GENCODE Super-track Settings
 
GENCODE Gene Annotation Tracks   (All Genes and Gene Predictions tracks)

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updated GENCODE V33lift37  GENCODE lifted annotations from V33lift37 (Ensembl 99)  
GENCODE V31lift37  GENCODE lifted annotations from V31lift37 (Ensembl 97)  
GENCODE V28lift37  GENCODE lifted annotations from V28lift37 (Ensembl 92)  
GENCODE Gene V27lift37  Gene Annotations from GENCODE Version 27lift37  
GENCODE Gene V24lift37  Gene Annotations from GENCODE Version 24lift37  
GENCODE Genes V19  Gene Annotations from GENCODE Version 19  
GENCODE Genes V17  Gene Annotations from ENCODE/GENCODE Version 17  
GENCODE Genes V14  Gene Annotations from ENCODE/GENCODE Version 14  
GENCODE Genes V7  Gene Annotations from ENCODE/GENCODE Version 7  


updated Note: Updated Feb. 11, 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 GRCh37 (hg19) genome assembly.

Experimental verification details are given in each descriptions for each track. Transcript Support Levels were determined for version 10 onwards based on evidence provided by GenBank mRNA and EST sequences. Versions 7 and 10 are being used in data analysis by the ENCODE consortium.

NOTE: Due to the UCSC Genome Browser using the NC_001807 mitochondrial genome sequence (chrM) and GENCODE annotating the NC_012920 mitochondrial sequence, the GENCODE mitochondrial sequences are not available in the UCSC Genome Browser. These annotations are available for download in the GENCODE GTF files.

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 hg19 are available in our downloads directory as wgEncodeGencode* 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 and on our blog.

Release Notes

GENCODE version 33lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 99.

GENCODE version 30lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 96.

GENCODE version 29lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 94.

GENCODE version 28lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 92.

GENCODE version 27lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 90.

GENCODE version 24lift37 (mapped from GRCh38 to GRCh37) corresponds to Ensembl 83.

GENCODE version 19 corresponds to Ensembl 74 and Vega 54.

GENCODE version 17 corresponds to Ensembl 72 and Vega 52.

GENCODE version 14 corresponds to Ensembl 69 and Vega 49

GENCODE version 7 corresponds to Ensembl 62 and Vega 42 and is used in ENCODE analysis.

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.