[Genome] gene position in Danio genome

[Kayla Smith]

Hello Josh,

The reason for the size discrepancy is that we have danRer4 out on our 
website (Sanger Zv6) and Ensembl has the Zv7 assembly (soon to be 
danRer5). When they created the Zv7 assembly, they removed over 200 Mb 
of duplicated sequence (since Zv6) so chr18 (and many other chromosomes) 
has shrunk.

You can look at the danRer5 browser on our test server, but keep in mind 
that data here has not yet gone through our rigorous QA processes:

http://genome-test.cse.ucsc.edu

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

Josh Gross wrote:
> Hello,
> 
> I have a question/comment about a particular gene in Danio,  
> somatolactin A (smtla). This is a duplicated gene with two forms (an  
> A and B form) in Danio that, when searched in the Danio UCSC genome,  
> yields a position on chromosome 18 (52,351,986 to 52,736,478). The  
> positions of this gene do not agree with physical characteristics of  
> chromosome 18 since the length of chromosome 18 in Danio (according  
> to Sanger/Ensembl) is only 49,281,368 bps.
> 
> Since this gene is of particular interest for a mapping project,  
> would someone please email me back why this type of thing happens  
> (i.e., incorrect position of a gene reported using your algorithms)?  
> I am interested in seeing if this type of thing occurs because the  
> algorithm is working with an outdated form of the draft genome?
> 
> I'm not complaining (I love your excellent website) -
> 
> Thanks,
> 
> Josh
> 
> 
> Joshua Gross, Ph.D.
> Post-doctoral Fellow in Genetics
> Harvard Medical School
> 77 Avenue Louis Pasteur
> New Research Building Room 360
> Boston, MA 02115
> 
> Phone: 617-432-6529
> Fax: 617-432-6525
> 
> 
> 
> _______________________________________________
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