All GENCODE Super-track Settings
 
All GENCODE transcripts include comprehensive set and previous versions Tracks   (All Genes and Gene Predictions tracks)

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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)
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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.

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 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 Jennifer Harrow
GENCODE Co-Principal Investigator Tim Hubbard
HAVANA manual annotation group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK Timothy Cutts, Bronwen Aken, James Gilbert, Jyoti Choudhary, Ed Griffiths, 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 Uszczyńska
Genome Bioinformatics, University of California Santa Cruz (UCSC), USA David Haussler, 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, Rachel Harte

Contact: GENCODE at the Sanger Institute

References

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

Publications

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.