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Nucleic Acids Res. 2019 Jan 8;47(D1):D766-D773. doi: 10.1093/nar/gky955.

GENCODE reference annotation for the human and mouse genomes.

Author information

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
Department of Medical Oncology, Inselspital, University Hospital, University of Bern, Bern, Switzerland.
Department of Biomedical Research (DBMR), University of Bern, Bern, Switzerland.
MIT Computer Science and Artificial Intelligence Laboratory, 32 Vasser St, Cambridge, MA 02139, USA.
Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Department of Bioscience, Brunel University London, Uxbridge UB8 3PH, UK.
Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, UK.
Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, E-08003 Catalonia, Spain.
Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA.
Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
Centre of New Technologies, University of Warsaw, Warsaw, Poland.
Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
Program in Computational Biology & Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.
Department of Computer Science, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.
Universitat Pompeu Fabra (UPF), Barcelona, E-08003 Catalonia, Spain.
Department of Medical and Molecular Genetics, King's College London, Guys Hospital, Great Maze Pond, London SE1 9RT, UK.


The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as

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