Hello, Phenix, The "strand" field of ESTs is always somewhat confusing.
Some labs reverse-complement the sequence from their sequencing experiment and so you cannot be sure if you are getting the mRNA or the template strand. We take the sequence as published in GenBank and align it to the genome and that is what is reported on the details page (http://genome.ucsc.edu/cgi-bin/hgc?db=hg19&g=intronEst&i=BG204397): BROWSER | SIZE IDENTITY CHROMOSOME STRAND START END ... -------------------------------------------------------------... browser | 641 99.3% 14 - 29859552 29905614 ... This is not necessarily the direction of transcription. The transcription direction will be pretty reliably indicated by the chevrons in the Browser image, which is left-to-right for this EST. You can see this for yourself if you click into the link, "EST sequence: BG204397" on the details page. Take the resulting sequence and use BLAT to align it to the hg19 genome and see that the alignment is on the bottom strand. I hope this helps you sort it out. And thanks for specifying the genome assembly (hg19) that you are looking at. It helps a lot. regards, --b0b kuhn ucsc genome bioinformatics group On 1/9/2012 5:40 PM, Phenix Hydra wrote: > Dear Sir or Madam, > I found that “BG204397” on genome browser (HG19) is “forward” while the > alignment strand is “-”. I think the inconsistent is unwonted. Please check > it. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
