New GENCODE gene tracks: Human V40 (hg19/hg38) - Mouse M29 (mm39)

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Luis Nassar

May 11, 2022, 5:05:01 PM5/11/22

We are pleased to announce new GENCODE Gene annotation tracks, which correspond to Ensembl 106, for three assemblies: hg19/GRCh37hg38/GRCh38, and mm39/GRCm39. For human, the GENCODE V40 annotations were mapped to hg38/GRCh38 and then back-mapped to the hg19/GRCh37 assembly. 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 tracks that are not available on hg19:

  • 2-way Pseudogenes - pseudogenes predicted by both the Yale Pseudopipe and UCSC Retrofinder pipelines.
  • 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.

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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