GENCODE
| Content | |
|---|---|
| Description | Encyclopædia of genes and gene variants |
| Data types captured |
All gene features in Human & mouse genome |
| Contact | |
| Research center | Wellcome Trust Sanger Institute |
| Authors | Harrow J, et al |
| Primary citation | PMID 22955987 |
| Release date | September 2012 |
| Access | |
| Website | www |
| Tools | |
| Web | {{|example.com|optional display text}} |
| Miscellaneous | |
| License | Open Access |
| Data release frequency |
Human - Quarterly Mouse - Half yearly |
| Version | Human - Release 24 (December 2015) Mouse - Release M8 (December 2015) |
GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project.
The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). Given the initial success of the project, GENCODE now aims to build an “Encyclopedia of genes and genes variants” by identifying all gene features in the human and mouse genome using a combination of computational analysis, manual annotation, and experimental validation, and annotating all evidence-based gene features in the entire human genome at a high accuracy.
The result will be a set of annotations including all protein-coding loci with alternatively transcribed variants,non-coding loci with transcript evidence, and pseudogenes.
GENCODE is currently progressing towards its goals in Phase 2 of the project, which are:
The most recent release of the Human geneset annotations is Gencode 20, with a freeze date of April 2014. This release utilises the latest GRCh38 human reference genome assembly, and corresponds to Ensembl release 76.
The latest release for the mouse geneset annotations is Gencode M3, also with a freeze date of April 2014.
Since September 2009, GENCODE has been the human gene set used by the Ensembl project and each new GENCODE release corresponds to an Ensembl release.
2003 September
The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The project was designed with three phases - Pilot, Technology development and Production phase. The pilot stage of the ENCODE project aimed to investigate in great depth, computationally and experimentally, 44 regions totaling 30 Mb of sequence representing approximately 1% of the human genome. As part of this stage, the GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. It was envisaged that the results of the first two phases will be used to determine the best path forward for analysing the remaining 99% of the human genome in a cost-effective and comprehensive production phase.
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