New GENCODE gene tracks: Human V42 (hg19/hg38) - Mouse VM31 (mm39)

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Gerardo Perez

Dec 14, 2022, 11:17:58 AM12/14/22

Hello Everyone,

We are pleased to announce new GENCODE Gene annotation tracks, which correspond to Ensembl 108, for three assemblies: hg19/GRCh37hg38/GRCh38, and mm39/GRCm39. For human, the GENCODE V42 annotations were mapped to hg38/GRCh38 and then back-mapped to the hg19/GRCh37 assembly. The hg38 GENCODE V42 and mm39 GENCODE VM31 releases now have an assigned rank for transcripts within the gene. The transcript rank may be used to filter the number of transcripts displayed in a principled manner. More details about transcript ranking can be found on the track description page. For all three assemblies, the gene sets contain the following tracks:

  • Basic - a subset of the Comprehensive set.
  • Comprehensive - all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations.
  • Pseudogenes - all annotations except polymorphic pseudogenes.

The hg38 and mm39 assemblies also include the following track that is not available on hg19:

  • PolyA - polyA signals and sites manually annotated on the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of transcripts containing at least 3 A's not matching the genome.

The 2-way Pseudogenes track has been dropped in these releases. Details on each release can be found on the GENCODE site. This includes statistics on each release.

We would like to thank the GENCODE project for providing these annotations. 

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