Entering edit mode
12 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!
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)
Yes my species of interest is Homo Sapiens GRCh38/hg38
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?