New GENCODE "KnownGene" V46 for human (hg38) and VM35 for mouse (mm39)
Gerardo Perez
Hello Everyone,
We are pleased to announce the release of the GENCODE V46 (hg38) and the GENCODE VM35 (mm39) gene tracks. The GENCODE "KnownGene" V46 and VM35 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. The track description pages for these tracks contain options for configuring the display such as also 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 v46 Release Stats | |||
|---|---|---|---|
| Genes | Observed | Transcripts | Observed |
| Protein-coding genes | 19,411 | Protein-coding transcripts | 89,581 |
| Long non-coding RNA genes | 20,310 | - full length protein-coding | 64,695 |
| Small non-coding RNA genes | 7,565 | - partial length protein-coding | 24,886 |
| Pseudogenes | 14,716 | Nonsense mediated decay transcripts | 21,774 |
| Immunoglobulin/T-cell receptor gene segments | 648 | Long non-coding RNA loci transcripts | 59,927 |
| Total No of distinct translations | 65,650 | Genes that have more than one distinct translations | 13,620 |
| GENCODE VM35 Release Stats | |||
|---|---|---|---|
| Genes | Observed | Transcripts | Observed |
| Protein-coding genes | 21,423 | Protein-coding transcripts | 58,457 |
| Long non-coding RNA genes | 15,126 | - full length protein-coding | 44,851 |
| Small non-coding RNA genes | 6,105 | - partial length protein-coding | 13,606 |
| Pseudogenes | 13,756 | Nonsense mediated decay transcripts | 7,243 |
| Immunoglobulin/T-cell receptor gene segments | 701 | Long non-coding RNA loci transcripts | 27,096 |
| Total No of distinct translations | 44,819 | Genes that have more than one distinct translations | 10,833 |
We would like to thank the GENCODE project for providing these annotations.