How to access the data

All the GENCODE project data is open access and can be accessed by any of the following methods. If you need help, please contact us.

1. The GENCODE release files can be found in this website or directly in our human and mouse FTP sites.
   • Release history for human and mouse.
   • Statistics about the current release for human and mouse.
   • FTP site README files for human and mouse.
   • Further information on the content and format of the Gencode GTF files.
   • Description of gene and transcript types and tags.
2. 

   Ensembl browser showing GENCODE annotation

   The current version of GENCODE is the default geneset in the Ensembl Genome Browser for human and mouse.

   The Ensembl data can also be accessed using the options listed below:

   • BioMart data retrieval system
   • Download from the FTP site
   • Access to MySQL public server
   • Perl interface
   • Access to REST server

3. The UCSC Genome Browser hosts selected GENCODE releases. GENCODE track data can also be downloaded from the Table Browser.

   The links below can be used to add GENCODE-related track hubs in the Ensembl or UCSC Genome Browsers:

   • GENCODE annotation updates: manual annotation updated since the last release.
   • GENCODE annotation releases: human releases since v7 and all mouse releases.
   • RACE-454seq on GENCODE lncRNAs: extension of human lncRNA transcripts by RACE coupled with long read high-throughput sequencing.
   • GENCODE CLS CaptureSeq: Capture Long-Seq (CLS) on human and mouse lincRNAs.
   • PhyloCSF: protein-coding potential based on comparative genomics.
4. We have created a custom long non-coding RNA expression array design with probes targeting the Gencode v15 human lncRNA annotation.