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<p>Hi Thomas,<br>
<br>
Thank you for a quick reply. I have looked into this case further,
and it only got more interesting.<br>
<br>
A <a moz-do-not-send="true"
href="https://www.nature.com/articles/ng1827">paper</a> in
Nature which led to the discovery of this gene states that there
are two transcripts spanning the (CTG)n repeat in 13q21.33 in the
opposite directions:</p>
<ol>
<li><b>ATXN8OS</b> (a. k. a. SCA8 & KLHL1AS), a lncRNA;<br>
</li>
<li><b>ATXN8,</b> a coding, nearly pure polyglutamine expansion
protein.</li>
</ol>
<p>The GenBank record <a
href="https://www.ncbi.nlm.nih.gov/nuccore/DQ641254?report=GenBank">DQ641254</a>
for ATXN8 has the comment: “The sequence is derived from 3'-RACE
analysis of the ATXN8 transcript. The 5'-end of ATXN8 mRNA is not
yet defined." So this is what the gene status seems to
reflect—that it does not have a <i>complete</i> genomic mapping
and annotation, not that it is invalid.</p>
<p>In the UCSC genome browser, this partial mRNA sequence is
displayed in the GENCODE v32 transcript set under the accession
AL160391.1:<br>
</p>
<img moz-do-not-send="false"
src="cid:part3.16D2FBBA.EC9587F7@ebi.ac.uk" alt="ATXN8 region in
UCSC genome browser" width="1148" height="424">
<div class="moz-signature"><font size="-1"><i>(In case mailing lists
won't keep the picture, here's a direct URL for a copy: </i></font><font
size="-1"><i><a href="https://i.imgur.com/iGVwihX.png">https://i.imgur.com/iGVwihX.png</a></i><i>)</i></font><br>
<br>
Now, if we follow up on accession AL160391.1, we will find that it
is linked to Ensembl gene <a moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000288330;r=13:70137831-70139431;t=ENST00000673087">ENSG00000288330</a>
with the same name (AL160391.1) and description "ataxin 8". This
appears to be the missing ATXN8 gene: it's there, it is just not
linked to the HGNC ID (<a moz-do-not-send="true"
href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:32925">HGNC:32925</a>)
and name. Also, the gene type is wrong: it is registered as
lncRNA, while in reality is it a mRNA. The record is stated to
have been manually annotated, so this appears to be a human error
caused by confusion between the ATXN8 and ATXN8OS (which really <i>is</i>
lncRNA and is correctly annotated as such).<br>
<br>
Please let me know what you think about this.<br>
<br>
Best,<br>
Kirill<br>
<br>
</div>
<div class="moz-cite-prefix">On 06/05/2020 00:09, Thomas Danhorn
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:alpine.DEB.2.11.2005051659280.7084@Ntebonpgrevhz.ybpny">
<pre class="moz-quote-pre" wrap="">Hi Kirill,
On the NCBI site for ATXN8 you linked to it says "not in current
annotation release", so it looks like it may have once been considered a
valid gene, but not anymore. I have also looked through a few of the
older Ensembl releases and none of them have ATXN8 on chromosome 13 (so
this is not an omission in the new release). The ones based on the
GRCh37/hg19 assembly (Ensembl versions 75 and older) have "ATXN8" as a
synonym of ENSG00000107815, but that is on chromosome 10, so I doubt that
is what you are looking for.
Hope this helps,
Thomas</pre>
</blockquote>
<br>
On Tue, 5 May 2020, Kirill Tsukanov wrote:
<blockquote type="cite" style="color: #000000;">
<pre class="moz-quote-pre" wrap="">Hi,
I have a quick question about a data issue. I noticed that Ensembl 100
includes ATXN8OS gene
<a class="moz-txt-link-rfc2396E" href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230223;r=13:70107213-70149092"><http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230223;r=13:70107213-70149092></a>
(opposite strand lncRNA), but not the ATXN8 gene itself. The latter is
present in NCBI Gene (<a class="moz-txt-link-freetext" href="https://www.ncbi.nlm.nih.gov/gene/724066">https://www.ncbi.nlm.nih.gov/gene/724066</a>), but not in
Ensembl. This is unfortunate because it means that I can't use it in an Open
Targets submission as it does not have an Ensembl gene ID associated with it.
Do you know if there's a specific reason why this gene is missing? Can we
expect it to be added in later Ensembl releases?
--
Best,
Kirill from the European Variation Archive
</pre>
</blockquote>
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