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How To Deal With Multiple Transcription Start Sites [Refseq || Chipseq]

Guys, How does the refSeq deals with the genes with multiple TSS. How is this information quoted into the list, which we obtain from the ucsc tables (refSeq table). If there is no information about this in the list, how the refSeq people decide which one is most stable or bound more by PolII. I want to stress that this is different from the same genes with different number of promoters. Is there any better database which gives this information. I am interested in Mouse.

Thanks

Sukhi

P.S. I was generating the protein's (factor) abundance plot at TSS and this might give a different result for the case which I asked above.

chip-seq rna-seq refseq ucsc genes
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updated by cdsouthan cdsouthan • written by Sukhi Singh Sukhi Singh

2 answers

When I was working on transcription start sites a couple of years ago, I used DBTSS for this information, as it was not available in the UCSC tables.

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written by Leonor Palmeira Leonor Palmeira

An important question but maybe needs clarifying, and an answer from a RefSeq spokesperson (please). I believe I have seem RefSeq NMs with different 3' UTRs. Are you are asking if/how they handle 5' UTRs ?

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written by cdsouthan cdsouthan

Is this a question or an answer to Sukhdeep Singh's question? If it is a new question, please post a new question and delete this answer. You probably need to clarify it also, it is a bit obscure for now...

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written by Leonor Palmeira Leonor Palmeira

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