Archive Page: GENCODE

Archive Page: GENCODE


This is an archive page and is no longer being updated. It is being maintained as a historical record of the Wellcome Sanger Institute's involvement in the GENCODE project.



In 2007 the US National Human Genome Research Institute ( NHGRI ) provided funding for the GENCODE sub-project, part of a programme to expand the ENCylcopedia Of DNA Elements ( ENCODE ) project. In 2013, after successfully delivering the definitive annotation of functional elements in the human genome, the GENCODE group was awarded a second grant to continue their human genome annotation work and expand GENCODE to include annotation of the mouse genome.

The aim of GENCODE is to annotate all evidence-based gene features in the entire human and mouse genomes at a high accuracy. The result will be a set of annotations including all protein-coding loci with alternatively transcribed variants, non-coding loci with transcript evidence and pseudogenes. The process to create this annotation involves manual curation, different computational analysis and targeted experimental approaches. Putative loci can be verified by wet-lab experiments and computational predictions are analysed manually.

The international team working in the GENCODE project was headed by Jennifer Harrow at the Wellcome Trust Sanger Institute and includes members from EMBL European Bioinformatics Institute, Centre de RegulacióGenòmica (CRG), Spanish National Cancer Research Centre (CNIO), The University of Lausanne, Massachusetts Institute of Technology, Yale University and The University of California, Santa Cruz.

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The ENCODE website is:

The GENCODE website is:


  • Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

    Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D et al.

    BMC genomics 2015;16 Suppl 8;S2

  • GENCODE pseudogenes.

    Frankish A and Harrow J

    Methods in molecular biology (Clifton, N.J.) 2014;1167;129-55

  • Functional transcriptomics in the post-ENCODE era.

    Mudge JM, Frankish A and Harrow J

    Genome research 2013;23;12;1961-73

  • The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

    Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S et al.

    Genome research 2012;22;9;1775-89

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

    Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M et al.

    Genome research 2012;22;9;1760-74

  • GENCODE: producing a reference annotation for ENCODE.

    Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK et al.

    Genome biology 2006;7 Suppl 1;S4.1-9

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