Hello, The results are correct. Transcripts on the negative strand are transcribed in the opposite direction from transcripts on the positive strand. This mean, that the 5' end of the gene will be on the "left" of the alignment if the viewer is set to display the --> positive strand. Flip the browser orientation to display data with respect to the negative strand <-- to see the reverse.
For a practical interpretation, for minus strand genes, the txtStart is really the txtEnd, the txtEnd is really the txtStart and the same goes for the cdsStart/End. Upstream means upstream of the known 5' end (the real start of the alignment, which would be in the txtEnd field in the data table for minus strand alignments) - and this is where the promoter might be, so you are doing the query correctly. We store all alignments with respect to the positive strand (smallest coordinate -> largest coordinate). Our tools know how to interpret this and switch the coordinates around for calculations. Some coordinate help: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms This is all a bit confusing at first, which I why I suggested trying to visualize the concept using the Assembly browser display (above) as a first step. Good luck, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Florian Wagner" <[email protected]> wrote: > From: "Florian Wagner" <[email protected]> > To: [email protected] > Sent: Thursday, December 3, 2009 10:11:36 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] fetching promotor sequences > > Dear Sir/Madam, > > I tried to fetch promotor sequences for all RefSeq genes (human, Mar > 2006) in a certain region, via the table browser, specifying > "upstream" > = 3.000 bp. > > However, when comparing the coordinates of the "upstream" sequences to > > the coordinates of the genes, I found that only for the genes on the + > > strand I got the upstream sequences. For genes on the - strand, I > obviously got 3 kb DOWNSTREAM of the transcriptional end. > > I am now confused about what "upstream" means in UCSC terminology. Can > > you please explain it a bit? > > Thank you, > Florian > > -- > Dr. Florian Wagner > Head, Microarray Service Unit > ATLAS Biolabs GmbH > Friedrichstraße 147 > 10117 Berlin > Germany > email: [email protected] > tel: +49 (0)30 319 89 66 41 > fax: +49 (0)30 700 143 12 26 > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
