Description

The GENCODE track is composed of all the gene models in the GENCODE v24 release. It includes both protein-coding genes and non-coding RNA genes.

Display Conventions and Configuration

This track in general follows the display conventions for gene prediction tracks. The exons for putative non-coding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. The following color key is used:

• Black -- feature has a corresponding entry in the Protein Data Bank (PDB)
• Dark blue -- transcript has been reviewed or validated by either the RefSeq or SwissProt staff
• Medium blue -- other RefSeq transcripts
• Light blue -- non-RefSeq transcripts

This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions.

Methods

All the GENCODE genes in the comprehensive set are downloaded from the GENCODE website. Data from other sources are correlated with the GENCODE data to build the knownTo tables.

Related Data

The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a downloadable file. These include tables that link GENCODE Genes transcripts to external datasets (such as knownToLocusLink, which maps GENCODE Genes transcripts to Entrez identifiers, previously known as Locus Link identifiers), and tables that detail some property of GENCODE Genes transcript sequences (such as knownToPfam, which identifies any Pfam domains found in the GENCODE Genes protein-coding transcripts). One can see a full list of the associated tables in the Table Browser by selecting GENCODE Genes from the track menu; this list is then available on the table menu. Note that some of these tables refer to GENCODE Genes by its former name of Known Genes, sometimes abbreviated as known or kg. While the complete set of annotation tables is too long to describe, some of the more important tables are described below.

• kgXref identifies the RefSeq, SwissProt, Rfam, or tRNA sequences (if any) which are associated with each transcript.
• knownToRefSeq identifies the RefSeq transcript that each GENCODE Genes transcript is most closely associated with. That RefSeq transcript is the RefSeq transcript that the GENCODE Genes transcript overlaps at the most bases.
• knownGeneMrna contains the genomic sequence for each of the GENCODE Genes models. This may not be the same as the actual mRNA used to validate the gene model.
• knownGenePep contains the protein sequences derived from the knownGeneMrna transcript sequences. Any protein-level annotations, such as the contents of the knownToPfam table, are based on these sequences.
• knownIsoforms maps each transcript to a cluster ID, a cluster of isoforms of the same gene.
• knownCanonical identifies the canonical isoform of each cluster ID or gene using the ENSEMBL gene IDs to define each cluster. The canonical transcript is chosen using the APPRIS principal transcript when available. If no APPRIS tag exists for any transcript associated with the cluster, then a transcript in the BASIC set is chosen. If no BASIC transcript exists, then the longest isoform is used.

Credits

The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a computational pipeline developed by Jim Kent and Brian Raney.

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.