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Old 10-05-2010, 11:31 AM   #6
jdanderson
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Location: Davis, CA

Join Date: Sep 2010
Posts: 45
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Hello Cliff,

Well I guess I figured the exonic boundaries would be the de facto splice sites (a script could parse the data for you). As for the promoter, that seems like a tough call. Even if by promoter you mean the core (~-35bp)and/or the proximal promoter (~-250-300) not all genes are well characterized in this fashion, to my knowledge (some TATA box, some CpG isl depending on type of gene). If by promoter you mean to include enhancer regions (as is sometimes the case in common language) this is even less well characterized and can be up to -100,000kb (and transcription factor prediction programs aren't much help in my experience). If its of any help you can also find the TSS, which may give some indication of where pol binds. Also, many genes have alternate promoters and TSS's that need to be taken into account.

Sorry if all of this is old news, just trying to throw some ideas out there. Wish I could be of more help. It sounds like you have an ambitious project in mind. I would be interested in hearing the results, especially on the regulatory side.

Regards,
Johnathon
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