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<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;" dir="ltr">
<p>Hi Carson,</p>
<p><br>
</p>
<p>for instance, if have this:</p>
<p><br>
</p>
<p></p>
<div>SCFXX<span style="white-space:pre"> </span>maker<span style="white-space:pre">
</span>five_prime_UTR<span style="white-space:pre"> </span>5164370<span style="white-space:pre">
</span>5164715<span style="white-space:pre"> </span>.<span style="white-space:pre">
</span>-<span style="white-space:pre"> </span>.<span style="white-space:pre"> </span>
ID=GENE-RA:five_prime_utr;Parent=GENE-RA;</div>
<div>SCFXX<span style="white-space:pre"> </span>maker<span style="white-space:pre">
</span>five_prime_UTR<span style="white-space:pre"> </span>5156091<span style="white-space:pre">
</span>5156136<span style="white-space:pre"> </span>.<span style="white-space:pre">
</span>-<span style="white-space:pre"> </span>.<span style="white-space:pre"> </span>
ID=GENE-RA:five_prime_utr;Parent=GENE-RA;</div>
<div><br>
</div>
<br>
<p></p>
<p>Does it mean that real coordinate of the 5' UTR is from <span>5156091 to <span>5164715 ?</span></span></p>
<p><br>
</p>
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<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
Patrick Tran Van<br>
<br>
Bioinformatician: Lab Chapuisat & Schwander <br>
Department of Ecology and Evolution<br>
University of Lausanne<br>
Lausanne - Switzerland<br>
Office 3206</div>
</div>
</div>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Carson Holt <carsonhh@gmail.com><br>
<b>Sent:</b> Wednesday, February 26, 2020 8:27:43 PM<br>
<b>To:</b> Patrick Tran Van<br>
<b>Cc:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: [maker-devel] Multiple UTR ?</font>
<div> </div>
</div>
<div>Sorry for the very slow reply. I found this way way down in my inbox.
<div class=""><br class="">
</div>
<div class="">The UTR features are the parts of the exons that are not CDS. So multiple UTR, means it spans multiple exons, and must assembled to generate the full UTR in a browser. Any exon that is fully non-coding will produce a UTR feature that mirrors
an exons coordinates, and if it’s partially coding the UTR will share the same start or end by will terminate somewhere in the middle with a CDS filling up the remains coordinates. The UTR and CDS features get tiled over the top of the exon features when
assembling a gene model. <br class="">
<div class=""><br class="">
</div>
<div class="">—Carson</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Dec 18, 2019, at 7:19 AM, Patrick Tran Van <<a href="mailto:Patrick.TranVan@unil.ch" class="">Patrick.TranVan@unil.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi Carson,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I have seen something strange in my annotation: multiple UTR. How can we explain this ? Thanks!</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>mRNA<span style="white-space: pre;" class=""> </span>12117462<span style="white-space: pre;" class="">
</span>12128433<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA;Parent=GENE_02395;Name=GENE_02395-RA;Alias=maker-Scaffold-augustus-gene-40.12-mRNA-3;_AED=0.02;_QI=5383|1|1|1|0.88|0.9|10|247|238;_eAED=0.02;Note=Protein of unknown function;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>exon<span style="white-space: pre;" class=""> </span>12128112<span style="white-space: pre;" class="">
</span>12128433<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:exon:571;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>exon<span style="white-space: pre;" class=""> </span>12117462<span style="white-space: pre;" class="">
</span>12118046<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RB:exon:569;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>exon<span style="white-space: pre;" class=""> </span>12118141<span style="white-space: pre;" class="">
</span>12118301<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RB:exon:568;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>exon<span style="white-space: pre;" class=""> </span>12118386<span style="white-space: pre;" class="">
</span>12118539<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RB:exon:567;Parent=GENE_02395-RB,GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>exon<span style="white-space: pre;" class=""> </span>12118818<span style="white-space: pre;" class="">
</span>12122493<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RB:exon:566;Parent=GENE_02395-RB,GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>exon<span style="white-space: pre;" class=""> </span>12123591<span style="white-space: pre;" class="">
</span>12123893<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RB:exon:565;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>exon<span style="white-space: pre;" class=""> </span>12123995<span style="white-space: pre;" class="">
</span>12124303<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RB:exon:564;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>exon<span style="white-space: pre;" class=""> </span>12125119<span style="white-space: pre;" class="">
</span>12125418<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RB:exon:563;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>exon<span style="white-space: pre;" class=""> </span>12126005<span style="white-space: pre;" class="">
</span>12126313<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RB:exon:562;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>exon<span style="white-space: pre;" class=""> </span>12127460<span style="white-space: pre;" class="">
</span>12127687<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RB:exon:561;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>five_prime_UTR<span style="white-space: pre;" class=""> </span>12128112<span style="white-space: pre;" class="">
</span>12128433<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>five_prime_UTR<span style="white-space: pre;" class=""> </span>12127460<span style="white-space: pre;" class="">
</span>12127687<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>five_prime_UTR<span style="white-space: pre;" class=""> </span>12126005<span style="white-space: pre;" class="">
</span>12126313<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>five_prime_UTR<span style="white-space: pre;" class=""> </span>12125119<span style="white-space: pre;" class="">
</span>12125418<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>five_prime_UTR<span style="white-space: pre;" class=""> </span>12123995<span style="white-space: pre;" class="">
</span>12124303<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>five_prime_UTR<span style="white-space: pre;" class=""> </span>12123591<span style="white-space: pre;" class="">
</span>12123893<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>five_prime_UTR<span style="white-space: pre;" class=""> </span>12118882<span style="white-space: pre;" class="">
</span>12122493<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>CDS<span style="white-space: pre;" class=""> </span>12118818<span style="white-space: pre;" class="">
</span>12118881<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>0<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>CDS<span style="white-space: pre;" class=""> </span>12118386<span style="white-space: pre;" class="">
</span>12118539<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>2<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>CDS<span style="white-space: pre;" class=""> </span>12118141<span style="white-space: pre;" class="">
</span>12118301<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>1<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>CDS<span style="white-space: pre;" class=""> </span>12117709<span style="white-space: pre;" class="">
</span>12118046<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>2<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;</div>
<div class="">Scaffold<span style="white-space: pre;" class=""> </span>maker<span style="white-space: pre;" class="">
</span>three_prime_UTR<span style="white-space: pre;" class=""> </span>12117462<span style="white-space: pre;" class="">
</span>12117708<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span>-<span style="white-space: pre;" class=""> </span>.<span style="white-space: pre;" class="">
</span><span class="Apple-converted-space"> </span>ID=GENE_02395-RA:three_prime_utr;Parent=GENE_02395-RA;</div>
<div class=""><br class="">
</div>
<br class="">
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<div name="divtagdefaultwrapper" style="font-family: Calibri, Arial, Helvetica, sans-serif; margin: 0px;" class="">
Patrick Tran Van<br class="">
<br class="">
Bioinformatician: Lab Chapuisat & Schwander<span class="Apple-converted-space"> </span><br class="">
Department of Ecology and Evolution<br class="">
University of Lausanne<br class="">
Lausanne - Switzerland<br class="">
Office 3206</div>
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