GENCODE (Ensembl) Tracks
GENCODE Gene Annotations (Ensembl) tracks   (All Annotation Tracks and External Data tracks)

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new All GENCODE V44  All GENCODE annotations from V44 (Ensembl 110)  
new All GENCODE V43  All GENCODE annotations from V43 (Ensembl 109)  
All GENCODE V42  All GENCODE annotations from V42 (Ensembl 108)  
All GENCODE V41  All GENCODE annotations from V41 (Ensembl 107)  
All GENCODE V28  All GENCODE annotations from V28 (Ensembl 92)  
All GENCODE V25  All GENCODE transcripts including comprehensive set V25  
GENCODE V22 (Ensembl 79)  Gene Annotations from GENCODE Version 22 (Ensembl 79)  
GENCODE V20 (Ensembl 76)  Gene Annotations from GENCODE Version 20 (Ensembl 76)  



The aim of the GENCODE Genes project (Harrow et al., 2006) is to produce a set of highly accurate annotations of evidence-based gene features on the human reference genome. This includes the identification of all protein-coding loci with associated alternative splice variants, non-coding with transcript evidence in the public databases (NCBI/EMBL/DDBJ) and pseudogenes. A high quality set of gene structures is necessary for many research studies such as comparative or evolutionary analyses, or for experimental design and interpretation of the results.

The GENCODE Genes tracks display the high-quality manual annotations merged with evidence-based automated annotations across the entire human genome. The GENCODE gene set presents a full merge between HAVANA manual annotation and Ensembl automatic annotation. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. With each release, there is an increase in the number of annotations that have undergone manual curation. This annotation was carried out on the GRCh38 (hg38) genome assembly.

Display Conventions

These are multi-view composite tracks that contain differing data sets (views). Instructions for configuring multi-view tracks are here. Only some subtracks are shown by default. The user can select which subtracks are displayed via the display controls on the track details pages. Further details on display conventions and data interpretation are available in the track descriptions.

Release Notes

GENCODE version 22 corresponds to Ensembl 79 and is the most current release.

GENCODE version 20 corresponds to Ensembl 76.

See also: The GENCODE Project Release History.


This GENCODE release is the result of a collaborative effort among the following laboratories: (contact: GENCODE at the Sanger Institute)

Lab/Institution Contributors
GENCODE Principal Investigator Tim Hubbard
HAVANA manual annotation group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Jennifer Harrow, Stephen Searle, Timothy Cutts, Bronwen Aken, James Gilbert, Jyoti Choudhary, Ed Griffiths, Ewan Birney, Jose Manuel Gonzalez, Electra Tapanari, Daniel Barrell, Adam Frankish, Andrew Berry, Alexandra Bignell, Veronika Boychenko, Claire Davidson, Gloria Despacio-Reyes, Mike Kay, Deepa Manthravadi, Gaurab Mukherjee, Catherine Snow, Gemma Barson, Matt Hardy, Joanne Howes
Centre de Regulació Genòmica (CRG), Barcelona, Spain Roderic Guigó, Julien Lagarde, Barbara Uszczy𑀪ska
Genome Bioinformatics, University of California Santa Cruz (UCSC), USA David Haussler, Rachel Harte, Mark Diekhans, Benedict Paten, Joel Armstrong
Computer Science and Artificial Intelligence Lab,Broad Institute of MIT and Harvard, USA Manolis Kellis, Irwin Jungreis
Computational Biology and Bioinformatics, Yale University (Yale), USA Mark Gerstein, Suganthi Balasubramanian, Ekta Khurana, Cristina Sisu, Baikang Pei, Yan Zhang, Mihali Felipe
Center for Integrative Genomics,University of Lausanne, Switzerland Alexandre Reymond, Cedric Howald, Anne-Maud Ferreira, Jacqueline Chrast
Structural Computational Biology Group, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain Alfonso Valencia, Michael Tress, José Manuel Rodríguez, Victor de la Torre
Former members of the GENCODE project Felix Kokocinski, Toby Hunt, Gary Saunders, Sarah Grubb, Thomas Derrien, Andrea Tanzer, Gang Fang, Mihali Felipe, Michael Brent, Randall Brown, Jeltje van Baren

Contact: GENCODE at the Sanger Institute


Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S et al. The GENCODE exome: sequencing the complete human exome. Eur J Hum Genet. 2011 Jul;19(7):827-31. PMID: 21364695; PMC: PMC3137498

Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S et al. Ensembl 2012. Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90. PMID: 22086963; PMC: PMC3245178

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7 Suppl 1:S4.1-9. PMID: 16925838; PMC: PMC1810553


Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J et al. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012;7(1):e28213. PMID: 22238572; PMC: PMC3251577

Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. Mol Biol Evol. 2012 Sep;29(9):2265-83. PMID: 22446687; PMC: PMC3424414

Publications link for the GENCODE project

Data Release Policy

GENCODE data are available for use without restrictions.