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~2kb up and down the gene start is commonly used for Human proximal
regulatory regions.<br>
As a broader region, you could use ~2kb around the whole gene.<br>
<br>
Daniel<br>
<br>
On 03/05/2011 13:02, Oliver, Gavin wrote:
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<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial; color: navy;">Thanks for
this!<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial; color: navy;">Is there any
sort of distance that is
recommended/has been previously utilized for
such purposes?<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial; color: navy;">Best, <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial; color: navy;">Gavin<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><b><font color="black"
face="Tahoma" size="2"><span style="font-size:
10pt; font-family: Tahoma; color:
windowtext; font-weight: bold;">From:</span></font></b><font
color="black" face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma;
color: windowtext;"> Daniel Sobral
[<a class="moz-txt-link-freetext" href="mailto:sobral@ebi.ac.uk">mailto:sobral@ebi.ac.uk</a>] <br>
<b><span style="font-weight: bold;">Sent:</span></b>
03 May 2011 12:56<br>
<b><span style="font-weight: bold;">To:</span></b>
<st1:personname w:st="on">Oliver, Gavin</st1:personname>;
dev ensembl<br>
<b><span style="font-weight: bold;">Subject:</span></b>
[SPAM] - Re:
[ensembl-dev] Quick question RE exons and
regulatory regions - Email found in
subject</span></font><font color="black"><span
style="color: windowtext;"><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="3"><span style="font-size: 12pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="3"><span style="font-size: 12pt;">At
the moment, we cannot associate a regulatory
region
to a specific gene.<br>
What you can do is get all regulatory regions
around a certain distance of the
gene.<br>
<br>
Hope that helps,<br>
Daniel<br>
<br>
On 03/05/2011 12:22, <st1:personname w:st="on">Oliver,
Gavin</st1:personname>
wrote: <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial;">Hi all, <u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial;"><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial;">Just wondering – using the
relevant APIs is it
possible to take a list of genes, extract all
associated exon coordinates and
also the coordinates of associated regulatory
regions?<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial;"><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial;">I know the exon bit is ok,
but it’s the
associated regulatory regions I’ve never looked
at before…<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial"
size="2"><span style="font-size: 10pt;
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<p class="MsoNormal"><font color="black" face="Arial"
size="2"><span style="font-size: 10pt;
font-family: Arial;">Cheers, <u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Arial"
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<p class="MsoNormal"><font color="black" face="Arial"
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font-family: Arial;">Gavin<u1:p></u1:p></span></font><o:p></o:p></p>
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<p class="MsoNormal"><strong><b><font color="black"
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<pre wrap=""><font color="black" face="Courier New" size="2"><span style="font-size: 10pt;"><o:p> </o:p></span></font></pre>
<pre><fieldset class="mimeAttachmentHeader"></fieldset><font color="black" face="Courier New" size="2"><span style="font-size: 10pt;"><o:p> </o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size: 10pt;">_______________________________________________<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size: 10pt;">Dev mailing list <a moz-do-not-send="true" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><o:p></o:p></span></font></pre>
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<pre><font color="black" face="Courier New" size="2"><span style="font-size: 10pt;">Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></span></font></pre>
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