Multiple UTR ?

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Multiple UTR ?

Patrick Tran Van-2

Hi Carson,


I have seen something strange in my annotation: multiple UTR. How can we explain this ?  Thanks!


Scaffold maker mRNA 12117462 12128433 . - . 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;
Scaffold maker exon 12128112 12128433 . - . ID=GENE_02395-RA:exon:571;Parent=GENE_02395-RA;
Scaffold maker exon 12117462 12118046 . - . ID=GENE_02395-RB:exon:569;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12118141 12118301 . - . ID=GENE_02395-RB:exon:568;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12118386 12118539 . - . ID=GENE_02395-RB:exon:567;Parent=GENE_02395-RB,GENE_02395-RA;
Scaffold maker exon 12118818 12122493 . - . ID=GENE_02395-RB:exon:566;Parent=GENE_02395-RB,GENE_02395-RA;
Scaffold maker exon 12123591 12123893 . - . ID=GENE_02395-RB:exon:565;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12123995 12124303 . - . ID=GENE_02395-RB:exon:564;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12125119 12125418 . - . ID=GENE_02395-RB:exon:563;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12126005 12126313 . - . ID=GENE_02395-RB:exon:562;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12127460 12127687 . - . ID=GENE_02395-RB:exon:561;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker five_prime_UTR 12128112 12128433 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12127460 12127687 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12126005 12126313 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12125119 12125418 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12123995 12124303 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12123591 12123893 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12118882 12122493 . - . ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker CDS 12118818 12118881 . - 0 ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;
Scaffold maker CDS 12118386 12118539 . - 2 ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;
Scaffold maker CDS 12118141 12118301 . - 1 ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;
Scaffold maker CDS 12117709 12118046 . - 2 ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;
Scaffold maker three_prime_UTR 12117462 12117708 . - . ID=GENE_02395-RA:three_prime_utr;Parent=GENE_02395-RA;



Patrick Tran Van

Bioinformatician: Lab Chapuisat & Schwander
Department of Ecology and Evolution
University of Lausanne
Lausanne - Switzerland
Office 3206

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Re: Multiple UTR ?

Patrick Tran Van-2

Hi Carson,


for instance, if have this:


SCFXX maker five_prime_UTR 5164370 5164715 . - . ID=GENE-RA:five_prime_utr;Parent=GENE-RA;
SCFXX maker five_prime_UTR 5156091 5156136 . - . ID=GENE-RA:five_prime_utr;Parent=GENE-RA;


Does it mean that real coordinate of the 5' UTR is from 5156091 to 5164715 ?


Patrick Tran Van

Bioinformatician: Lab Chapuisat & Schwander
Department of Ecology and Evolution
University of Lausanne
Lausanne - Switzerland
Office 3206

From: Carson Holt <[hidden email]>
Sent: Wednesday, February 26, 2020 8:27:43 PM
To: Patrick Tran Van
Cc: [hidden email]
Subject: Re: [maker-devel] Multiple UTR ?
 
Sorry for the very slow reply. I found this way way down in my inbox.

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. 

—Carson



On Dec 18, 2019, at 7:19 AM, Patrick Tran Van <[hidden email]> wrote:

Hi Carson,

I have seen something strange in my annotation: multiple UTR. How can we explain this ?  Thanks!

Scaffold maker mRNA 12117462 12128433 . - .  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;
Scaffold maker exon 12128112 12128433 . - .  ID=GENE_02395-RA:exon:571;Parent=GENE_02395-RA;
Scaffold maker exon 12117462 12118046 . - .  ID=GENE_02395-RB:exon:569;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12118141 12118301 . - .  ID=GENE_02395-RB:exon:568;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12118386 12118539 . - .  ID=GENE_02395-RB:exon:567;Parent=GENE_02395-RB,GENE_02395-RA;
Scaffold maker exon 12118818 12122493 . - .  ID=GENE_02395-RB:exon:566;Parent=GENE_02395-RB,GENE_02395-RA;
Scaffold maker exon 12123591 12123893 . - .  ID=GENE_02395-RB:exon:565;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12123995 12124303 . - .  ID=GENE_02395-RB:exon:564;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12125119 12125418 . - .  ID=GENE_02395-RB:exon:563;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12126005 12126313 . - .  ID=GENE_02395-RB:exon:562;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker exon 12127460 12127687 . - .  ID=GENE_02395-RB:exon:561;Parent=GENE_02395-RB,GENE_02395-RC,GENE_02395-RA;
Scaffold maker five_prime_UTR 12128112 12128433 . - .  ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12127460 12127687 . - .  ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12126005 12126313 . - .  ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12125119 12125418 . - .  ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12123995 12124303 . - .  ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12123591 12123893 . - .  ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker five_prime_UTR 12118882 12122493 . - .  ID=GENE_02395-RA:five_prime_utr;Parent=GENE_02395-RA;
Scaffold maker CDS 12118818 12118881 . - 0  ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;
Scaffold maker CDS 12118386 12118539 . - 2  ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;
Scaffold maker CDS 12118141 12118301 . - 1  ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;
Scaffold maker CDS 12117709 12118046 . - 2  ID=GENE_02395-RA:cds;Parent=GENE_02395-RA;
Scaffold maker three_prime_UTR 12117462 12117708 . - .  ID=GENE_02395-RA:three_prime_utr;Parent=GENE_02395-RA;



Patrick Tran Van

Bioinformatician: Lab Chapuisat & Schwander 
Department of Ecology and Evolution
University of Lausanne
Lausanne - Switzerland
Office 3206
_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org