Mostra el registre parcial de l'element Harrow, Jennifer Denoeud, France Frankish, Adam Reymond, Alexandre Chen, Chao-Kung Chrast, Jacqueline Lagarde, Julien Gilbert, James Storey, Roy Swarbreck, David Rossier, Colette Ucla, Catherine Hubbard, Tim J. Antonarakis, Stylianos E. Guigó Serra, Roderic
dc.contributor.other Universitat Pompeu Fabra 2011-10-26T11:07:50Z 2011-10-26T11:07:50Z 2006
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.issn 1465-6906
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.language.iso eng
dc.publisher BioMed Central
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 (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is also available at
dc.subject.other Bioinformàtica
dc.subject.other Biologia molecular -- Tècnica
dc.title GENCODE: producing a reference annotation for ENCODE
dc.type info:eu-repo/semantics/article
dc.subject.keyword GENCODE
dc.subject.keyword ENCODE
dc.subject.keyword cDNA
dc.subject.keyword RACE
dc.subject.keyword Gene Loci
dc.type.version info:eu-repo/semantics/publishedVersion

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