GENCODE: producing a reference annotation for ENCODE

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• dc.contributor.author Harrow, Jenniferca
• dc.contributor.author Denoeud, Franceca
• dc.contributor.author Frankish, Adamca
• dc.contributor.author Reymond, Alexandreca
• dc.contributor.author Chen, Chao-Kungca
• dc.contributor.author Chrast, Jacquelineca
• dc.contributor.author Lagarde, Julienca
• dc.contributor.author Gilbert, Jamesca
• dc.contributor.author Storey, Royca
• dc.contributor.author Swarbreck, Davidca
• dc.contributor.author Rossier, Coletteca
• dc.contributor.author Ucla, Catherineca
• dc.contributor.author Hubbard, Tim J.ca
• dc.contributor.author Antonarakis, Stylianos E.ca
• dc.contributor.author Guigó Serra, Rodericca
• dc.date.accessioned 2011-10-26T11:07:50Z
• dc.date.available 2011-10-26T11:07:50Z
• dc.date.issued 2006ca
• dc.description.abstract Background: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual/nannotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results./nResults: The GENCODE gene features are divided into eight different categories of which only/nthe first two (known and novel coding sequence) are confidently predicted to be protein-coding/ngenes. 5’ rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally/nverify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been/nsequenced. They supported 5’ extensions of 30 loci and new splice variants in 50 loci. In addition,/n46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15/nputative transcripts. We assessed the comprehensiveness of the GENCODE annotation by/nattempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out/nof 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two/nof them in intergenic regions./nConclusions: In total, 487 loci, of which 434 are coding, have been annotated as part of the/nGENCODE reference set available from the UCSC browser. Comparison of GENCODE/nannotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within/nthe two sets, which is a reflection of the high number of alternative splice forms with unique/nexons annotated. Over 50% of coding loci have been experimentally verified by 5’ RACE for/nEGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human/ngenome with the aid of experimental validation.
• dc.format.mimetype application/pdfca
• dc.identifier.citation Harrow J, Denoeud F, Frankish A, Reymond A, Chen C, Chrast J, Lagarde J, Gilbert J G, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis S E, Guigo R. GENCODE: producing a reference annotation for ENCODE. Genome Biology. 2006;7 Supl 1:S4. DOI: 10.1186/gb-2006-7-s1-s4
• dc.identifier.doi http://dx.doi.org/10.1186/gb-2006-7-s1-s4
• dc.identifier.issn 1465-6906
• dc.identifier.uri http://hdl.handle.net/10230/12925
• dc.language.iso engca
• dc.publisher BioMed Centralca
• dc.relation.ispartof Genome Biology. 2006;7 Supl 1:S4
• dc.rights © 2006 Harrow et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is also available at http://genomebiology.com/2006/7/S1/S4ca
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/2.0
• dc.subject.keyword GENCODE
• dc.subject.keyword ENCODE
• dc.subject.keyword cDNA
• dc.subject.keyword RACE
• dc.subject.keyword Gene Loci
• dc.subject.other Bioinformàtica
• dc.subject.other Biologia molecular -- Tècnica
• dc.title GENCODE: producing a reference annotation for ENCODEca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionen