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<p>Hi<br>
</p>
<p>The database and VEP caches are in sync. NM_004448.3 is in the
database and VEP caches.<br>
</p>
<p>Running VEP for a variant using the database without a cache
NM_004448.3 is returned e.g.</p>
<p>./vep --database --assembly GRCh37 --port 3337 --input_data
rs1456994901 --refseq<br>
</p>
<p>The schema has not changed and NM_004448.3 can be queried using
the transcript and the xref table <a
class="moz-txt-link-freetext"
href="https://www.ensembl.org/info/docs/api/core/core_schema.html#xref">https://www.ensembl.org/info/docs/api/core/core_schema.html#xref</a></p>
<p>SELECT stable_id<br>
FROM transcript <br>
WHERE stable_id like '%NM_004448%'<br>
</p>
<p>It is best to query using the API instead of querying the
database directly.</p>
<p>See core API: <a class="moz-txt-link-freetext"
href="https://www.ensembl.org/info/docs/api/core/index.html">https://www.ensembl.org/info/docs/api/core/index.html</a>)
<br>
</p>
<p>The core tutorial <a class="moz-txt-link-freetext"
href="https://www.ensembl.org/info/docs/api/core/core_tutorial.html#xrefs">https://www.ensembl.org/info/docs/api/core/core_tutorial.html#xrefs</a></p>
<p>FAQ: How do I access RefSeq annotation in Ensembl?
grch37.ensembl.org/Help/Faq</p>
<p> </p>
<p>Regards</p>
<p>Helen</p>
<div class="moz-cite-prefix">On 08/06/2020 07:54, Wallace Ko wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20200608065617.133AD1344FB_EDDE111B@hx-mx2.ebi.ac.uk">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi,
<div><br>
</div>
<div>I have some variants on the gene ERBB2 annotated by VEP 100
(GRCh37) transcripts NM_004448.3, which seems to be a
record from the new RefSeq release.<br>
However, when I tried to query the transcript table in the
MySQL (<a
href="http://ensembldb.ensembl.org:3337/homo_sapiens_otherfeatures_100_37"
moz-do-not-send="true">ensembldb.ensembl.org:3337/homo_sapiens_otherfeatures_100_37</a>)
, there's no result for this stable_id.<br>
<br>
When querying all transcripts of the accession without version
(<font face="monospace">select * from transcript where
stable_id like 'NM_004448%'</font>), there are only results
for NM_004448.2.<br>
<br>
Are the database and cache not in sync yet? Or is the database
schema changed so that I'll need to query in another way?<br>
</div>
<div><br clear="all">
<div>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">Regards,
<div>Wallace Ko</div>
</div>
</div>
</div>
</div>
</div>
<br>
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