<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Duarte, Magali,<div><br></div><div>The clone AL133414.4 containing this gene was identified as misassembled. </div><div><br></div><div>It has since been fixed (AL133414.5) and incorporated into one of the many KIR haplotypes we added to GRCh38. You will be able to find it in the new relase in ALT_REF_LOCI_35, patch contig name HSCHR19KIR_RP5_B_HAP_CTG3_1, see <a href="http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?ID=HG-196">http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?ID=HG-196</a>.</div><div><br></div><div>Hope this helps,</div><div><br></div><div>Kerstin </div><div><br></div><div><br></div><div> <br><div><div>On 25 Sep 2013, at 12:11, Magali <<a href="mailto:mr6@ebi.ac.uk">mr6@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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Hi Duarte,<br>
<br>
The NCBI entry you are referring to was updated on the 14th
September this year, so 10 days ago.<br>
The Ensembl gene set displayed on the browser was last updated in
June.<br>
<br>
It could be that additional biological evidence as been made
available since, which could be incorporated in our next gene set
update.<br>
<br>
Additionally, there is a vega annotation for that gene.<br>
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charset=ISO-8859-1">
<a href="http://vega.sanger.ac.uk/Homo_sapiens/Gene/Summary?db=core;g=OTTHUMG00000151665;r=19-COX_2:194318-203659;t=OTTHUMT00000323417">http://vega.sanger.ac.uk/Homo_sapiens/Gene/Summary?db=core;g=OTTHUMG00000151665;r=19-COX_2:194318-203659;t=OTTHUMT00000323417</a><br>
The annotation says that there is no ungapped mapping available for
this gene in GRCh37.<br>
This would prevent us from annotating a full length model.<br>
<br>
Hopefully this will be fixed with the new assembly GRCh38 and will
allow us to annotate the full gene model, as well as assign it its
correct name.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 25/09/13 12:01, Duarte Molha wrote:<br>
</div>
<blockquote cite="mid:CAGqkoEKJYXoZ6skszA0ojC9RV1bg0t5JXtYXDCWXHK8o12fOTg@mail.gmail.com" type="cite">
<div dir="ltr">Dear Magali
<div><br>
</div>
<div>I am still confused... if you look in this gene <span style="font-family:arial,sans-serif;font-size:13.333333969116211px">KIR2DL5A
in NCBI</span>:</div>
<div><br>
</div>
<div><a moz-do-not-send="true" href="http://www.ncbi.nlm.nih.gov/gene/57292">http://www.ncbi.nlm.nih.gov/gene/57292</a><br>
</div>
<div><br>
</div>
<div>In the section "Links to other resources" there are links
to several other services.</div>
<div><br>
</div>
<div>If you click on the UCSC link it takes you to the gene with
the same name:</div>
<div><a moz-do-not-send="true" href="http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=NM_020535">http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=NM_020535</a><br>
</div>
<div><br>
</div>
<div>However if you click on the ensembl link</div>
<div><br>
</div>
<div><a moz-do-not-send="true" href="http://www.ensembl.org/Homo_sapiens/geneview?gene=NM_020535">http://www.ensembl.org/Homo_sapiens/geneview?gene=NM_020535</a><br>
</div>
<div><br>
</div>
<div>it redirects you automatically to this other gene:</div>
<div><br>
</div>
<div><a moz-do-not-send="true" href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000215764;r=GL000209.1:7891-96246">http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000215764;r=GL000209.1:7891-96246</a><br>
</div>
<div><br>
</div>
<div>So both NCBI and UCSC agree on the existence of this gene
but not ensembl?</div>
<div><br>
</div>
<div>My apologies to insist on this but I want to understand
Ensembl disagrees with these other sources and the gene simply
is missing from ENSEMBL because it has merged it into <span style="color:rgb(51,51,51);font-family:'Luxi
Sans',Helvetica,Arial,Geneva,sans-serif;font-size:1.5em">KIR2DL2
- </span><span style="font-family:arial,sans-serif;font-size:13.333333969116211px"> </span><span style="font-family:arial,sans-serif;font-size:13.333333969116211px">ENSG00000215764</span></div>
<div><br>
</div>
<div>Best regards</div>
<div><br>
Duarte</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br>
</font>
<div><font style="background-color:rgb(255,255,255)" color="#999999"> <a moz-do-not-send="true" href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
<br>
<br>
<div class="gmail_quote">On Wed, Sep 25, 2013 at 11:46 AM,
Magali <span dir="ltr"><<a moz-do-not-send="true" href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi Duarte,<br>
<br>
Looking at the HGNC entry for KIR2DL5A, there is no link
there to any Ensembl annotation.<br>
If there was, we would be able to assign the HGNC name
directly to the Ensembl gene.<br>
<br>
For ENSG00000215764, we were able to align a refseq entry,
NM_014219.2<br>
<a moz-do-not-send="true" href="http://www.ncbi.nlm.nih.gov/nuccore/NM_014219.2" target="_blank">http://www.ncbi.nlm.nih.gov/nuccore/NM_014219.2</a><br>
<br>
This entry in turn links back to the HGNC entry for
KIR2DL2, which is where the Ensembl gene gets its name
from.<br>
<br>
If you have any biological evidence that ENSG00000215764
corresponds to KIR2DL5A, we would be most grateful if you
could submit it to HGNC.<br>
This would allow them to update their records regarding
KIR2DL5A and in turn we would be able to assign the
correct name.<br>
<br>
<br>
Regards,<br>
Magali
<div>
<div class="h5"><br>
<br>
<div>On 25/09/13 11:32, Duarte Molha wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<div dir="ltr"><p>Dear developers</p><p> I have a question regarding a gene that I
would like your help with </p><p> I have a Gene called KIR2DL5A.. This is the
most up-to-date name in HGNC for this gene:</p><p> <a moz-do-not-send="true" href="http://www.genenames.org/data/hgnc_data.php?hgnc_id=16345" target="_blank">http://www.genenames.org/data/hgnc_data.php?hgnc_id=16345</a></p><p> <span style="font-family:Calibri,sans-serif;font-size:11pt">However,
ensembl calls it: KIR2DL2</span></p><p><span><a moz-do-not-send="true" href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000215764;r=GL000209.1:7891-96246" target="_blank">http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000215764;r=GL000209.1:7891-96246</a></span></p>
<h1 style="margin:0cm 0cm 12pt"><span style="font-size:11pt;font-family:Calibri,sans-serif;font-weight:normal"> </span><span style="font-family:Calibri,sans-serif;font-size:11pt;font-weight:normal">This
is not the correct name, and it is not even an
alias of the gene of interest.... </span><span style="font-family:Calibri,sans-serif;font-size:11pt;font-weight:normal">What
is going on here?</span></h1>
<h1 style="margin:0cm 0cm 12pt"><span style="font-size:11pt;font-family:Calibri,sans-serif;font-weight:normal"> </span><span style="font-family:Calibri,sans-serif;font-size:11pt;font-weight:normal">Best
regards</span></h1><p> Duarte</p>
</div>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
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</pre>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
</div>
_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote></div><br><div apple-content-edited="true">
<div>---<br>Dr. Kerstin Howe<br>Senior Scientific Manager<br>Genome Reference Informatics<br><a href="mailto:kerstin@sanger.ac.uk">kerstin@sanger.ac.uk</a><br><br>Wellcome Trust Sanger Institute<br>Hinxton, Cambridge CB10 1SA, UK</div>
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