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
