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<p class="MsoNormal">Dear all,</p>
<p class="MsoNormal">Ensembl is reviewing how we provide access to
pseudoautosomal regions (PAR) in human, and we'd like your input.
<o:p></o:p></p>
<p class="MsoNormal"><o:p></o:p>Please let us know how our current
PAR strategy works for you. What do you like and what is
difficult? If our current strategy (explained below) is not
working for you, please let us know why. <span
style="mso-spacerun:yes"> </span>(If it does work for you, we’d
also like to know why!)<o:p></o:p> </p>
<p class="MsoNormal"><o:p></o:p>The pseudoautosomal regions (PAR),
where chromosome X and Y share homologous sequence, are defined by
the GRC for human. In Ensembl, the full-length Y chromosome is
displayed on our browser. However, within our core human database,
the Y chromosome is divided into five regions:<o:p></o:p> </p>
<p class="MsoNormal"><o:p></o:p>chromosome:GRCh38:Y:1:10000:1 unique
to Y<o:p></o:p><br>
chromosome:GRCh38:Y:10001:2781479:1 PAR1<o:p></o:p><br>
chromosome:GRCh38:Y:2781480:56887902:1 unique to Y<o:p></o:p><br>
chromosome:GRCh38:Y:56887903:57217415:1 PAR2<o:p></o:p><br>
chromosome:GRCh38:Y:57217416:57227415:1 unique to Y<o:p></o:p> </p>
<p class="MsoNormal"><o:p></o:p>We store sequence for only the three
unique regions of Y in our database. The DNA for PAR1 and PAR2 are
stored with the sequence for chromosome X. The full-length
chromosome Y can be generated on-the-fly by our API, where we
stitch in the shared PAR sequence from X.<o:p></o:p> </p>
<p class="MsoNormal"><o:p></o:p>What does this mean practically?<o:p></o:p>
</p>
<p class="MsoNormal"><o:p></o:p>- chr Y PARs are identical (ie. same
set of contigs in the same order) for human X and Y. When aligning
data such as RNA-seq to the genome, masking out the PAR on Y
avoids duplicate mappings. This impacts mapping scores.<o:p></o:p>
</p>
<p class="MsoNormal"><o:p></o:p>- Genes are only built on the X PAR
regions only. (The genes you see in the Y PAR regions are
identical to the genes annotated on X.)<o:p></o:p> </p>
<p class="MsoNormal"><o:p></o:p>Accessing PARs on the Y chromosome:<o:p></o:p>
</p>
<p class="MsoNormal"><o:p></o:p>- Our Perl API provides a range of
methods that allow you to fetch only the unique regions of Y or
the whole of Y<o:p></o:p> </p>
<p class="MsoNormal"><o:p></o:p>- Our websites (e.g. <a
class="moz-txt-link-abbreviated" href="http://www.ensembl.org">www.ensembl.org</a>)
show genomic sequence for chr Y PAR<o:p></o:p> </p>
<p class="MsoNormal"><o:p></o:p>- Our FTP site provides a fasta file
for the whole length of Y, with PARs replaced with Ns<o:p></o:p> </p>
<p class="MsoNormal"><o:p></o:p>Do feedback any comments by
responding to this post, or let us know what you think on helpdesk
(at) ensembl.org<br>
</p>
<p class="MsoNormal">Best wishes,<br>
Giulietta (Ensembl Outreach)<br>
</p>
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