[Genome] Mouse assembly differences

[Kayla Smith]

Hello Dixie,

The coordinates that you have provided for the Feb. 2006 (mm8) assembly 
correspond to the following position for the July 2007 (mm9) assembly:

chr13:67,703,567-67,851,638  (and there are no gaps in this region)

The way you can get this yourself is when you have the mm8 browser open 
to the position of your choice, you can click on "Convert" on the blue 
bar on the top of the page.   Alternatively you could click on 
"Utilities" and then "LiftOver" on the blue bar on the left side of the 
main page.

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

Dixie Mager wrote:
> Hello,
>    I have a question about a certain region of the mouse genome assembly.
> In the July 2007 version, there is a large gap of about 50,000 bp in the
> middle of this region:
> chr13:68,101,733-68,249,804
> 
> The previous version (Feb. 2006) shows no such gap.  I am interested in this
> region so I would be willing to sequence a BAC that spans the gap if
> necessary.  However, because of the discrepancy in assemblies, I thought I
> would check to determine if the July 2007 assembly is correct before going
> to the expense of sequencing. Also, if it is truly a gap, is there a way to
> find out when it might be closed?
> 
> Thanks very much.
> 
> Sincerely,
> Dixie Mager
> 
> 
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