Hello,
I would like to know how to find conserved regulatory elements among different genomes. I am interested in finding such sequences in Silurana tropicalis, I already have a list of genes of interest and I would like to know more about their regulation but, first of all, I need to know which of them are already predicted as regulative.
Thanks in advance.
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Anima Mundi
The TRASNFAC and JASPAR databases will give you a few transcription factor binding sites (TFBS) for Xenopus but you won't find too many and those databases are certainly quite sparse for other frogs. I would try to load your sequence data into the UCSC genome browser and look for spikes of conservation from a couple/few kbp upstream of the gene's transcription start into and through intron 1. Regions of conservation are likely to harbor regulatory elements - TFBS or enhancer binding.
Well, Silurana is a subgenus of Xenopus. Hence, you can find a lot of information on the Xenbase. By the way, Xenbase use the annotation of promoters in the Database of Evolutionary Conserved Regions. They're the best reference for this (sub)genus. But, I think that more esoteric elements (enhacers, silencers, insulators, siRNAs) aren't well represented (not so sure).
Certainly, the more esoteric elements, like enhancers, are notoriously difficult to spot by sequence comparison. A good reason for this is their location is not conserved. This drives one to look for over-representation of 5-, 6-, 7- 8- or 9-bp motifs.
I've tried a statistical approach before. A sequence can act as a enhancer (or not) depending on the context. Now, I'm trying a (possibly stochastic) context free grammar scheme to find such esoteric elements that depend on long range interactions to work.
For a look at conserved regulatory regions there are several resources available. You might want to try out rVISTA. The UCSC Genome Browser and Ensembl have several annotation tracks that might be of use.
Regulatory element is quite a broad notion. If you are looking for transcription factors and their binding sites, maybe the JASPER database can help.
Thank you all. I am looking for generic non-coding conserved sequences; I would use these sequences as a starting pool to identify TFBSs.
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You should provide a little bit more of details. What kind of REs? Things at the promoter? Enhacers? Insulators?