GENCODE: the reference human genome annotation for The ENCODE Project.

TitleGENCODE: the reference human genome annotation for The ENCODE Project.
Publication TypeJournal Article
Year of Publication2012
AuthorsHarrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JManuel, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ
JournalGenome Res
Volume22
Issue9
Pagination1760-74
Date Published2012 Sep
ISSN1549-5469
KeywordsAnimals, Computational Biology, Databases, Genetic, DNA, Complementary, Evolution, Molecular, Exons, Genetic Loci, Genome, Human, Genomics, Humans, Internet, Models, Molecular, Molecular Sequence Annotation, Open Reading Frames, Pseudogenes, Quality Control, Reproducibility of Results, RNA Splice Sites, RNA, Long Noncoding, Untranslated Regions
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.

DOI10.1101/gr.135350.111
Alternate JournalGenome Res.
PubMed ID22955987
PubMed Central IDPMC3431492
Grant List095908 / / Wellcome Trust / United Kingdom
5U54HG004555 / HG / NHGRI NIH HHS / United States
WT098051 / / Wellcome Trust / United Kingdom
Research Reference: 
Gene Annotation