[Genome] BLAT vs browser discrepancy

[Brooke Rhead]

Hi Judy,

I looked at the region of Trim12 and Trim34 on the mm8 assembly.  It 
appears that Trim12 is a gene on the - strand that resides within the 
much larger Trim34 gene, which is on the + strand.  I'm looking at the 
RefSeq Genes track in approximately this region: 
chr7:104,115,813-104,213,106.)

As far as I can tell, the Trim12 mRNA is aligning twice to - strand in 
this area, once to the annotated Trim12 gene and once adjacent to the 
annotated gene.  Both of these alignments happen to lie within the same 
region as a large intron of the Trim34 gene, which is on the + strand.

I hope this explanation helps.  If you have further questions, or if you 
would like to send us some specific troublesome coordinates of this BLAT 
alignment, please do not hesitate to contact us again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

We invite you to give us your feedback on the UCSC Genome Browser
through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177


judy singer sam wrote:
> I just performed a BLAT search for the mouse gene Trim12, using mm8 build.
> I found homology with Trim34, a nearby gene, which the BLAT table lists as
> being on the - strand.  However, in the UCSC genome browser the arrows show
> Trim34 to be on the + strand.  Why the discrepancy?
> 
> Thank you.
> 
> Judy Singer-Sam
> Biology Division
> City of Hope
> Duarte, CA 91010
> email: jsam at coh.org
> tel. 626-301-8241
> 
> 
> "EMF <COH.org>" made the following annotations.
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