The GENCODE Project: Encyclopædia of genes and gene variants

Current GENCODE version

The current version in Human is Gencode 21, released on the 2nd October 2014.

For more information about the human releases please see the README.txt file.

The current version in Mouse is Gencode M4, released on the 3rd December 2014.

For more information about the mouse releases please see the README.txt file.


** NEW ** The annotation files are now available in GFF3 format too!

** NEW ** BioDalliance Genome Browser is now embedded in website!

Two publications are out on our RNASeq genome annotation assessment project (RGASP):

  • Assessment of transcript reconstruction methods for RNA-seq.

    Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P and RGASP Consortium

    Nature methods 2013;10;12;1177-84

  • Systematic evaluation of spliced alignment programs for RNA-seq data.

    Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P and RGASP Consortium

    Nature methods 2013;10;12;1185-91


The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. After a successful pilot phase on 1% of the genome, the scale-up to the entire genome is now underway. The Wellcome Trust Sanger Institute was awarded a grant to carry out a scale-up of the GENCODE project for integrated annotation of gene features.

Having been involved in successfully delivering the definitive annotation of functional elements in the human genome, the GENCODE group were awarded a second grant in 2013 in order to continue their human genome annotation work and expand GENCODE to include annotation of the mouse genome.

The international team working in the GENCODE project is headed by Tim Hubbard at the Wellcome Trust Sanger Institute, and includes members from Centre de Regulació Genòmica, Spanish National Cancer Research Centre, The University of Lausanne, Massachusetts Institute of Technology, Yale University and The University of California, Santa Cruz .

The GENCODE gene sets are used by the entire ENCODE consortium and by many other projects (eg. 1000 Genomes) as reference gene sets.


The GENCODE project is funded through an NHGRI ENCODE grant with additional funding from the Wellcome Trust.

When referencing, please use "Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project" (PubMed).


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