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Magali,Daniel,
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<div>Thank you for your e-mails. Quarterly updated cDNA alignments would be sufficient for my purposes if the mouse gene builds are likely to be old (~1.5 years in this case).</div>
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<div>However, I still cannot find an ENA track that displays <span style="font-family: AdvTT3713a231; font-size: 9pt; ">JX682706, JX682707, and JX682708 (from Aug '13). I only see AK144630 under the mouse cDNAs (Refseq/ENA) track. </span></div>
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<div><a href="http://www.ensembl.org/Mus_musculus/Location/View?r=1:150159043-150164948">http://www.ensembl.org/Mus_musculus/Location/View?r=1%3A150159043-150164948</a></div>
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<div>The Ensembl 'whats new in 75' page suggests that ENA sequences are more recent than Aug '13:</div>
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<div><a href="http://www.ensembl.org/Mus_musculus/Info/WhatsNew?db=core#change_1343">http://www.ensembl.org/Mus_musculus/Info/WhatsNew?db=core#change_1343</a></div>
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<p class="MsoNormal">Relevant text from what new:</p>
<p class="MsoNormal">Mouse: updated cDNA alignments (Mouse)<o:p></o:p></p>
<p class="MsoNormal">A new cdna database was created for e75: The latest set of cDNAs for mouse (as of January 2013) from the European Nucleotide Archive and NCBI RefSeq (release 62) were aligned to the current genome using Exonerate.</p>
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<div apple-content-edited="true">
<div>Daniel <br>
</div>
<div><br>
</div>
</div>
<br>
<div>
<div>On Feb 28, 2014, at 9:51 AM, mag <<a href="mailto:mr6@ebi.ac.uk">mr6@ebi.ac.uk</a>></div>
<div> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div text="#000000" bgcolor="#FFFFFF">Hi Daniel,<br>
<br>
There are two separate RefSeq tracks, representing two separate sets of data.<br>
<br>
The 'RefSeq/ENA' track represents the set of cDNA sequences which were used to build the latest gene set for a given species.<br>
For mouse, the last full build was for release 68.<br>
This means this track would only have sequences which were available at the time, around February 2012.<br>
<br>
As a full genebuild is very time consuming, we cannot re-annotate every single genome in its entirety every release.<br>
To provide a more recent set, we import the full RefSeq set dumped by NCBI every release, currently only for human and mouse.<br>
That data is available with the 'RefSeq import' track.<br>
<br>
<br>
Hope that makes sense,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 28/02/2014 14:48, Daniel Barrell wrote:<br>
</div>
<blockquote cite="mid:5310A1CC.7030309@ebi.ac.uk" type="cite">Hi Daniel,<br>
<br>
e!75 currently contains RefSeq data from a dump that the NCBI did for us on November 14th 2013. I've just looked at the human gff files and they do not include NR_110375<br>
<br>
All the best<br>
<br>
Daniel <br>
<br>
On 28/02/14 14:39, Caffrey, Daniel wrote:
<blockquote cite="mid:20140228143940.E74DB22F47A_3109FACB@hx-mx1.ebi.ac.uk" type="cite">
Hi Magali,
<div><br>
</div>
<div>If Ensembl 75 is using refseq sequences from December this probably explains the missing refseqs. However, the genbank/ENA accessions (<span style="font-family:
AdvTT3713a231; font-size: 9pt;">JX682706, JX682707, and JX682708)</span><font size="3" face="AdvTT3713a231"> </font> were
released in Aug 2013 . As the track is named refseq/ ENA I would expect them to be included (assuming version 75 is using ENA from December '13). </div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
<div apple-content-edited="true">
<div>Daniel <br>
<br>
</div>
<div><br>
</div>
<br class="Apple-interchange-newline">
</div>
<br>
<div>
<div>On Feb 28, 2014, at 6:44 AM, mag <<a moz-do-not-send="true" href="mailto:mr6@ebi.ac.uk">mr6@ebi.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div text="#000000" bgcolor="#FFFFFF">Hi Daniel,<br>
<br>
The two RefSeq entries you are referring to have been last updated early February 2014 and mention a paper from late January 2014.<br>
Could it be that these entries have only been recently created, hence would not have made it in our database at the time of update?<br>
<br>
The RefSeq track displayed in Ensembl 75 was updated end of last year, so any more recent RefSeq entries would not be included here.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 27/02/2014 19:15, Caffrey, Daniel wrote:<br>
</div>
<blockquote cite="mid:49AFC403-426E-4298-B964-17C7EA32EE94@umassmed.edu" type="cite">
Hi,
<div><br>
</div>
<div>Does anyone know why the following refseq sequences/alignments do not appear in version 75 (or other versions) of the cDNAs (Refseq/ENA) track on the location tabs</div>
<div><br>
</div>
<div>
<div>REFSEQ: NR_110420</div>
</div>
<div>mouse 1:150159043-150164948</div>
<div><br>
</div>
<div> </div>
<div><br>
</div>
<div>REFSEQ: NR_110375</div>
<div>human: 12:125509989-125511939</div>
<div><br>
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<div>There appear to be similar issues with other transcripts - They are all lincRNAs and perhaps this is the reason?</div>
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<div> Related to this, I know there are at least 3 splice variants/transcripts for the mouse gene in genbank (<span style="font-family: AdvTT3713a231;
font-size: 9pt;">JX682706, JX682707, and JX682708)</span><font size="3" face="AdvTT3713a231"> but
Ensembl/gencode only lists a </font><font face="AdvTT3713a231">single</font><font size="3" face="AdvTT3713a231"> transcript </font>ENSMUST00000181308. Presumably cDNA data is sufficient evidence for inclusion within gencode?</div>
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<div>Thanks</div>
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<div>Daniel <br>
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