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+ ++We are excited to announce the release of the +GENCODE +"KnownGene" v45lift37 gene track for hg19. With this release, the previous 2013 UCSC +Genes track will be frozen and made available in the +GENCODE/UCSC Genes Archive superTrack for reproducibility. +As new GENCODE tracks are made available, previous versions will also be available in the archive. +Beginning with this update, the "KnownGene" track will use GENCODE v45 gene models +lifted to hg19, which replaces the old UCSC transcript IDs with the official GENCODE IDs. +
++The following is an example of some GENCODE IDs that will replace the UCSC IDs in the update: +
++oldId newId +uc003qfo.3 ENST00000341911.10_8 +uc003jsk.2 ENST00000462279.5_3 +uc003umk.1 ENST00000318238.9_6 +uc003gzi.3 ENST00000682860.1_2 +uc011dpu.2 ENST00000375023.3_6 +uc021raj.2 ENST00000258149.11_6 +uc002fxp.3 ENST00000341657.9_12 +uc010xhp.1 ENST00000429344.7_6 +uc003zze.3 ENST00000242285.11_9+
+For each transcript ID, the _# portion is part of the +official hg19 backmap ID, so they are not confused with the gene/transcript they +are derived from in hg38. Between hg38 and hg19, the two IDs are not always in the same sequence and +may not be a one-to-one mapping. +
++The GENCODE +"KnownGene" V45lift37 gene track is 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 the GENCODE v45 release. +For more details visit the GENCODE site. +
+| GENCODE v45 Release Stats | |||
|---|---|---|---|
| Genes | Observed | Transcripts | Observed |
| Protein-coding genes | 19,395 | Protein-coding transcripts | 89,110 |
| Long non-coding RNA genes | 20,424 | - full length protein-coding | 64,028 |
| Small non-coding RNA genes | 7,565 | - partial length protein-coding | 25,082 |
| Pseudogenes | 14,719 | Nonsense mediated decay transcripts | 21,427 |
| Immunoglobulin/T-cell receptor gene segments | 648 | Long non-coding RNA loci transcripts | 59,719 |
| Total No of distinct translations | 65,357 | Genes that have more than one distinct translations | 13,600 |
+We would like to thank the GENCODE project for providing these +annotations. We would also like to thank Brian Raney, Mark Diekhans, and Jairo Navarro for the +development and release of these tracks. +
+We are pleased to announce the release of the EVA SNP release 6 track for 37 assemblies. These tracks contain mappings of single nucleotide variants and small insertions and deletions (indels) — collectively Simple Nucleotide Variants (SNVs) — from the European Variation Archive (EVA) Release 6. The full list of assemblies that contain the EVA SNP release 6 track is below: