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Can any person tell me if there are free software programs to predict the regulatory elements of genes?
Second question : what i know about regulatory elements of gene is that they include Promoter, Poly A signal and Splice site. Is there any regulatory elements other than these??
"Regulatory elements" as I understand them are modules containing transcription factor binding sites that can be very far (>10kb) from the gene's "promoter" (the region just upstream of the transcription start site where RNA polymerase binds). Binding of transcription factors at these sites influences transcription through looping of DNA that brings the bound TFs into the proximity of the promoter, where they can help to recruit or initiate the polymerase.
One way to identify regulatory elements is to align genome sequences (from the region surrounding the gene) from closely-related species (10-100My divergence, say) using MussaGL, for example. You can predict that since these intergenic sequences don't encode a gene, they should accumulate mutations and indels rapidly, unless they have a regulatory function and need to be conserved. When you align the sequences you may see patches of conservation that don't correspond to exons of genes. Those are potential regulatory elements. To get a better idea of whether the regulatory element might be functional, you can just take the sequence within the conservation patch and feed it into a program designed to identify potential transcription factor binding sites, like Consite. (http://asp.ii.uib.no:8090/cgi-bin/CONSI ... put_single) Consite will tell you which transcription factors are capable of binding in your conserved patch, and if you have preexisting knowledge about which TFs might regulate your gene, then you can look for enrichment of that type of binding site in the conserved patch.
Titus Brown has an awesome webpage that describes all of that much better. It's at http://ivory.idyll.org/articles/intro-c ... e-analysis
Where are you looking for regulatory elements and for what purpose?
4 posts • Page 1 of 1
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