GENCODE: The reference human genome annotation for The ENCODE Project

  1. Tim J. Hubbard1,9
  1. 1Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, United Kingdom;
  2. 2University of California, Santa Cruz, California 95064, USA;
  3. 3Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
  4. 4Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland;
  5. 5Centre for Genomic Regulation (CRG) and UPF, 08003 Barcelona, Catalonia, Spain;
  6. 6Yale University, New Haven, Connecticut 06520-8047, USA;
  7. 7Spanish National Cancer Research Centre (CNIO), E-28029 Madrid, Spain;
  8. 8Center for Genome Sciences & Systems Biology, St. Louis, Missouri 63130, USA

    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.

    Footnotes

    • 9 Corresponding authors

      E-mail jla1{at}sanger.ac.uk

      E-mail th{at}sanger.ac.uk

    • [Supplemental material is available for this article.]

    • Article and supplemental material are at http://www.genome.org/cgi/doi/10.1101/gr.135350.111.

      Freely available online through the Genome Research Open Access option.

    • Received November 25, 2011.
    • Accepted May 22, 2012.

    This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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