My gene X has several transcript variants. Through UCSC genome Browser, I found the promoter sequence of each variant.But now I am a little bit confused because I do not know among all of those which one should I choose for transcription factor binding assay. I have searched that is any isoform more prevalent in my tissue but I did not get any result.So, finally I have choosed the highest and the lowest ranges so that all promoters of all isoforms must fall in this total sequence. When I have through JASPAR database , some of the result match in some isoforms others are not.What should I do ?
If you get yourself the actual transcripts from your tissue (e.g. by sequencing it), just use that.
If you want to decrease your search space, I would rely on the JASPAR result.
You may also check if some of these isoforms are predicted. In that case, you may choose to ignore them. Still, predicted data does not mean it cannot exist.
If it is possible and not to many, I would consider testing all (except, like said, if you have some sequence information of your tissue available).
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