New GENCODE "knownGene" V49 for human (hg38/hg19) and VM38 for mouse (mm39)
Gerardo Perez
Hello Everyone,
We are happy to announce the new GENCODE gene annotation tracks, corresponding to Ensembl release 115, along with GENCODE knownGene V49 for human (hg38/GRCh38 and hg19/GRCh37) and GENCODE knownGene VM38 for mouse (mm39/GRCm39). The GENCODE "knownGene" V49 and VM38 tracks were built using the UCSC knownGene pipeline 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 v49 Release Stats | |||
|---|---|---|---|
| Genes | Observed | Transcripts | Observed |
| Protein-coding genes | 19,433 | Protein-coding transcripts | 211,446 |
| Long non-coding RNA genes | 35,899 | - full length protein-coding | 186,646 |
| Small non-coding RNA genes | 7,563 | - partial length protein-coding | 24,800 |
| Pseudogenes | 14,701 | Nonsense mediated decay transcripts | 21,949 |
| Immunoglobulin/T-cell receptor gene segments | 649 | Long non-coding RNA loci transcripts | 191,079 |
| Total No of distinct translations | 129,801 | Genes that have more than one distinct translations | 15,498 |
| GENCODE VM38 Release Stats | |||
|---|---|---|---|
| Genes | Observed | Transcripts | Observed |
| Protein-coding genes | 21,530 | Protein-coding transcripts | 58,647 |
| Long non-coding RNA genes | 36,108 | - full length protein-coding | 45,050 |
| Small non-coding RNA genes | 6,105 | - partial length protein-coding | 13,597 |
| Pseudogenes | 13,809 | Nonsense mediated decay transcripts | 7,250 |
| Immunoglobulin/T-cell receptor gene segments | 701 | Long non-coding RNA loci transcripts | 155,914 |
| Total No of distinct translations | 44,974 | Genes that have more than one distinct translations | 10,853 |
We would like to thank the GENCODE project for providing these annotations.