[Genome] gene annotation - Oct2

[Hiram Clawson]

Good Afternoon Elias:

What you can do is take the protein sequence from the Ensembl browser:
 >Pou2f2
MVHSSMGAPEIRMSKPLEAEKQSLDSPSEHTDTERNGPDINHQNPQNKASPFSVSPTGPS
TKIKAEDPSGDSAPAAPPPPQPAQPHLPQAQLMLTGSQLAGDIQQLLQLQQLVLVPGHHL
QPPAQFLLPQAQQSQPGLLPTPNLFQLPQQTQGALLTSQPRAGLPTQPPKCLEPPSHPEE
PSDLEELEQFARTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCK
LKPLLEKWLNDAETMSVDSSLPSPNQLSSPSLGFDGLPGRRRKKRTSIETNVRFALEKSF
LANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKRINPCSAAPMLPSPGKPTSYSPH
LVTPQGGAGTLPLSQASSSLSTTVTTLSSAVGTLHPSRTAGGGGGGGGAAPPQFHPLCHS
PTPGHHQQHKPEPSRQPLGYWLVGPEPQRGPWPLVEPCPLPALMAAGTWCWGQPVRPQGV
PA

And use blat on the UCSC mouse genome to find where this protein exists.
It will be found located in the region with the other transcripts of Pou2f2,
but it does not match perfectly to the genome sequence.
It is found at the location: chr7:25877926-25906241 on the minus strand.

If you turn on the Mouse mRNAs track, you can see the supporting evidence
for the UCSC gene predictions.  It isn't clear to me where this 15th exon from
the Ensembl prediction would be located.  Perhaps you can see where it is.

--Hiram


Elias Theodorou wrote:
> Hi,
> 
> I would like to get some help figuring out the exon sequence for a 
> particular mouse splice form of Pou2f2, specifically Oct-2.5/Oct2b (X57940).
> 
> There his a difference in the annotation that is used in Ensembl where 
> there are two isoforms, where one isoform includes 13 exons and another 
> includes 15 exons. I thought that the 15 exon isoform might have been 
> what I was looking for, but on UCSC's browser (chr7:25877675-25917479) I 
> am only getting 14 exons total. I can't get the 15th exon that has been 
> published in one paper and that shows up on the Ensembl site. What's in 
> Ensembl doesn't seem to match what has been published as far as exon 
> size. Would it be possible to help me find out the sequence of all 15 
> exons in full?
> 
> 
> http://www.ensembl.org/Mus_musculus/exonview?db=core;transcript=ENSMUST00000085970
> 
> Thank you for your time,
> Elias
> 
> Laboratory of Michael Snyder
> Yale University
> Dept of MCDB, KBT 950
> 266 Whitney Ave
> New Haven, CT 06511
> 
> phone (203) 432-3515
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