Hi Peng,
you can only retrieve upstream TSS by selecting flank transcript and
specifying your upstream coordinates. for downstream, you need to do
some calculations on the transcript sequence itself and take out the
downstream length out of the transcript sequence. Here you need to be
careful whether you want the downstream sequence out of transcript as a
whole, coding region, or unspliced transcript. whihc ever is required,
choose the appropriate sequence type.
the flanking would work correctly for the respective strand, Positive
for positive and negative for negative.
Cheers
Syed
Peng Yu wrote:
I want to get the DNA sequence between -5kb and 500bp around TSS of a gene.
I went to
http://www.ensembl.org/biomart/martview/a90f00892a48e04d438f762f551bf48a/a90f00892a48e04d438f762f551bf48a
select Ensembl56 as database, Mus Musculus as species, go to Filters
and fill the 'Id list limit' form to add the required geneIds, then go
to Attributes, select Sequences (Unspliced (Gene)) and then check
'Upstream Flank -
5000'.
If the gene is in the negative strand, I'm wondering whether it gives
me the negative strand or the positive strand.