Retrieve Promoter Sequences by GeneID
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19 months ago

Hello! I want to retrieve promoter sequences starting from a list of Gene_ID, i had try to used RSAT-retrieve sequence, but the problem is that they retrieve the sequence from the start codon or the stop codon, but i want retrieve the sequence 1500bp before the TSS and 500bp after the stop codon of the last exon... there is a tool that is able to do that? Thank you!

GeneID by Sequences Retrieve Promoter • 933 views
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There is a good reason why those regions are mostly linked to start&stop codon (== those we can quite accurately determine). TSS can also be determined but then only experimentally and as such they will only be present for a very limited number of species (and/or genes in the genome) .

So if your species of interest is human or such it can work, if it is anything else you'll have very little chance to have those transcription start/stop determined and hence you will have to fall back to the start/stop codon (== translation boundaries)

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Yes my species of interest is Homo Sapiens GRCh38/hg38

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then you might be in luck ...

though I can't immediately point you to tools that can do this ... perhaps you can look into biomart or entrez or such?

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