Schema for GENCODE V41 - GENCODE V41
  Database: hg38    Primary Table: knownGene    Row Count: 272,352   Data last updated: 2022-05-15
Format description: GENCODE bigGenePred
fieldexampleSQL type info description
name ENST00000619216.1varchar(255) values Ensembl ID
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 17368int(10) unsigned range  
txEnd 17436int(10) unsigned range  
cdsStart 17368int(10) unsigned range  
cdsEnd 17368int(10) unsigned range  
exonCount 1int(10) unsigned range  
exonStarts 17368,longblob    
exonEnds 17436,longblob    
proteinID  varchar(40) values  
alignID uc031tla.1varchar(255) values  

Connected Tables and Joining Fields
        hg38.bioCycPathway.kgID (via knownGene.name)
      hg38.ccdsKgMap.geneId (via knownGene.name)
      hg38.ceBlastTab.query (via knownGene.name)
      hg38.dmBlastTab.query (via knownGene.name)
      hg38.drBlastTab.query (via knownGene.name)
      hg38.foldUtr3.name (via knownGene.name)
      hg38.foldUtr5.name (via knownGene.name)
      hg38.gnfAtlas2Distance.query (via knownGene.name)
      hg38.gnfAtlas2Distance.target (via knownGene.name)
      hg38.gnfU95Distance.query (via knownGene.name)
      hg38.gnfU95Distance.target (via knownGene.name)
      hg38.humanHprdP2P.query (via knownGene.name)
      hg38.humanHprdP2P.target (via knownGene.name)
      hg38.humanVidalP2P.query (via knownGene.name)
      hg38.humanVidalP2P.target (via knownGene.name)
      hg38.humanWankerP2P.query (via knownGene.name)
      hg38.humanWankerP2P.target (via knownGene.name)
      hg38.keggPathway.kgID (via knownGene.name)
      hg38.kgAlias.kgID (via knownGene.name)
      hg38.kgColor.kgID (via knownGene.name)
      hg38.kgProtAlias.kgID (via knownGene.name)
      hg38.kgSpAlias.kgID (via knownGene.name)
      hg38.kgTargetAli.qName (via knownGene.name)
      hg38.kgXref.kgID (via knownGene.name)
      hg38.knownAttrs.kgID (via knownGene.name)
      hg38.knownBlastTab.query (via knownGene.name)
      hg38.knownBlastTab.target (via knownGene.name)
      hg38.knownCanonical.transcript (via knownGene.name)
      hg38.knownCds.name (via knownGene.name)
      hg38.knownGeneMrna.name (via knownGene.name)
      hg38.knownGenePep.name (via knownGene.name)
      hg38.knownIsoforms.transcript (via knownGene.name)
      hg38.knownToEnsembl.name (via knownGene.name)
      hg38.knownToGnfAtlas2.name (via knownGene.name)
      hg38.knownToHprd.name (via knownGene.name)
      hg38.knownToKeggEntrez.name (via knownGene.name)
      hg38.knownToLocusLink.name (via knownGene.name)
      hg38.knownToLynx.name (via knownGene.name)
      hg38.knownToMrna.name (via knownGene.name)
      hg38.knownToMrnaSingle.name (via knownGene.name)
      hg38.knownToMupit.name (via knownGene.name)
      hg38.knownToNextProt.name (via knownGene.name)
      hg38.knownToPfam.name (via knownGene.name)
      hg38.knownToRefSeq.name (via knownGene.name)
      hg38.knownToSuper.gene (via knownGene.name)
      hg38.knownToTag.name (via knownGene.name)
      hg38.knownToU133.name (via knownGene.name)
      hg38.knownToU95.name (via knownGene.name)
      hg38.knownToVisiGene.name (via knownGene.name)
      hg38.knownToWikipedia.name (via knownGene.name)
      hg38.mmBlastTab.query (via knownGene.name)
      hg38.rnBlastTab.query (via knownGene.name)
      hg38.scBlastTab.query (via knownGene.name)
      hg38.ucscRetroInfo9.kgName (via knownGene.name)
      hg38.ucscScop.ucscId (via knownGene.name)

Sample Rows
 
namechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsproteinIDalignID
ENST00000619216.1chr1-17368174361736817368117368,17436,uc031tla.1
ENST00000473358.1chr1+29553310972955329553329553,30563,30975,30039,30667,31097,uc057aty.1
ENST00000469289.1chr1+30266311093026630266230266,30975,30667,31109,uc057atz.1
ENST00000607096.1chr1+30365305033036530365130365,30503,uc031tlb.1
ENST00000417324.1chr1-34553360813455334553334553,35276,35720,35174,35481,36081,uc001aak.4
ENST00000461467.1chr1-35244360733524435244235244,35720,35481,36073,uc057aua.1
ENST00000641515.2chr1+65418715856556470008365418,65519,69036,65433,65573,71585,A0A2U3U0J3uc001aal.2
ENST00000466430.5chr1-892941209328929489294489294,92090,112699,120774,91629,92240,112804,120932,uc057aub.1
ENST00000495576.1chr1-89550911058955089550289550,90286,90050,91105,uc057auc.1
ENST00000477740.5chr1-922291292179222992229492229,112699,120720,129054,92240,112804,120932,129217,uc057aud.1

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

GENCODE V41 (knownGene) Track Description
 

Description

The GENCODE Genes track (version 41, December 2021) 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 v41 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 v41 Release Stats
GenesObservedTranscriptsObserved
Protein-coding genes19,370Protein-coding transcripts88,780
Long non-coding RNA genes19,095- full length protein-coding63,370
Small non-coding RNA genes7,566- partial length protein-coding25,410
Pseudogenes14,736Nonsense mediated decay transcripts20,933
Immunoglobulin/T-cell receptor gene segments410Long non-coding RNA loci transcripts54,291

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
  • non-coding
  • pseudogene
  • problem

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.

Methods

The GENCODE v41 track was built from the GENCODE downloads file gencode.v41.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.