Hi Eric, The sequences you're looking at are on the negative strand (i.e. strand=-). In the browser, both of the isoforms 'start' in the same location (+ strand), 67278574, but they 'end' in different locations, 67340620 and 67356505. The start coordinate in our tables is always the lowest (left-most) number, and the end coordinate is always the highest number, regardless of strand. When a gene is on the negative strand, however, the sequence that is retrieved is the reverse complement of the the region containing the gene, and it is the 5' to 3' sequence of the gene. The 5' end of the _negative_ strand of uc009waw.2 is at 67340620, while the 5' end of the _negative_ strand of uc009wax.2 is at 67356505. Since you're reading 5' to 3', so you would expect the sequence to be different.
Just to make the point, if you search go to cords chr1:67278574-67340620 (uc009waw.2 ) in the genome browser and then click the DNA button in the top blue bar, check Reverse complement, and then "get DNA" and look at the sequence, it'll match what you have pasted below. It's starting then at position 67340620, and moving to 67340619, and so on...on the negative strand. Hope that helps. Let us know if you have any other questions. - Greg Roe UCSC Genome Bioinformatics Group On 2/28/11 11:13 AM, Eric Foss wrote: > I am trying to get sequence information from the genome browser. I want human > DNA sequence with the coordinates according to build 37 (the most recent > build). I enter a series of regions and a text file is downloaded with > sequence information. However, sometimes that information is contradictory. > For example, here are some sequences from chromosome 1 that are supposed to > be starting with the same nucleotide (67278574), but they clearly aren't: > > >> hg19_knownGene_uc009waw.2 range=chr1:67278574-67340620 5'pad=0 3'pad=0 >> strand=- repeatMasking=none ATTTGCAAGTTATA >> hg19_knownGene_uc009wax.2 range=chr1:67278574-67356505 5'pad=0 3'pad=0 >> strand=- repeatMasking=none TTCCTCTTCTTTTCCTCTTC > > I noticed a difference of "waw" versus "wax" following the "uc009" and > searched for information on that, but couldn't find it. Can someone point out > what I'm doing wrong? > > Thanks very much. > > Eric > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
