I have a question about how to interpret the coordinates of negative-sense exons in the UCSC genome browser.
Specifically, suppose that I'm given exon coordinates 10-16 and sequence ATGCCT (negative sense). Presumably, even though coordinates 10-16 are the negative sense strand, we're given the start codon in the opposite direction. Does this mean that the actual sequence in positions 10-16 is the reverse complement of ATGCCT?
This is critical for me, because I have vcf files that call a mutation in (say) position 11. Is this a mutation in the "T" of this strand, or of its reverse complement (G as complement to C)?
Thanks you for the reply - UCSC's annotation is rather muddled. I already have a lot of scripts written that "commit" me to doing it the long way, so if I understand you correctly, in my example, a mutation in position X from a vcf means position X in the forward strand, so to reconstruct the CDS, I need the reverse complement. Correct?
In other words, if I'm given coordinates 10-15 for ATGCCT, position 11 corresponds to the G in the reverse complement forward strand, not to the T (nor its complementary A).
Yes, you're right.