[Genome] (no subject)

[Heather Trumbower]

Ken:

It's possible that you are seeing SNPs in the pseudoautosomal regions 
on the ends of chrX and chrY.

In the latest human assembly, the Y chromosome pseudoautosomal regions 
(PARs) are at chrY:1-2709520 and chrY:57443438-57772954. These sequences 
were taken from the corresponding regions in the X chromosome and are 
exact duplications of the X chromosome sequences at chrX:1-2709520 and
chrX:154584237-154913754, respectively.

For example, rs34557243 is displayed in our SNP track at chrX:425-425 and 
chrY:425-425.  dbSNP assigns it to these same positions, using the 
ref_assembly for chrX and the ref_par for chrY.

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs34557243

If this does not account for what you are seeing, please send us specific 
examples.

Thank you.

Heather Trumbower
UCSC Genome Bioinformatics Group


On Thu, 23 Nov 2006, Ken McELREAVEY wrote:

> Hi
>
> I have a problem concerning the identification of Y chromosome
> specific SNPs. In many, but not all cases, the SNP marked as being
> specific for the Y chromosome is indicated as being on both X and Y
> chromosome when I go to the dbSNP database. Is there any way to
> resolve this discrepancy ?
>
> Many thanks
>
> Ken
>
> Ken McElreavey
> Reproduction, Fertility and Populations Unit
> Institut Pasteur
> 25 rue du Dr Roux
> Paris
> France
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