[genome-announce] New GENCODE "knownGene" V48 for human (hg38/hg19) and VM37 for mouse (mm39)
Jairo Navarro Gonzalez
We are pleased to announce the release of the GENCODE Genes V48 for human (hg38/GRCh38 & hg19/GRCh37) and the GENCODE Genes VM37 for mouse (mm39/GRCm39). The GENCODE "knownGene" V48 and VM37 gene tracks were built using a UCSC pipeline (knownGene) and the GENCODE comprehensive gene set to generate high-quality manual annotations merged with evidence-based automated annotations. The GENCODE "knownGene" tracks are our default gene tracks, which have extensive associations to external sources. This allows for additional metadata on every item as well as external links. The track description pages contain options for configuring the display, such as showing non-coding genes, splice variants, and pseudogenes.
Below is a summary of the contents found in each release. For more details, visit the GENCODE site.
| GENCODE v48 Release Stats | |||
|---|---|---|---|
| Genes | Observed | Transcripts | Observed |
| Protein-coding genes | 19,435 | Protein-coding transcripts | 89,843 |
| Long non-coding RNA genes | 35,901 | - full length protein-coding | 65,024 |
| Small non-coding RNA genes | 7,563 | - partial length protein-coding | 24,819 |
| Pseudogenes | 14,695 | Nonsense mediated decay transcripts | 21,902 |
| Immunoglobulin/T-cell receptor gene segments | 649 | Long non-coding RNA loci transcripts | 191,076 |
| Total No of distinct translations | 65,814 | Genes that have more than one distinct translations | 13,646 |
| GENCODE VM37 Release Stats | |||
|---|---|---|---|
| Genes | Observed | Transcripts | Observed |
| Protein-coding genes | 21,529 | Protein-coding transcripts | 58,636 |
| Long non-coding RNA genes | 36,111 | - full length protein-coding | 45,038 |
| Small non-coding RNA genes | 6,105 | - partial length protein-coding | 13,598 |
| Pseudogenes | 13,790 | Nonsense mediated decay transcripts | 7,247 |
| Immunoglobulin/T-cell receptor gene segments | 701 | Long non-coding RNA loci transcripts | 155,932 |
| Total No of distinct translations | 44,964 | Genes that have more than one distinct translations | 10,850 |
We would like to thank the GENCODE project for providing these annotations.
Jairo Navarro
UCSC Genome Browser
UC Santa Cruz Genomics Institute
Revealing life’s code.
Google Scholar | Twitter | Facebook | YouTube