This release of the GENCODE Genes track (Version 3c, October 2009) shows high-quality manual annotations in the ENCODE regions generated by the GENCODE project.
Version 3 of the GENCODE gene set presents a full merge between HAVANA and ENSEMBL, giving priority to the manually curated Havana objects and using ENSEMBL objects where they are different or fall into un-annotated regions. The annotation was carried out on genome assembly GRCh37 (hg19), features are projected back to NCBI36 (hg18) where possible. GENCODE 3c is a small update of version 3b (July 09 freeze) mainly for chromosomes 3 & 4 for which the latest annotation was held back and QC'ed again to be used in the RNASeq Genome Annotation Assessment Project. Statistics about this release can be found here.
NOTE: The release cycles for GENCODE, Havana and Ensembl differ. Users are cautioned to compare release dates to determine which annotation is most current.
The gene annotations are colored based on the HAVANA annotation type and the confidence level. See the table below for the color key, as well as more detail about the transcript and feature types.
Class | Color | Description | Transcript Types (see Vega Transcript Types) |
---|---|---|---|
Validated_coding | Dark Orange | Level 1 Validated: coding regions | protein_coding |
Validated_processed | Light Orange | Level 1 Validated: processed | processed_transcript |
Validated_processed_pseudogene | Dark Pink | Level 1 Validated: processed pseudogenes | processed_pseudogene, processed_transcript, transcribed_processed_pseudogene |
Validated_unprocessed_pseudogene | Medium Pink | Level 1 Validated: unprocessed pseudogenes | transcribed_unprocessed_pseudogene, unprocessed_pseudogene |
Validated_pseudogene | Light Pink | Level 1 Validated: pseudogenes | IG_pseudogene, polymorphic_pseudogene, pseudogene, retrotransposed, unitary_pseudogene |
Havana_coding | Dark Orange | Level 2 Manual annotation: coding | IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,protein_coding |
Havana_nonsense | Medium Orange | Level 2 Manual annotation: nonsense | nonsense_mediated_decay |
Havana_non_coding | Light Orange | Level 2 Manual annotation: non-coding | ambiguous_orf, antisense, non_coding, processed_transcript, retained_intron |
Havana_polyA | Black | Level 2 Manual annotation: polyA | polyA_signal, polyA_site, pseudo_polyA |
Havana_processed_pseudogene | Dark Pink | Level 2 Manual annotation: processed pseudogene | processed_pseudogene, transcribed_processed_pseudogene |
Havana_unprocessed_pseudogene | Medium Pink | Level 2 Manual annotation: unprocessed pseudogene | transcribed_unprocessed_pseudogene, unprocessed_pseudogene |
Havana_pseudogene | Light Pink | Level 2 Manual annotation: pseudogene | IG_pseudogene, TR_pseudogene, polymorphic_pseudogene, pseudogene, retrotransposed, unitary_pseudogene |
Havana_TEC | Grey | Level 2 Manual annotation: TEC | TEC, artifact |
Ensembl_coding | Dark Red | Level 3 Automated annotation: coding | IG_C_gene, IG_D_gene, IG_J_gene, IG_V_gene, protein_coding |
Ensembl_non_coding | Light Orange | Level 3 Automated annotation: non-coding | antisense, non_coding, processed_transcript, retained_intron |
Ensembl_pseudogene | Dark Pink | Level 3 Automated annotation: pseudogene | IG_pseudogene, miRNA_pseudogene, misc_RNA_pseudogene, pseudogene, retrotransposed, unitary_pseudogene |
Ensembl_processed_pseudogene | Medium Pink | Level 3 Automated annotation: processed pseudogene | processed_pseudogene |
Ensembl_unprocessed_pseudogene | Light Pink | Level 3 Automated annotation: unprocessed pseudogene | unprocessed_pseudogene |
Ensembl_RNA | Light Red | Level 3 Automated annotation: RNA transcripts | Mt_rRNA, Mt_tRNA, Mt_tRNA_pseudogene, miRNA, misc_RNA, rRNA, rRNA_pseudogene, scRNA_pseudogene, snRNA, snRNA_pseudogene, snoRNA, snoRNA_pseudogene, tRNA_pseudogene, tRNAscan |
2way_consensus_pseudogene | Dark Purple | Level 3 Automated annotation: pseudogenes | pseudogenes |
This track uses filtering by category to select subsets of transcripts and has additional advanced features. Help with these features can be found here.
We aim to annotate all evidence-based gene features at high accuracy on the human reference sequence. This includes identifying all protein-coding loci with associated alternative variants, non-coding loci which have transcript evidence, and pseudogenes. We integrate computational approaches (including comparative methods), manual annotation and targeted experimental verification.
For a detailed description of the methods and references used, see Harrow et al (2006).
See Harrow et al. (2006) for information on verification techniques.
The data can be downloaded at the GENCODE ftp site here.
This GENCODE release is the result of a collaborative effort among the following laboratories: (contact: GENCODE at the Sanger Institute. )
Lab/Institution |
Contributors |
HAVANA annotation group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK | Adam Frankish, James Gilbert, Jennifer Harrow,
Felix Kokocinski, Stephen Trevanion, Tim Hubbard (GENCODE Principal Investigator) |
Genome Bioinformatics Lab (CRG), Barcelona, Spain | Thomas Derrien, Tyler Alioto, Andrea Tanzer, Roderic Guigó |
Genome Bioinformatics, University of California Santa Cruz (UCSC), USA | Rachel Harte, Mark Diekhans, Robert Baertsch, David Haussler |
Comp. Genomics Lab, Washington University St. Louis (WUSTL), USA | Jeltje van Baren, Charlie Comstock, David Lu, Michael Brent |
Computer Science and Artificial Intelligence Lab, Broad Institute of MIT and Harvard, USA | Mike Lin, Manolis Kellis |
Bioinformatics, Yale University (Yale), USA | Philip Cayting, Mark Gerstein |
Center for Integrative Genomics, University of Lausanne, Switzerland | Cedric Howald, Alexandre Reymond |
ENSEMBL genebuild group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK | Bronwen Aken, Julio Fernandez Banet, Stephen Searle |
Structural Computational Biology Group, Centro Natcional de Investigaciones Oncologicas (CNIO), Madrid, Spain | Manuel Rodríguez José, Jan-Jaap Wesselink, Michael Tress, Alfonso Valencia |
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. European Journal of Human Genetics. March 2011;19 827-831. [Epub ahead of print]
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.
GENCODE data are available for use without restrictions. The full data release policy for ENCODE is available here.