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<p>Hi Beat,</p>
<p><br>
</p>
<p>The GRCh37 GFF file does not contain any MANE_Select tag. </p>
<p><br>
</p>
<p>We need to consider whether it is worth adding a partial set of
MANE Select tags or it might be confusing where users could be
expecting the whole set. <br>
</p>
<p><br>
</p>
<p>Thanks,<br>
</p>
<p>Jose</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 24/09/2023 14:22, Wolf Beat wrote:<br>
</div>
<blockquote type="cite"
cite="mid:GVAP278MB0391FEBA7BC24D325C7CFFAEE8FDA@GVAP278MB0391.CHEP278.PROD.OUTLOOK.COM">
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<div
style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"
class="elementToProof"> Thank you for the answer.</div>
<div
style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"
class="elementToProof"> The question though is, does the GRCH37
GFF file contain the MANE_SELECT tag for the transcripts that do
match?</div>
<div
style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"
class="elementToProof"> <br>
</div>
<div
style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"
class="elementToProof"> Kind regards</div>
<div
style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"
class="elementToProof"> <br>
</div>
<div
style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);"
class="elementToProof"> Beat Wolf</div>
<div class="elementToProof">
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<br>
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<p style="margin-top:0px; margin-bottom:0px"><b><span
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data-lt-sig="">Dr Beat Wolf, PhD ▪ Assistant
Professor ▪ Member of iCoSys Institute<br>
</span></b><span
style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont"
data-lt-sig="">University of Applied Sciences
and Arts Western Switzerland ▪ Pérolles 80 ▪
CH-1700 Fribourg<br>
Member of University of Applied Sciences of
Western Switzerland<br>
</span><span
style="margin: 0px; font-size: 8pt; font-family: Arial, sans-serif, serif, EmojiFont; color: blue;"
lang="FR"><a href="https://eia-fr.ch/"
target="_blank" rel="noopener noreferrer"
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lang="EN-GB">https://www.heia-fr.ch</span></a></span><span
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style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont"
data-lt-sig="">▪ <a href="https://icosys.ch/"
target="_blank" rel="noopener noreferrer"
style="margin:0px" data-lt-sig=""
moz-do-not-send="true"
class="moz-txt-link-freetext">https://icosys.ch/</a></span></p>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>Von:</b> Jose
Gonzalez <a class="moz-txt-link-rfc2396E"
href="mailto:jmgonzalez@ebi.ac.uk"><jmgonzalez@ebi.ac.uk></a><br>
<b>Gesendet:</b> Donnerstag, 14. September 2023 11:02<br>
<b>An:</b> Ensembl developers list <a
class="moz-txt-link-rfc2396E" href="mailto:dev@ensembl.org"><dev@ensembl.org></a>;
Wolf Beat <a class="moz-txt-link-rfc2396E"
href="mailto:Beat.Wolf@hefr.ch"><Beat.Wolf@hefr.ch></a><br>
<b>Betreff:</b> Re: [ensembl-dev] Declaration of Intentions
for Ensembl release 111 and Ensembl Genomes release 58</font>
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<div>Sie erhalten nicht oft eine E-Mail von <a
class="moz-txt-link-abbreviated moz-txt-link-freetext"
href="mailto:jmgonzalez@ebi.ac.uk">jmgonzalez@ebi.ac.uk</a>.
<a
href="https://aka.ms/LearnAboutSenderIdentification"
moz-do-not-send="true"> Erfahren Sie, warum dies
wichtig ist</a></div>
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style="width:75px; background-color:#EAEAEA; padding:7px 5px 7px 5px; font-family:wf_segoe-ui_normal,Segoe UI,Segoe WP,Tahoma,Arial,sans-serif; font-size:12px; font-weight:normal; color:#212121; text-align:left; word-wrap:break-word"
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<p>Hi Beat,</p>
<p><br>
</p>
<p>As far as I know, the only update is the RefSeq annotation
in our GRCh37 otherfeatures database, which has been
imported using the file below:<br>
<a class="x_moz-txt-link-freetext moz-txt-link-freetext"
href="https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz"
moz-do-not-send="true">https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz</a><br>
<br>
The Ensembl GRCh37 annotation hasn't been updated, so only a
fraction of the RefSeq MANE v1.0 transcripts will be exactly
matched by Ensembl transcripts.</p>
<p><br>
</p>
<p>Thanks,<br>
Jose<br>
</p>
<p><br>
</p>
<p><br>
</p>
<div class="x_moz-cite-prefix">On 13/09/2023 15:31, Wolf Beat
wrote:<br>
</div>
<blockquote type="cite">
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<div class="x_elementToProof"
style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
The mane 1.0 inclusion into grch37 sounds great. Related
to this, will the gff file for grch37 also include this
information? I know the grch38 does already do that.</div>
<div class="x_elementToProof"
style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div class="x_elementToProof"
style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Kind regards</div>
<div class="x_elementToProof"
style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div class="x_elementToProof"
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Beat Wolf</div>
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<br>
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<p style="margin-top:0px; margin-bottom:0px"><b><span
data-lt-sig=""
style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont">Dr
Beat Wolf, PhD ▪ Assistant Professor ▪
Member of iCoSys Institute<br>
</span></b><span data-lt-sig=""
style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont">University
of Applied Sciences and Arts Western
Switzerland ▪ Pérolles 80 ▪ CH-1700
Fribourg<br>
Member of University of Applied Sciences
of Western Switzerland<br>
</span><span
style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont; color:blue"
lang="FR"><a href="https://eia-fr.ch/"
target="_blank"
rel="noopener noreferrer"
style="margin:0px"
moz-do-not-send="true"><span
data-lt-sig="" style="margin:0px"
lang="EN-GB">https://www.heia-fr.ch</span></a></span><span
style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont; color:blue"> </span><span
data-lt-sig=""
style="margin:0px; font-size:8pt; font-family:Arial,sans-serif,serif,EmojiFont">▪ <a
href="https://icosys.ch/"
target="_blank"
rel="noopener noreferrer"
data-lt-sig=""
class="x_moz-txt-link-freetext moz-txt-link-freetext" style="margin:0px"
moz-do-not-send="true">https://icosys.ch/</a></span></p>
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<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" face="Calibri, sans-serif"
color="#000000"><b>Von:</b> Dev <a
class="x_moz-txt-link-rfc2396E"
href="mailto:dev-bounces@ensembl.org"
moz-do-not-send="true"><dev-bounces@ensembl.org></a>
im Auftrag von Benjamin Moore <a
class="x_moz-txt-link-rfc2396E"
href="mailto:bmoore@ebi.ac.uk" moz-do-not-send="true"><bmoore@ebi.ac.uk></a><br>
<b>Gesendet:</b> Mittwoch, 13. September 2023 16:15<br>
<b>An:</b> Ensembl developers list <a
class="x_moz-txt-link-rfc2396E"
href="mailto:dev@ensembl.org" moz-do-not-send="true">
<dev@ensembl.org></a><br>
<b>Betreff:</b> [ensembl-dev] Declaration of Intentions
for Ensembl release 111 and Ensembl Genomes release 58</font>
<div> </div>
</div>
<div>
<div class="" style="margin:0cm 0cm 0.0001pt">Dear all,</div>
<div class="" style="margin:0cm 0cm 0.0001pt"> </div>
<div class="" style="margin:0cm 0cm 0.0001pt">Ensembl
release 111 and Ensembl Genomes release 58 are scheduled
for November 2023.</div>
<div class="" style="margin:0cm 0cm 0.0001pt"> </div>
<div class="" style="margin:0cm 0cm 0.0001pt">Please find
the summary of the declarations of intentions in our
blog:</div>
<div class="" style="margin:0cm 0cm 0.0001pt"><a
class="x_x_moz-txt-link-freetext x_moz-txt-link-freetext moz-txt-link-freetext"
href="https://www.ensembl.info/2023/09/13/whats-coming-in-ensembl-111-ensembl-genomes-58/"
moz-do-not-send="true">https://www.ensembl.info/2023/09/13/whats-coming-in-ensembl-111-ensembl-genomes-58/</a><br>
</div>
<div class="" style="margin:0cm 0cm 0.0001pt"> </div>
<div class="" style="margin:0cm 0cm 0.0001pt"><span
class="" style="background-color:white">As with all
releases, please note that these are intentions and
are not guaranteed to make it into the releases. </span></div>
<div class="" style="margin:0cm 0cm 0.0001pt"> </div>
<div class="" style="margin:0cm 0cm 0.0001pt">Best wishes</div>
<div class="" style="margin:0cm 0cm 0.0001pt"> </div>
<div class="" style="margin:0cm 0cm 0.0001pt">Ben</div>
<div class="" style="margin:0cm 0cm 0.0001pt">On behalf of
the Ensembl team</div>
<pre class="x_x_moz-signature" cols="72">--
Dr. Ben Moore (he/him)
Ensembl Outreach Manager
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK
<a
class="x_x_moz-txt-link-abbreviated x_moz-txt-link-freetext moz-txt-link-freetext"
href="mailto:bmoore@ebi.ac.uk" moz-do-not-send="true">bmoore@ebi.ac.uk</a>
+44 (0)1223 494265</pre>
</div>
<br>
<fieldset class="x_moz-mime-attachment-header"></fieldset>
<pre class="x_moz-quote-pre">_______________________________________________
Dev mailing list <a
class="x_moz-txt-link-abbreviated moz-txt-link-freetext"
href="mailto:Dev@ensembl.org" moz-do-not-send="true">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a
class="x_moz-txt-link-freetext moz-txt-link-freetext"
href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org"
moz-do-not-send="true">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a>
Ensembl Blog: <a class="x_moz-txt-link-freetext moz-txt-link-freetext"
href="http://www.ensembl.info/" moz-do-not-send="true">http://www.ensembl.info/</a>
</pre>
</blockquote>
<pre class="x_moz-signature" cols="72">--
Dr Jose M. Gonzalez
GENCODE Bioinformatician (Genome Interpretation Team)
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton, CB10 1SD, UK</pre>
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