[Genome] Browser shows complement, unexpectedly?

Thomas D. Moloshok Thomas.Moloshok at fccc.edu
Wed Apr 25 08:33:33 PDT 2007


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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