title: GENCODE: the reference human genome annotation for The ENCODE Project.
abstract: The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, United Kingdom. jla1@sanger.ac.uk
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authors.lastname: Diekhans
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authors.lastname: Saunders
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authors.lastname: Derrien
authors.forename: Jacqueline
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authors.lastname: Chrast
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authors.forename: Suganthi
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authors.lastname: Balasubramanian
authors.forename: Baikang
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authors.forename: Jose Manuel
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authors.lastname: Rodriguez
authors.forename: Iakes
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authors.lastname: Ezkurdia
authors.forename: Jeltje
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authors.lastname: van Baren
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authors.lastname: Brent
authors.forename: David
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authors.lastname: Haussler
authors.forename: Manolis
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authors.lastname: Kellis
authors.forename: Alfonso
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authors.lastname: Valencia
authors.forename: Alexandre
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authors.lastname: Reymond
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mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005091:Exons; D056426:Genetic Loci; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D011544:Pseudogenes; D011786:Quality Control; D022821:RNA Splice Sites; D062085:RNA, Long Noncoding; D015203:Reproducibility of Results; D020506:Untranslated Regions
chemical_list: D018076:DNA, Complementary; D022821:RNA Splice Sites; D062085:RNA, Long Noncoding; D020506:Untranslated Regions