All GENCODE Super-track Settings
 
All GENCODE transcripts, including comprehensive set and previous version Tracks   (All Genes and Gene Predictions tracks)

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new All GENCODE V34  All GENCODE annotations from V34 (Ensembl 100)  
All GENCODE V33  All GENCODE annotations from V33 (Ensembl 99)  
All GENCODE V31  All GENCODE annotations from V31 (Ensembl 97)  
All GENCODE V29  All GENCODE annotations from V29 (Ensembl 94)  
All GENCODE V28  All GENCODE annotations from V28 (Ensembl 92)  
All GENCODE V27  All GENCODE annotations from V27 (Ensembl 90)  
All GENCODE V26  All GENCODE annotations from V26 (Ensembl 88)  
All GENCODE V25  All GENCODE transcripts including comprehensive set V25  
All GENCODE V24  All GENCODE transcripts including comprehensive set V24  
All GENCODE V23  All GENCODE transcripts including comprehensive set V23  
All GENCODE V22  All GENCODE transcripts including comprehensive set V22  
GENCODE V20 (Ensembl 76)  Gene Annotations from GENCODE Version 20 (Ensembl 76)  


p12 Note: Includes annotations on GRCh38.p12 patch sequences
updated Note: Updated May. 22, 2020 wgEncodeGencodeSuper

Description

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.

For more information on the different gene tracks, see our Genes FAQ.

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.

Data access

GENCODE Genes and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. The GENCODE data files for hg38 are available in our downloads directory as wgEncodeGencode* files in genePred format. All the tables can also be queried directly from our public MySQL servers, with instructions on this method available on our MySQL help page as well as on our blog.

Release Notes

GENCODE version 34 corresponds to Ensembl 100.

GENCODE version 33 corresponds to Ensembl 99.

GENCODE version 30 corresponds to Ensembl 96.

GENCODE version 29 corresponds to Ensembl 94.

GENCODE version 28 corresponds to Ensembl 92.

GENCODE version 27 corresponds to Ensembl 90.

GENCODE version 26 corresponds to Ensembl 88.

GENCODE version 24 corresponds to Ensembl 84.

GENCODE version 23 corresponds to Ensembl 81.

GENCODE version 22 corresponds to Ensembl 79.

GENCODE version 20 corresponds to Ensembl 76.

See also: The GENCODE Project Release History.

Credits

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, EMBL European Bioinformatics Institute, Cambridge, UK Paul Flicek
GENCODE Co-Principal Investigator, EMBL European Bioinformatics Institute, Cambridge, UK Adam Frankish
GENCODE Co-Principal Investigator, Wellcome Trust Sanger Institute (WTSI), Cambridge, UK Bronwen Aken
Kings College, London, UK Tim Hubbard
HAVANA manual annotation group, EMBL European Bioinformatics Institute, Cambridge, UK Timothy Cutts, Jyoti Choudhary, Ed Griffiths, Ewan Birney, Jose Manuel Gonzalez, Stephen Fitzgerald, Andrew Berry, Alexandra Bignell, Claire Davidson, Gloria Despacio-Reyes, Mike Kay, Deepa Manthravadi, Gaurab Mukherjee, Gemma Barson, Matt Hardy, Angela Macharia
Ensembl, EMBL European Bioinformatics Institute, Cambridge, UK Carlos Garcia, Fergal Martin, Osagie Izuogu
Centre de Regulació Genòmica (CRG), Barcelona, Spain Roderic Guigó, Julien Lagarde, Barbara Uszczyńska
UC Santa Cruz Genomics Institute, University of California Santa Cruz (UCSC), USA David Haussler, Mark Diekhans, Benedict Paten, Joel Armstrong, Ian Fiddes
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, 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 Jennifer Harrow, James Gilbert, Electra Tapanari, Stephen Searle, Rachel Harte, Daniel Barrell, Felix Kokocinski, Veronika Boychenko, Toby Hunt, Catherine Snow, Gary Saunders, Sarah Grubb, Thomas Derrien, Andrea Tanzer, Gang Fang, Mihali Felipe, Joanne Howes, Reena Halai, Pablo Roman-Garcia, Michael Brent, Randall Brown, Jeltje van Baren

References

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012 Sep;22(9):1760-74. PMID: 22955987; PMC: PMC3431492

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

A full list of GENCODE publications are available at The GENCODE Project web site.

Data Release Policy

GENCODE data are available for use without restrictions.