. Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments. ECO:0000299 eco mchibucos A type of cleavage arrested development that arises after treatment with cytochalasin. ECO:MCC green fluorescent protein immunolocalization evidence 2011-01-11T03:48:50Z A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker. ECO:0000300 GFP immunolocalization evidence This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript". eco mchibucos A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker. ECO:MCC beta-galactosidase protein immunolocalization evidence 2011-01-11T04:06:40Z A type of immunolocalization evidence that was generated using LacZ protein as a marker. ECO:0000301 LacZ protein immunolocalization evidence This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript". eco mchibucos A type of immunolocalization evidence that was generated using LacZ protein as a marker. ECO:MCC author statement used in manual assertion 2011-01-20T02:26:47Z A type of author statement that is used in a manual assertion. ECO:0000302 eco mchibucos A type of author statement that is used in a manual assertion. ECO:MCC non-traceable author statement used in manual assertion 2011-01-20T02:29:50Z A type of non-traceable author statement that is used in a manual assertion. ECO:0000303 GOECO:NAS NAS eco mchibucos non-traceable author statement non-traceable author statement GOECO:NAS A type of non-traceable author statement that is used in a manual assertion. ECO:MCC GOECO:NAS non-traceable author statement GOECO:NAS NAS traceable author statement used in manual assertion 2011-01-20T02:31:03Z A type of traceable author statement that is used in a manual assertion. ECO:0000304 GOECO:TAS TAS eco mchibucos traceable author statement traceable author statement GOECO:TAS GOECO:TAS traceable author statement GOECO:TAS TAS A type of traceable author statement that is used in a manual assertion. ECO:MCC curator inference used in manual assertion 2011-01-20T02:33:32Z A type of curator inference that is used in a manual assertion. ECO:0000305 GOECO:IC eco mchibucos inferred by curator GOECO:IC A type of curator inference that is used in a manual assertion. ECO:MCC inference from background scientific knowledge used in manual assertion 2011-01-20T02:35:11Z A type of inference from background scientific knowledge that is used in a manual assertion. ECO:0000306 eco mchibucos A type of inference from background scientific knowledge that is used in a manual assertion. ECO:MCC no biological data found used in manual assertion 2011-01-20T02:43:18Z A type of no biological data found that is used in a manual assertion. ECO:0000307 GOECO:ND eco mchibucos no biological data available GOECO:ND A type of no biological data found that is used in a manual assertion. ECO:MCC biological aspect of ancestor evidence 2011-02-04T05:41:26Z A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene. ECO:0000308 First, a characteristic of the most recent common ancestor (MRCA) is inferred from experimental evidence in descendants; this is followed by inferring a characteristic of a descendant of the MRCA. This type of evidence can be used in support of both positive and "not" GO annotations. eco mchibucos A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene. ECO:MCC cap analysis of gene expression evidence 2011-02-17T01:33:09Z A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system. CAGE ECO:0000309 cDNA is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed. eco mchibucos A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system. ECO:MCC CAGE PMID:16489339 nano-cap analysis of gene expression evidence 2011-02-17T01:33:34Z A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching. ECO:0000310 NanoCAGE captures the 5' ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5' full length cDNAs is extended upon hybridization of the riboguanosine-tailed template switching oligonucleotides to these extra cytosines. In semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers, which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template switching, semisuppressive PCR, and EcoP151 cleavage, 25-bp tags are ligated to bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA. eco mchibucos nanoCAGE A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching. ECO:MCC PMID:20543846 nanoCAGE imported information 2011-03-02T05:24:13Z An evidence type that is based on work performed by a person or group prior to a use by different person or group. ECO:0000311 eco mchibucos An evidence type that is based on work performed by a person or group prior to a use by different person or group. ECO:MCC imported information used in manual assertion 2011-03-02T05:29:44Z A type of imported information that is used in a manual assertion. ECO:0000312 eco mchibucos A type of imported information that is used in a manual assertion. ECO:MCC imported information used in automatic assertion 2011-03-02T05:33:43Z A type of imported information that is used in an automatic assertion. ECO:0000313 eco mchibucos A type of imported information that is used in an automatic assertion. ECO:MCC direct assay evidence used in manual assertion 2011-10-28T04:59:31Z A type of direct assay evidence that is used in a manual assertion. ECO:0000314 GOECO:IDA IDA eco inferred from direct assay mchibucos A type of direct assay evidence that is used in a manual assertion. ECO:MCC inferred from direct assay GOECO:IDA GOECO:IDA IDA GOECO:IDA inferred from direct assay mutant phenotype evidence used in manual assertion 2011-10-28T05:12:49Z A type of mutant phenotype evidence that is used in a manual assertion. ECO:0000315 GOECO:IMP IMP eco inferred from mutant phenotype mchibucos inferred from mutant phenotype GOECO:IMP GOECO:IMP inferred from mutant phenotype A type of mutant phenotype evidence that is used in a manual assertion. ECO:MCC GOECO:IMP IMP genetic interaction evidence used in manual assertion 2011-10-28T05:14:42Z A type of genetic interaction experiment evidence that is used in a manual assertion. ECO:0000316 GOECO:IGI IGI eco inferred from genetic interaction mchibucos GOECO:IGI inferred from genetic interaction GOECO:IGI IGI inferred from genetic interaction GOECO:IGI A type of genetic interaction experiment evidence that is used in a manual assertion. ECO:MCC genomic context evidence used in manual assertion 2011-10-28T05:22:53Z A type of genomic context evidence that is used in a manual assertion. ECO:0000317 GOECO:IGC IGC eco inferred from genomic context mchibucos A type of genomic context evidence that is used in a manual assertion. ECO:MCC inferred from genomic context GOECO:IGC GOECO:IGC inferred from genomic context GOECO:IGC IGC biological aspect of ancestor evidence used in manual assertion 2011-10-28T05:23:51Z A type of biological aspect of ancestor evidence that is used in a manual assertion. ECO:0000318 GOECO:IBA IBA eco inferred from biological aspect of ancestor mchibucos GOECO:IBA inferred from biological aspect of ancestor A type of biological aspect of ancestor evidence that is used in a manual assertion. ECO:MCC inferred from biological aspect of ancestor GOECO:IBA GOECO:IBA IBA biological aspect of descendant evidence used in manual assertion 2011-10-28T05:25:09Z A type of biological aspect of descendant evidence that is used in a manual assertion. ECO:0000319 GOECO:IBD IBD eco inferred from biological aspect of descendant mchibucos GOECO:IBD inferred from biological aspect of descendant GOECO:IBD IBD A type of biological aspect of descendant evidence that is used in a manual assertion. ECO:MCC inferred from biological aspect of descendant GOECO:IBD phylogenetic determination of loss of key residues evidence used in manual assertion 2011-10-28T05:25:48Z A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion. ECO:0000320 GOECO:IKR GOECO:IMR IKR IMR eco inferred from key residues inferred from missing residues mchibucos GOECO:IKR inferred from missing residues GOECO:IKR inferred from key residues inferred from missing residues GOECO:IMR inferred from key residues GOECO:IKR GOECO:IKR IKR A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion. ECO:MCC GOECO:IKR IMR rapid divergence from ancestral sequence evidence used in manual assertion 2011-10-28T05:26:42Z A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion. ECO:0000321 GOECO:IRD IRD eco inferred from rapid divergence mchibucos GOECO:IRD IRD GOECO:IRD inferred from rapid divergence A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion. ECO:MCC inferred from rapid divergence GOECO:IRD imported manually asserted information used in automatic assertion 2011-12-13T12:04:48Z ECO:0000322 Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion. eco mchibucos ECO:MCC Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion. imported automatically asserted information used in automatic assertion 2011-12-13T02:06:25Z ECO:0000323 Evidence that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion. eco mchibucos ECO:MCC Evidence that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion. imaging assay evidence 2012-02-23T12:01:43Z Direct assay evidence derived from analysis of an image. ECO:0000324 eco mchibucos Direct assay evidence derived from analysis of an image. ECO:MCC chromatography evidence 2012-05-16T11:46:27Z A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase. ECO:0000325 chromatographic evidence eco mchibucos A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase. ECO:MCC transcript splice pattern evidence 2012-06-08T11:03:59Z A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript. ECO:0000326 eco mchibucos A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript. ECO:MCC whole transcript splice pattern evidence 2012-06-08T11:11:24Z A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features. ECO:0000327 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. eco mchibucos A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features. ECO:MCC coding sequence splice pattern evidence 2012-06-08T11:21:57Z A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript. ECO:0000328 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. eco mchibucos A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript. ECO:MCC whole transcript splice pattern evidence used in manual assertion 2012-06-08T11:40:03Z A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion. ECO:0000329 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. eco mchibucos A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion. ECO:MCC coding sequence splice pattern evidence used in manual assertion 2012-06-08T11:43:47Z A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion. ECO:0000330 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. eco mchibucos A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion. ECO:MCC coding sequence splice pattern evidence used in automatic assertion 2012-06-08T11:48:09Z A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion. ECO:0000331 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. eco mchibucos A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion. ECO:MCC whole transcript splice pattern evidence used in automatic assertion 2012-06-08T11:49:17Z A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion. ECO:0000332 This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. eco mchibucos A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion. ECO:MCC sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence 2012-07-31T14:56:43Z A type of protein assay evidence where proteins are separated according to their electrophoretic mobility. ECO:0000333 Electrophoretic mobility is a function of both the length and charge of a protein. The protein sample is linearized with sodium dodecyl sulfate (SDS), an anionic detergent. Typically, polypeptides bound with SDS possess an even distribution of charge per unit mass, and subsequent fractionation is by size. SDS-PAGE evidence eco mchibucos A type of protein assay evidence where proteins are separated according to their electrophoretic mobility. ECO:MCC PubMed:4861258 particle size and count assay evidence 2012-07-31T15:19:32Z A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined. An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system. ECO:0000334 eco mchibucos A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined. ECO:MCC substance quantification evidence 2012-07-31T15:52:46Z A type of direct assay evidence where the quantity of a substance used as part of an assay is measured. ECO:0000335 Two examples of substance quantification assay are (i) measuring how much of a radiolabelled compound is taken up by a cell and (ii) measuring how much of a substrate is turned over by a given enzyme. eco mchibucos A type of direct assay evidence where the quantity of a substance used as part of an assay is measured. ECO:MCC competitive growth assay evidence 2012-08-24T12:03:58Z A type of biological assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed. ECO:0000336 eco fitness profiling mchibucos GOC:MAH PMID:20537132 fitness profiling A type of biological assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed. GOC:MAH PMID:14718172 PMID:20537132 gel electrophoresis evidence 2012-08-24T12:11:51Z A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field. ECO:0000337 Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch. eco mchibucos A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field. ECO:MCC wikipedia:Gel_electrophoresis pulsed-field gel electrophoresis evidence 2012-08-24T12:34:01Z ECO:0000338 Gel electrophoresis evidence that employs alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous, to separate large DNA molecules on an agarose gel. PFGE eco mchibucos Gel electrophoresis evidence that employs alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous, to separate large DNA molecules on an agarose gel. PMID:6373014 two-dimensional agarose gel electrophoresis evidence 2-D agarose gel electrophoresis 2012-08-24T12:42:37Z ECO:0000339 Gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide. The first dimension gel is intentionally run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape. eco mchibucos Gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide. PMID:8594382 plasmid maintenance assay evidence 2012-08-24T13:27:58Z ECO:0000340 Experimental evidence from an assay in which a mitotically stable plasmid (or minichromosome) is introduced into cells, cells are grown without selection for several generations, the proportion of cells that retain the plasmid is then determined (by comparing colony numbers on selective versus non-selective media), and the loss per generation calculated. eco mchibucos minichromosome maintenance assay evidence ECO:MCC Experimental evidence from an assay in which a mitotically stable plasmid (or minichromosome) is introduced into cells, cells are grown without selection for several generations, the proportion of cells that retain the plasmid is then determined (by comparing colony numbers on selective versus non-selective media), and the loss per generation calculated. PMID:6323245 PMID:6323245 minichromosome maintenance assay evidence specific protein inhibition by antibody evidence 2012-08-24T13:48:24Z A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody. ECO:0000341 eco mchibucos A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody. ECO:MCC Support of intron position by RNA-seq alignment evidence 2013-04-03T16:22:05Z A type of transcript splice pattern evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence. ECO:0000342 RNA-seq alignment intron location evidence is used by NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq). Exon-exon boundaries (or intron locations) of a RefSeq transcript, as determined by aligning the transcript to a reference chromosome, are compared to intron locations supported by RNAseq data. eco mchibucos A type of transcript splice pattern evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence. ECO:MCC Full support of intron position by RNA-seq alignment evidence 2013-04-03T16:41:48Z A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript. ECO:0000343 Full support entails that all exon pairs represented in the transcript are supported. For example, for a transcript containing five exons, if liver RNA-seq reads support all four introns but brain RNA-seq supports only three introns, then the liver data fully support the transcript exons whereas the brain data do not. eco mchibucos A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript. ECO:MCC Partial support of intron position by RNA-seq alignment evidence 2013-04-03T16:50:46Z A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript. ECO:0000344 Partial support can occur in two ways. First, one or more exon-exon pair (intron) is not supported by any RNA-seq sample included in the analysis. Second, no single RNA-seq sample provides support for all exon-exon pairs (introns) represented in a transcript, but all represented exons are supported by at least one sample. eco mchibucos A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript. ECO:MCC single exon transcript confirmation via alignment evidence 2013-04-03T17:10:34Z ECO:0000345 eco mchibucos Support of intron position by RNA-seq alignment evidence used in manual assertion 2013-04-04T16:37:35Z A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:0000346 eco mchibucos A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC Support of intron position by RNA-seq alignment evidence used in automatic assertion 2013-04-04T16:38:45Z A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:0000347 eco mchibucos A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC Full support of intron position by RNA-seq alignment evidence used in automatic assertion 2013-04-04T16:40:19Z A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:0000348 eco mchibucos A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC Full support of intron position by RNA-seq alignment evidence used in manual assertion 2013-04-04T16:41:34Z A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:0000349 eco mchibucos A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC Partial support of intron position by RNA-seq alignment evidence used in automatic assertion 2013-04-04T16:42:53Z A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:0000350 eco mchibucos A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion. ECO:MCC Partial support of intron position by RNA-seq alignment evidence used in manual assertion 2013-04-04T16:43:56Z A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:0000351 eco mchibucos A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion. ECO:MCC evidence used in automatic assertion A type of evidence that is used in an automatic assertion. ECO:0000501 GOECO:IEA GO_REF:0000004 GO_REF:0000023 IEA cjm eco inferred from electronic annotation Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping. GO_REF:0000023 Gene Ontology annotation based on Swiss-Prot keyword mapping. GO_REF:0000004 GOECO:IEA IEA inferred from electronic annotation GOECO:IEA GOECO:IEA inferred from electronic annotation A type of evidence that is used in an automatic assertion. ECO:cjm