Description

The GENCODE Genes track (version 43, February 2023) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the GENCODE project. By default, only the basic gene set is displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts that GENCODE believes will be useful to the majority of users.

The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes are not displayed by default. It contains annotations on the reference chromosomes as well as assembly patches and alternative loci (haplotypes).

The following table provides statistics for the v43 release derived from the GTF file that contains annotations only on the main chromosomes. More information on how they were generated can be found in the GENCODE site.

GENCODE v43 Release Stats
Genes	Observed	Transcripts	Observed
Protein-coding genes	19,393	Protein-coding transcripts	89,411
Long non-coding RNA genes	19,928	- full length protein-coding	64,004
Small non-coding RNA genes	7,566	- partial length protein-coding	25,407
Pseudogenes	14,737	Nonsense mediated decay transcripts	21,354
Immunoglobulin/T-cell receptor gene segments	410	Long non-coding RNA loci transcripts	58,023
Total No of distinct translations	65,519	Genes that have more than one distinct translations	13,618

For more information on the different gene tracks, see our Genes FAQ.

Display Conventions and Configuration

By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. It includes options to display the entire GENCODE set and pseudogenes. To customize these options, the respective boxes can be checked or unchecked at the top of this description page.

This track also includes a variety of labels which identify the transcripts when visibility is set to "full" or "pack". Gene symbols (e.g. NIPA1) are displayed by default, but additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene and transcript names can be found in our FAQ.

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.

Coloring for the gene annotations is based on the annotation type:

• coding: protein coding transcripts, including polymorphic pseudogenes
• non-coding: non-protein coding transcripts
• pseudogene: pseudogene transcript annotations
• problem: problem transcripts (Biotypes of retained_intron, TEC, or disrupted_domain)

This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. There is also an option to display the data as a density graph, which can be helpful for visualizing the distribution of items over a region.

Squishy-pack Display

Within a gene using the pack display mode, transcripts below a specified rank will be condensed into a view similar to squish mode. The transcript ranking approach is preliminary and will change in future releases. The transcripts rankings are defined by the following criteria for protein-coding and non-coding genes:

1. MANE or Ensembl canonical
   • 1st: MANE Select / Ensembl canonical
   • 2nd: MANE Plus Clinical
2. Coding biotypes
   • 1st: protein_coding and protein_coding_LoF
   • 2nd: NMDs and NSDs
   • 3rd: retained intron and protein_coding_CDS_not_defined
3. Completeness
   • 1st: full length
   • 2nd: CDS start/end not found
4. CARS score (only for coding transcripts)
5. Transcript genomic span and length (only for non-coding transcripts)

1. Transcript biotype
   • 1st: transcript biotype identical to gene biotype
2. Ensembl canonical
3. GENCODE basic
4. Transcript genomic span
5. Transcript length

Methods

The GENCODE v43 track was built from the GENCODE downloads file gencode.v43.chr_patch_hapl_scaff.annotation.gff3.gz. Data from other sources were correlated with the GENCODE data to build association tables.

Related Data

The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a downloadable file.

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.

Data access

GENCODE Genes and its associated tables can be explored interactively using the REST API, the Table Browser or the Data Integrator. The genePred format files for hg38 are available from our downloads directory or in our GTF download directory. All the tables can also be queried directly from our public MySQL servers, with more information available on our help page as well as on our blog.

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 is available at The GENCODE Project web site.

Data Release Policy

GENCODE data are available for use without restrictions.