<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">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=""><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" class=""><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></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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;" class=""><a href="mailto:maker-devel@yandell-lab.org" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">maker-devel@yandell-lab.org</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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;" class=""><a href="http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></div></div></body></html>