[Genome] X and Y Pseudoautosomal Regions

[Ann Zweig]

Hello Patrick,

	Good question.  Note that the full name of the Segmental Duplications 
track is "Duplications of >1000 Bases of Non-RepeatMasked Sequence". 
For a region to be included in the track, at least 1 Kb of the total 
sequence (containing at least 500 bp of non-RepeatMasked sequence) had 
to align and a sequence identity of at least 90% was required.

	In the case of the PARs, they pass both the length and identity 
requirements.  However, those locations are full of repeats.  You can 
turn on the Repeat Masker track to get a sense of just how many repeats 
there are.  That would be my gut feel for why there isn't a 100% match 
in the Seg Dups track.

	You might want to contact the lab that produced the track to verify. 
You can get the contact information from the track description page.

	As an alternative solution, you could make a Custom Track and display 
that in the browser, so you would always be aware if you were in that 
region.  Here's a simple Custom Track annotation that would work.

browser position chrX:154580000-154913754
track name=PARs description="chrX and chrY pseudoautosomal regions" 
visibility=2
chrY 1 2709520
chrX 1 2709520
chrY 57443438 57772954
chrX 154584237 154913754

	For details on using the Custom Track tool, see:
http://genome.ucsc.edu/goldenPath/help/customTrack.html


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

Gonzales, Patrick R. wrote:
> Why are the ~100% identical pseudoautosomal regions on Xp/Yp and Xq/Yq
> not fully shown in the "Segmental Duplications" track of the genome
> browser?  This would be very helpful to investigators interested in
> these regions to have them clearly demarcated.  You mention the defined
> coordinates under the "Genomes" tab.  Thanks!
> 
> Pat
> 
> 
> Patrick R. Gonzales, MS
> 
> Clinical Development Technologist
> Cytogenetics Array CGH
> Mayo Clinic
> Hilton 932
> (507)284-8338
> gonzales.patrick at mayo.edu
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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