[GET-dev] Re: Interesting tidbit: genomes on GET variant pages and dbSNP
krobasky at gmail.com
Tue May 25 10:44:16 EDT 2010
I stand corrected once again (thanks Madeleine!):
The key is to notice the reported sequence on dbSNP is '- strand', so
I needed to take the reverse complement to find the genomic sequence:
CTG->CCG becomes CAG->CGG
So for '+ strand', the sequence would be the same as genomic dna.
Incidently, this also clears up my confusion below over why the dbSNP
sequence uses T instead of U :)
On Tue, May 25, 2010 at 10:14 AM, Kimberly Robasky <krobasky at gmail.com> wrote:
> After clicking through to dbSNP, I erroneously thought the GET variant
> pages were linking to the wrong genomes. So that others will avoid my
> mistake, here was the thought process:
> Take as example: http://evidence.personalgenomes.org/PARP4-L1550P
> Click the dbSNP link:
> Scroll down about 1/4-way to 'GeneView' table, and see the codons that
> represent the SNPs at this locus:
> CTG to CAG corresponds to L to Q mutation
> CTG to CCG " " L to P "
> CTG to CGG " " L to R "
> So I expected the L to P mutation to pull genomes that are het/hom for
> C, as in CTG->CCG above.
> But the PARP4-L155P GET page has genomes that are het/hom for G.
> I missed the fact that dbSNP states that it reports the CTG->CCG
> sequences as mRNA. I'm still unsure why they didn't use CUG->CCG,
> wouldn't it be more correct to state it's reported as cDNA? Anyway,
> the corresponding DNA in the genome is GAC->GGC, in which case, you'd
> want to pull the het G genomes, which is exactly what GET does.
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