Hi David, I see what you are seeing now! If I first zoom in on the 5' exon, I see the numbering starting at 66798504 for "Genomic chr1", but then just below that, under "Side by Side Alignment", the numbering for the genomic sequence starts at 66797793.
This looks like a bug. I will report it to our engineers. Thank you for pointing it out! -- Brooke Rhead UCSC Genome Bioinformatics Group David F Barker wrote on 10/5/10 6:52 AM: > Hi Brooke, > > Thanks for the reply. I'll keep that in mind and see if that's what > I've missed, but I'm not sure that explains it, because it seems to me > that I've seen the exact same sequences (i.e. the 5' ends of specific > mRNAs) aligned with differently numbered genomic segments, and of > course, the genomic numeration should not be variable. > > David B. > > >>>> Brooke Rhead <[email protected]> 10/4/2010 9:19 PM >>> > Hi David, > > The "View details of parts of alignment within browser window" link > changes when you zoom in or out on a region in the Genome Browser. If > > the entire mRNA alignment fits into your Browser window, both alignment > > links on the RefSeq Genes page will be the same. However, if you are > zoomed in on only part of the alignment, you will see only that part > when you click on "View details of parts of alignment within browser > window". > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > David F Barker wrote on 10/4/10 2:18 PM: >> I have noticed a couple of times now that mRNA sequence genome >> alignments obtained by different avenues in the Genome Browser do > not >> always agree. >> >> For example, go to: >> >> >> > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=170596672&o=66797792&t=66840262&g=refGene&i=NM_001037339 > >> and under mRNA alignment, this information appears: >> >> mRNA/Genomic Alignments >> BROWSER | SIZE IDENTITY CHROMOSOME STRAND START END > >> QUERY START END TOTAL >> > ----------------------------------------------------------------------------------------------------- >> browser | 3876 100.0% 1 + 66797793 66840262 > >> NM_001037339 1 3876 3882 >> >> >> But if you click on the link on this page: >> >> View details of parts of alignment within browser window. >> >> and look at the enumeration of the alignment with the genomic > sequence >> the mRNA begins at 66798504 (NOT 66797793)--although the sequence >> appears to be the same. >> >> By other alignment approaches--i.e. BLAT of the relevant mRNA > sequence, >> one obtains the + 66797793 66840262 alignment. >> >> >> Is this due to use of different versions of the human genome > sequence? >> Is there a cue that I am missing? >> >> Thanks, >> >> David Barker >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
