Hello Yesim, Please be advised that there is only limited annotation available thus for for our hg19 assembly. In particular, the UCSC Genes track, that you are working with, is not yet available.
If you like, you can use our liftOver tool to translate between hg18 and hg19 coordinates. For example, if you are on hg18, and you have the uc003qms.2 gene in view, click on the "Convert" button on the blue bar on the top of the main page, and convert from hg18 --> hg19. Unfortunately, I can't comment on your PCR results. I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance with the Genome Browser. Kayla Smith UCSC Genome Bioinformatics Group ----- "Yesim Negis" <[email protected]> wrote: > Dear UCSC, > > > > I am working on human KATNA1 promoter region. I retrieved the > promoter > sequence by using table browser, (1000 bp upstream/5'-UTR). In March > 2006 > assembly, under UCSC genes, two different predicted promoter regions > were > available for katanin p60 subunit A1, (hg18_knownGene_uc003qms.2 > range=chr6:150001377-150012543 and hg18_knownGene_uc003qmr.1 > range=chr6:150001377-150002421 5). However, in the new Feb. 2009 > assembly, > hg18 _uc003qms.2 sequence has been removed from the system (in which > the > last 13 bases of this sequence were not matching anywhere in the > genome). My > point is, according to what this change has been made and if the > predicted > promoter site in 2009 assembly is accurate. We had designed primers > using > hg18 _uc003qms.2 sequence (before Feb 2009 release), however none of > them > give any product (all kind of optimization were done). Do you think > that it > is related with the sequence? > > > > Thank you very much for your help > > > > Yesim Negis > > > > Istanbul Technical University > > Turkey > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
