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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>
<meta http-equiv="content-type" content="text/html;
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>
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