Hi Tania, The upstream and downstream sequences are strand specific and adjusted according to the strand. For negative (-1) strand the sequences are reverse complemented. The upstream sequences are always reported 5' from the gene both for (1) and (-1) strands.
I am cc'ing the users mailing list in case my answer is not clear enough and someone wants to chip in. a On Mon, Aug 6, 2012 at 9:51 AM, Dottorini, Tania <[email protected] > wrote: > Dear Arek, > > I have a question concerning sequences downloadable from Biomart. If I > have to take a putative promoter sequence of a gene that is on the reverse > strand, once I ask Biomart for the sequence of that putative promoter (the > sequence at the 5' start of the gene) , Biomart will provide me with the > exact 5'UTR fasta sequence of the reverse strand, or will provide me with > the reverse complement of the original sequence present in the reverse > strand? > is that correct if I say that the promoter is identified at the start of > the gene if the latter is located in the forward strand (+1), or at the end > if located in the backward strand (-1); in other words the it reports the > upstream from the perspective of the gene (ie, 3' on the chromosome) > > thank you very much for your help > tania Dottorini > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead www.biomart.org
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