Hello Thomas,<div><br></div><div><span class="Apple-style-span" style="color: rgb(85, 85, 85); font-family: Arial, Helvetica, sans-serif; font-size: 14px; line-height: 18px; background-color: rgb(255, 255, 255); ">The Ensembl gene start and end coordinates correspond to the outermost transcript start and end coordinates. These can be part of the same transcript or belong to two different transcripts. An example of the latter is the human BRCA2 gene (<a href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000139618;r=13:32889611-32973805">http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000139618;r=13:32889611-32973805</a>), where the start coordinate corresponds to the start coordinate of transcript ENST00000380152 (BRCA2-001) and the end coordinate to the end coordinate of transcript ENST00000544455 (BRCA2-201).</span></div>
<div><span class="Apple-style-span" style="color: rgb(85, 85, 85); font-family: Arial, Helvetica, sans-serif; font-size: 14px; line-height: 18px; background-color: rgb(255, 255, 255); "><br></span></div><div><span class="Apple-style-span" style="color: rgb(85, 85, 85); font-family: Arial, Helvetica, sans-serif; font-size: 14px; line-height: 18px; background-color: rgb(255, 255, 255); ">Also note that by definition the start coordinate is always less than the end coordinate, so for reverse strand genes the start coordinate corresponds to the 3' end of the gene, not the 5' end!</span></div>
<div><span class="Apple-style-span" style="color: rgb(85, 85, 85); font-family: Arial, Helvetica, sans-serif; font-size: 14px; line-height: 18px; background-color: rgb(255, 255, 255); "><br></span></div><div><span class="Apple-style-span" style="color: rgb(85, 85, 85); font-family: Arial, Helvetica, sans-serif; font-size: 14px; line-height: 18px; background-color: rgb(255, 255, 255); ">Absolute genomic start and end coordinates you can retrieve using seq_region_start and seq_region_end.</span></div>
<div><font class="Apple-style-span" color="#555555" face="Arial, Helvetica, sans-serif"><span class="Apple-style-span" style="font-size: 14px; line-height: 18px;"><br></span></font></div><div><font class="Apple-style-span" color="#555555" face="Arial, Helvetica, sans-serif"><span class="Apple-style-span" style="font-size: 14px; line-height: 18px;">Hope this helps,</span></font></div>
<div><font class="Apple-style-span" color="#555555" face="Arial, Helvetica, sans-serif"><span class="Apple-style-span" style="font-size: 14px; line-height: 18px;">Bert<br></span></font><br><div class="gmail_quote">On Tue, Sep 27, 2011 at 10:40 AM, Thomas Juettemann <span dir="ltr"><<a href="mailto:juettemann@gmail.com">juettemann@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Dear All,<br>
<br>
I was wondering how the chromosomal location of a gene is defined in Ensembl.<br>
Are start and end the lowest and highest start coordinate found in all<br>
of the genes transcripts?<br>
And does the function "seq_region_end()" from the Perl API return these values?<br>
<br>
Many thanks,<br>
Thomas<br>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Bert Overduin, Ph.D.<br>Vertebrate Genomics Team<br><br>EMBL - European Bioinformatics Institute<br>Wellcome Trust Genome Campus<br>Hinxton, Cambridge CB10 1SD<br>
United Kingdom<br><br><a href="http://www.ebi.ac.uk/~bert" target="_blank">http://www.ebi.ac.uk/~bert</a><div><p style="margin-bottom:0in;margin-bottom:.0001pt"><font face="Arial"></font></p><p style="margin-bottom:0in;margin-bottom:.0001pt">
<font face="Arial">
</font></p><p style="margin-top:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt"><font face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:black">Ensembl
browser: <a href="http://www.ensembl.org/" target="_blank"><span style="color:blue">http://www.ensembl.org</span></a></span><span style="font-size:10.0pt;font-family:Arial"></span></font></p><font face="Arial">
<p style="margin-top:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:Arial;color:black">Mailing
lists: </span><span style="font-size:10.0pt;font-family:Arial;color:blue"><a href="http://www.ensembl.org/info/about/contact/mailing.html" target="_blank"><span style="color:blue">http://www.ensembl.org/info/about/contact/mailing.html</span></a></span><span style="font-size:10.0pt;font-family:Arial;color:black"></span></p>
<p style="margin-top:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:Arial;color:black">Blog: </span><span style="font-size:10.0pt;font-family:Arial;color:blue"><a href="http://www.ensembl.info/" target="_blank"><span style="color:blue">http://www.ensembl.info</span></a></span><span style="font-size:10.0pt;font-family:Arial;color:black"></span></p>
<p style="margin-top:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:Arial;color:black">YouTube: </span><span style="font-size:10.0pt;font-family:Arial;color:#000099"><a href="http://www.youtube.com/user/EnsemblHelpdesk" target="_blank"><span style="color:blue">http://www.youtube.com/user/EnsemblHelpdesk</span></a></span><span style="font-size:10.0pt;font-family:Arial;color:black"><br>
Facebook: </span><span style="font-size:10.0pt;font-family:Arial;color:blue"><a href="http://www.facebook.com/Ensembl.org" target="_blank"><span style="color:blue">http://www.facebook.com/Ensembl.org</span></a></span><span style="font-size:10.0pt;font-family:Arial;color:black"><br>
Twitter: </span><span style="font-size:10.0pt;font-family:Arial;color:blue"><a href="http://twitter.com/Ensembl" target="_blank"><span style="color:blue">http://twitter.com/Ensembl</span></a> </span><span style="font-size:10.0pt;font-family:Arial;color:black"></span></p>
<p></p>
</font><p></p><font face="Arial" size="2">
</font><p></p>
</div><br>
</div>