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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Hi
Rhoda,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>The
first gene I noticed this issue was with BCORL1/ENSG00000085185. Specifying
Genomic Coding Start/End gives me UTR coordinates as well.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Thanks
for looking into this.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Simon.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Rhoda
Kinsella<br>
<b>Sent:</b> Thursday, May 24, 2012 1:00 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] Biomart Genomic Coding Start/End<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi Simon<o:p></o:p></p>
<div>
<p class=MsoNormal>Yes this is likely to be related to the issue below. Can you
send me a specific example so that I can check that this? We have rerun the
calculations and are in the process of testing to make sure all id okay before
copying the fixed mart to the live site. I will send an email once the fix has
been made live.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Regards<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Rhoda<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<p class=MsoNormal>On 23 May 2012, at 18:06, Simon Chan wrote:<o:p></o:p></p>
</div>
<p class=MsoNormal><br>
<br>
<o:p></o:p></p>
<div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Hello,</span><span style='color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> </span><span style='color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>I'm using BioMart to fetch all protein coding portions of all
exons of all transcripts of my favourite gene (Ensembl Genes 67, Homo sapiens
genes GRCh37.p7). In the past, 'Genomic coding start' and 'Genomic coding
end' would give me all exon coordinates minus UTRs. However, now it seems
to return the UTR coordinates as well. Perhaps this is related to the UTR
issue reported by Beat below?</span><span style='color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> </span><span style='color:black'><o:p></o:p></span></p>
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<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Thank you.</span><span style='color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Simon.</span><span style='color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> </span><span style='color:black'><o:p></o:p></span></p>
</div>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:black'>From:</span></b><span class=apple-converted-space><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> </span></span><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'><a
href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [<a
href="mailto:dev-bounces@ensembl.org">mailto:dev-bounces@ensembl.org</a>]<span
class=apple-converted-space> </span><b>On Behalf Of<span
class=apple-converted-space> </span></b>Rhoda Kinsella<br>
<b>Sent:</b><span class=apple-converted-space> </span>Tuesday, May 22,
2012 3:38 AM<br>
<b>To:</b><span class=apple-converted-space> </span>Ensembl developers
list<br>
<b>Subject:</b><span class=apple-converted-space> </span>Re: [ensembl-dev]
Ensembl release 67 is out!</span><span style='color:black'><o:p></o:p></span></p>
</div>
</div>
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<div>
<p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='color:black'>Hi Beat<o:p></o:p></span></p>
</div>
<div>
<div>
<p class=MsoNormal><span style='color:black'>We are currently looking into why
this has occurred but it is certainly a bug in our mart databases. I will
respond as soon as we have a fix in place. Thank you for reporting this and
apologies for any inconvenience.<o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><span style='color:black'>Regards<o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><span style='color:black'>Rhoda<o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p>
</div>
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<div>
<div>
<p class=MsoNormal><span style='color:black'>On 19 May 2012, at 15:55, Beat
Wolf wrote:<o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal><span style='color:black'><br>
<br>
<br>
<o:p></o:p></span></p>
</div>
<div>
<div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'>Hi,</span><span
style='color:black'><o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'> </span><span
style='color:black'><o:p></o:p></span></p>
</div>
<div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'>i'm a computer
scientist and not a biologist, so perhaps i missed something about the DMD gene
changing recently.</span><span style='color:black'><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'>I have an
automated unit test for my application that uses biomart. It happens to test
the DMD-001 transcript of the DMD gene.</span><span style='color:black'><o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'>I</span><span
style='font-size:9.0pt;color:#1F1C1B'>n the 66 version of enembl, the UTR3
coordinates of the exon number 79 where:</span><span style='color:black'><o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'> </span><span
style='color:black'><o:p></o:p></span></p>
</div>
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<td style='padding:0in 0in 0in 0in'>
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<div>
<p class=MsoNormal><span style='font-size:13.5pt;color:#1F1C1B'>31137345</span><o:p></o:p></p>
</div>
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<td style='padding:0in 0in 0in 0in'>
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<div>
<p class=MsoNormal><span style='font-size:13.5pt;color:#1F1C1B'>to 31140035</span><o:p></o:p></p>
</div>
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</td>
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<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:#1F1C1B'>which was
correct. Now with the version 67 of ensembl, the UTR3 region in the same exon
is:</span><span style='color:black'><o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'> </span><span
style='color:black'><o:p></o:p></span></p>
</div>
<table class=MsoNormalTable border=0 cellpadding=0>
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<td style='padding:0in 0in 0in 0in'>
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<p class=MsoNormal><span style='font-size:13.5pt;color:#1F1C1B'>31137345 to</span><o:p></o:p></p>
</div>
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<td style='padding:0in 0in 0in 0in'>
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<div>
<p class=MsoNormal><span style='font-size:13.5pt;color:#1F1C1B'>31137344</span><o:p></o:p></p>
</div>
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<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'>Which can not be
correct, because that means that UTR3 has a length of 1. The other numbers
don't match up either.</span><span style='color:black'><o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'> </span><span
style='color:black'><o:p></o:p></span></p>
</div>
<div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'>Did the DMD gene
change? Is the information stored differently in ensembl? What values do i need
to reconstruct the true UTR3 region? Or is this a bug in the new ensembl
version. If yes, how many other genes are affected? Currently i will stay on
the 66 version thanks to the archives, but i have some connection issues with
it, it seems to be much less stable than the 67 version.</span><span
style='color:black'><o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'> </span><span
style='color:black'><o:p></o:p></span></p>
</div>
<div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'>Greetings</span><span
style='color:black'><o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'> </span><span
style='color:black'><o:p></o:p></span></p>
</div>
<div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'>Beat Wolf</span><span
style='color:black'><o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;color:black'> </span><span
style='color:black'><o:p></o:p></span></p>
</div>
</div>
</div>
</div>
<p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";
color:black'>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
List admin (including subscribe/unsubscribe):<span class=apple-converted-space> </span><a
href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog:<span class=apple-converted-space> </span><a
href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Rhoda Kinsella Ph.D.<o:p></o:p></span></p>
</div>
<div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Ensembl Production Project Leader,<o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>European Bioinformatics Institute (EMBL-EBI),<br>
Wellcome Trust Genome Campus, <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Hinxton<br>
Cambridge CB10 1SD,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>UK.<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
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