Configuring Genes to show exons and UTRs

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Configuring Genes to show exons and UTRs

John Portwood
Hello,

I'm having an issue trying to render exons and UTRs together. Here is a
sample of the GFF3 I'm working with:

/Chr10   Ensembl_AGPv3   gene    1720611 1722779 .       +       .      
Name=GRMZM2G129907;biotype=protein_coding;description=Uncharacterized%20protein%20%20[Source:UniProtKB/TrEMBL%3BAcc:B4FHQ6];logic_name=genebuilder;ID=GRMZM2G129907
Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .      
Name=GRMZM2G129907_T02;Parent=GRMZM2G129907;biotype=protein_coding;description=cdna|est|omrna;logic_name=genebuilder;ID=GRMZM2G129907_T02
Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .      
Name=GRMZM2G129907_T01;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T01
Chr10   Ensembl_AGPv3   mRNA    1721887 1722779 .       +       .      
Name=GRMZM2G129907_T03;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T03
Chr10   Ensembl_AGPv3   exon    1720611 1720931 .       +       .      
Name=GRMZM2G129907_E02;Parent=GRMZM2G129907_T01;ensembl_end_phase=2;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E02
Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .      
Parent=GRMZM2G129907_T01;
Chr10   Ensembl_AGPv3   CDS     1720714 1720931 .       +       0      
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=1;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   CDS     1721395 1721501 .       +       0      
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=2;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   exon    1721395 1721501 .       +       .      
Name=GRMZM2G129907_E04;Parent=GRMZM2G129907_T01;ensembl_end_phase=1;ensembl_phase=2;rank=2;ID=GRMZM2G129907_E04
Chr10   Ensembl_AGPv3   CDS     1722296 1722459 .       +       0      
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=3;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .      
Name=GRMZM2G129907_E03;Parent=GRMZM2G129907_T01;ensembl_end_phase=-1;ensembl_phase=1;rank=3;ID=GRMZM2G129907_E03
Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .      
Parent=GRMZM2G129907_T01;
Chr10   Ensembl_AGPv3   exon    1720611 1721501 .       +       .      
Name=GRMZM2G129907_E06;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E06
Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .      
Parent=GRMZM2G129907_T02;
Chr10   Ensembl_AGPv3   CDS     1720714 1720935 .       +       0      
Name=GRMZM2G129907_P02;Parent=GRMZM2G129907_T02;rank=1;ID=GRMZM2G129907_P02
Chr10   Ensembl_AGPv3   three_prime_UTR 1720936 1722779 .       +       .      
Parent=GRMZM2G129907_T02;
Chr10   Ensembl_AGPv3   exon    1721994 1722055 .       +       .      
Name=GRMZM2G129907_E05;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E05
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .      
Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=3;ID=GRMZM2G129907_E01
Chr10   Ensembl_AGPv3   exon    1721887 1722055 .       +       .      
Name=GRMZM2G129907_E07;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E07
Chr10   Ensembl_AGPv3   five_prime_UTR  1721887 1722363 .       +       .      
Parent=GRMZM2G129907_T03;
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .      
Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E01
Chr10   Ensembl_AGPv3   CDS     1722364 1722459 .       +       0      
Name=GRMZM2G129907_P03;Parent=GRMZM2G129907_T03;rank=1;ID=GRMZM2G129907_P03
Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .      
Parent=GRMZM2G129907_T03;/

Using the gene glyph produces this rendering:
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/geneModelsv3_UTRs.png>

This is close to what I want, but the inner exons aren't showing. When I use
"sub_part=exon" in this track's stanza, the exons show but the gray UTRs
disappear:
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/genModelsv3_Exons.png>

I want to render a display that looks exactly like the image above, but with
the grayed UTR regions showing in the exons. Any help on accomplishing this
would be greatly appreciated.

Thanks,
John




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Re: Configuring Genes to show exons and UTRs

Scott Cain
Hi John,

I think your GFF is inconsistent: when you (or Gramene) specify all of exons, CDSes and UTRs in a GFF file, it is over specified.  That is, you really only need two out of the three of those items to specify where the coding and non coding regions of a transcript are.  The features in the third transcript have these ranges:

exon                     1721887 1722055
five_prime_UTR   1721887 1722363
exon                     1722296 1722779
CDS                      1722364 1722459
three_prime_UTR 1722460 1722779

If you look at the coordinates of the UTRs and CDS, you'll see that it covers everything from the start to the finish of the transcript, which is why you're getting a single glyph with no sign of there being two exons, which is what I would guess is supposed to happen given the exon boundaries.  The problem is GBrowse doesn't know which boundaries to pay attention to: the exons or the CDS/UTR.  I would say, the exon features should probably just go away and and be replaced with this:

five_prime_UTR   1721887 1722055
five_prime_UTR   1722296 1722363
CDS                      1722364 1722459
three_prime_UTR 1722460 1722779

Which I think is right (ie, the 5' utr stretches over two exons and the CDS and 3' utr are in the second exon).  I imagine you'll find the same sort of thing in the second transcript, but deciphering cut and pasted GFF is somewhat tedious :-)

Scott



On Thu, Apr 17, 2014 at 1:47 PM, John Portwood <[hidden email]> wrote:
Hello,

I'm having an issue trying to render exons and UTRs together. Here is a
sample of the GFF3 I'm working with:

/Chr10   Ensembl_AGPv3   gene    1720611 1722779 .       +       .
Name=GRMZM2G129907;biotype=protein_coding;description=Uncharacterized%20protein%20%20[Source:UniProtKB/TrEMBL%3BAcc:B4FHQ6];logic_name=genebuilder;ID=GRMZM2G129907
Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .
Name=GRMZM2G129907_T02;Parent=GRMZM2G129907;biotype=protein_coding;description=cdna|est|omrna;logic_name=genebuilder;ID=GRMZM2G129907_T02
Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .
Name=GRMZM2G129907_T01;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T01
Chr10   Ensembl_AGPv3   mRNA    1721887 1722779 .       +       .
Name=GRMZM2G129907_T03;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T03
Chr10   Ensembl_AGPv3   exon    1720611 1720931 .       +       .
Name=GRMZM2G129907_E02;Parent=GRMZM2G129907_T01;ensembl_end_phase=2;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E02
Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .
Parent=GRMZM2G129907_T01;
Chr10   Ensembl_AGPv3   CDS     1720714 1720931 .       +       0
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=1;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   CDS     1721395 1721501 .       +       0
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=2;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   exon    1721395 1721501 .       +       .
Name=GRMZM2G129907_E04;Parent=GRMZM2G129907_T01;ensembl_end_phase=1;ensembl_phase=2;rank=2;ID=GRMZM2G129907_E04
Chr10   Ensembl_AGPv3   CDS     1722296 1722459 .       +       0
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=3;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .
Name=GRMZM2G129907_E03;Parent=GRMZM2G129907_T01;ensembl_end_phase=-1;ensembl_phase=1;rank=3;ID=GRMZM2G129907_E03
Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .
Parent=GRMZM2G129907_T01;
Chr10   Ensembl_AGPv3   exon    1720611 1721501 .       +       .
Name=GRMZM2G129907_E06;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E06
Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .
Parent=GRMZM2G129907_T02;
Chr10   Ensembl_AGPv3   CDS     1720714 1720935 .       +       0
Name=GRMZM2G129907_P02;Parent=GRMZM2G129907_T02;rank=1;ID=GRMZM2G129907_P02
Chr10   Ensembl_AGPv3   three_prime_UTR 1720936 1722779 .       +       .
Parent=GRMZM2G129907_T02;
Chr10   Ensembl_AGPv3   exon    1721994 1722055 .       +       .
Name=GRMZM2G129907_E05;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E05
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .
Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=3;ID=GRMZM2G129907_E01
Chr10   Ensembl_AGPv3   exon    1721887 1722055 .       +       .
Name=GRMZM2G129907_E07;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E07
Chr10   Ensembl_AGPv3   five_prime_UTR  1721887 1722363 .       +       .
Parent=GRMZM2G129907_T03;
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .
Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E01
Chr10   Ensembl_AGPv3   CDS     1722364 1722459 .       +       0
Name=GRMZM2G129907_P03;Parent=GRMZM2G129907_T03;rank=1;ID=GRMZM2G129907_P03
Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .
Parent=GRMZM2G129907_T03;/

Using the gene glyph produces this rendering:
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/geneModelsv3_UTRs.png>

This is close to what I want, but the inner exons aren't showing. When I use
"sub_part=exon" in this track's stanza, the exons show but the gray UTRs
disappear:
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/genModelsv3_Exons.png>

I want to render a display that looks exactly like the image above, but with
the grayed UTR regions showing in the exons. Any help on accomplishing this
would be greatly appreciated.

Thanks,
John




--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Configuring-Genes-to-show-exons-and-UTRs-tp5712467.html
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------------------------------------------------------------------------------
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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
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http://p.sf.net/sfu/NeoTech
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
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