Hi all,
Is there a way to get a list of the start and end base pair positions of all known regulatory sequences (cis, trans, promotors, etc) in the human genome? Many thanks in advance!
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written
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Abdel
4 answers
see the ENCODE project: http://genome.ucsc.edu/ENCODE/downloads.html ( good luck...)
If you define X kb upstream of a gene to be a promoter, you can get this using the UCSC table browser as follows: Hg19 Promoters .Bed File
Either the ENCODE project or any other FAIRE-seq (http://en.wikipedia.org/wiki/FAIRE-Seq) public dataset deeply sampled on human tissues would be a good approximation. The current estimates is that 20% of the human genome is doing something (TM).
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written
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2184687-1231-83-
All Ensembl regulatory features can be obtained from biomart using this query.
Email the Ensembl helpdesk if the following page does not answer your question: http://www.ensembl.org/info/docs/funcgen/index.html
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