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Does Ensembl have promoters or regulatory regions?

Known promoters are not available for most genes in Ensembl. However, for mouse and human you can find possible promoters and enhancers based on experiments from the ENCODE project. See the Ensembl Regulatory Build documentation for more. Data from genome-wide studies (ChIP-Seq) are used to generate Regulatory Features, which amongst other classifications, can be annotated as 'Promoter Associated'. Regulatory features are accessible as follows:

1. Turn on one of the Regulatory Features tracks in the Location view. See the 'Regulation' menu in the configuration panel. Clicking on a regulatory feature in this track will show a stable ID with a link to the Regulation view. Other menu choices show the specific transcription factor binding sites (TFBS) or histone modications, for example, in the region.

2. The Gene tab also has a Regulation view (available in the left hand menu). This page displays regulatory features based on ENCODE data as described above. Where available, there are additional features for human, mouse, and fly (e.g. cisRED, miRNA targets, VISTA enhancers, and REDfly).

Other access to these data uses the Perl API to query the functional genomics database. Alternatively, use BioMart.

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