[Genome] Browser shows complement, unexpectedly?

[Brooke Rhead]

Hello Thomas,

The Base Position track, which displays genomic sequence, has a control 
on the left-hand side that looks like this: "--->".  Clicking on the 
control causes the complement sequence (the negative strand) to be 
displayed.  The arrow turns the other direction, "<---", and the bases 
appear in gray rather than black.

I think this may explain what you are seeing.  If you have further 
questions, please do not hesitate to contact us again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Thomas D. Moloshok wrote:
> Hi,
> Yesterday I was looking for the potential stop codon of Mouse (mm8) Pax1
>     Chr2:147056501-147066487
> Having downloaded the sequence using the DNA link of the browser  
> ("5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none"),
> I found that one is ATTAAA
>     Chr2:147066098-147066103
> Viewing this location in the browser shows:
>     TAATTT
> i.e., the complement!
> 
> When I looked at the stop codon of the known gene: TAG
>     Chr2:147066098-147066103
> Again, I see the complement: ATC
> which would actually code for Ile.
> 
> These are not the reverse-complement, and Pax1 is listed as reading  
> on the + strand.
> 
> Any suggestion of what I am doing, or is going, wrong?
> 
> Thanks,
> Tom
> 
> <<<o>
>     Thomas Moloshok, Ph.D.
>     Director, Bioinformatics
>     Fox Chase Cancer Center
>     333 Cottman Avenue
>     Philadelphia, PA 19111-2497
>     215-214-1417
> 
> 
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