## Description

The Gencode Genes track (version 4, May 2010) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. The Gencode gene set presents a full merge between HAVANA and ENSEMBL. Priority is given to the manually curated HAVANA annotation, using predicted ENSEMBL annotations when there are no corresponding manual annotations. The annotation was carried out on genome assembly GRCh37 (hg19).

## Display Conventions and Configuration

The annotations are divided into separate tracks based on source/confidence. The Gencode project recommends that the annotations from level 1 & 2 be used for in-depth analysis in "finished" regions, combined levels 1, 2 and 3 should be used for all methods that analyze the entire genome and require a full gene set.

- Level 1: validated

  This level is comprised of pseudogene loci that were predicted independently by the analysis-pipelines from Yale, UCSC, and HAVANA manual annotation (WTSI) and transcripts that were verified by the Gencode experimental pipeline.

- Level 2: manual annotation

  This level is comprised of HAVANA manual annotation from WTSI. The following regions are considered "fully annotated", although they will still be updated: chromosomes 1, 2, 3, 4, 6, 9, 10, 13, 20, 21, 22, X, Y, ENCODE pilot regions, chr11:2353995-3878750.

- Level 3: automated annotation

  This level is comprised of ENSEMBL annotation in regions where no HAVANA annotation or additional isoforms can be found.

NOTE: We try and synchronize the release cycles for Gencode, Havana and Ensembl. This Gencode version 4 corresponds to Ensembl 58 and Vega 38. Also see: GENCODE project.

The gene annotations are colored based on the 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_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.

## Methods

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).

## Verification

See Harrow et al. (2006) for information on verification techniques.

## Credits

This GENCODE release is the result of a collaborative effort among the following laboratories: (contact: Felix Kokocinski)

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, 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
Computational Biology and 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 | Steve Searle, Bronwen Aken, Amonida Zadissa, Daniel Barrell
Structural Computational Biology Group, Centro Natcional de Investigaciones Oncologicas (CNIO), Madrid, Spain | José Manuel Rodríguez, Michael Tress, Alfonso Valencia

## References

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.

Flicek et al. Ensembl 2011 Nucleic Acids Research 2011 39 Database issue:D800-D806

## Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.