[maker-devel] Multiple UTR ?

Tue May 26 12:51:52 MDT 2020

The UTR is split across two exons. The intron is not considered part of the UTR. The UTR exists in the post splicing mRNA, so the corresponding genomic coordinates will have gaps because the introns that exist in the genome have been spliced out of the mRNA. So while the UTR is continuous in the mRNA, it is punctuated in the genome.

—Carson

> On May 3, 2020, at 5:39 AM, Patrick Tran Van <Patrick.TranVan at unil.ch> wrote:
> 
> 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 <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Sent: Wednesday, February 26, 2020 8:27:43 PM
> To: Patrick Tran Van
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> 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 <Patrick.TranVan at unil.ch <mailto:Patrick.TranVan at unil.ch>> 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
>> _______________________________________________
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