[ensembl-dev] Exon order in header

[Thomas Maurel]

Dear Genomeo,

1) The "2;4;3;1" numbers in the header refer to the Exon rank. If you add the "Ensembl Exon ID" attribute to your query, you will get the exon stable ID in the header (please see attached screenshot1).

For this example you will get the following back:
>GRM3|ENSG00000198822|ENST00000546348|ENSP00000444064|ENSE00000700691;ENSE00002307238;ENSE00003523712;ENSE00002052628|2;4;3;1|1416

In this example the Exon rank is the following in the sequence header:
2) ENSE00000700691
4) ENSE00002307238
3) ENSE00003523712
1) ENSE00002052628

You can see that the Ranking match the ensembl website: http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000198822;r=7:86273706-86493917;t=ENST00000546348

Biomart won't return the Exon stable ID in the rank order but the "Exon Rank in Transcript" attribute will help you know the actual Exon rank order.

2) The "Constitutive Exon" attribute in biomart correspond to the Exons that are not spliced out, therefore present in all the Transcripts of a given gene (please see: http://www.ensembl.org/Help/Glossary?id=471).
I am sorry, I can't see the "Ensembl Exon ID" in your screenshot. Could you please send me a screenshot of the result page or the Exon stable ID?

The "Structure" section can help you to see if an Exon is constitutive or not (please see last column of the attached screenshot2). 

Hope this helps,
Regards,
Thomas
On 28 Apr 2014, at 12:54, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi,
> 
> (1)
> 
> Using biomart it is possible to retrieve a sequence of a transcript with information in the header about Exon Ranks in Transcript (see image below). In this example, I wonder what order, it is correct to assume that 2;5;4;3;1 refer to some indices of the exons as defined based on the canonical transcript? but what is the meaning of this unordered indices here for this particular transcript?
> 
> >GRM3|ENSG00000198822|ENST00000546348|ENSP00000444064|1416|2;4;3;1
> MRRTNHEPEPGCRLTAAAATAVSSSSCQELSVRAPFNPNKDADSIVKFDTFGDGMGRYNV
> FNFQNVGGKYSYLKVGHWAETLSLDVNSIHWSRNSVPTSQCSDPCAPNEMKNMQPGDVCC
> WICIPCEPYEYLADEFTCMDCGSGQWPTADLTGCYDLPEDYIRWEDAWAIGPVTIACLGF
> MCTCMVVTVFIKHNNTPLVKASGRELCYILLFGVGLSYCMTFFFIAKPSPVICALRRLGL
> GSSFAICYSALLTKTNCIARIFDGVKNGAQRPKFISPSSQVFICLGLILVQIVMVSVWLI
> LEAPGTRRYTLAEKRETVILKCNVKDSSMLISLTYDVILVILCTVYAFKTRKCPENFNEA
> KFIGFTMYTTCIIWLAFLPIFYVTSSDYRVQTTTMCISVSLSGFVVLGCLFAPKVHIILF
> QPQKNVVTHRLHLNRFSVSGTGTTYSQSSASTYVPTVCNGREVLDSTTSSL*
> 
> 
> (2)
> 
> What is Constitutive Exon feature in Biomart?  See bottom of picture. For ENSG00000198822, exon 1 appears in all transcript but is not flagged as constitutive by this feature.
> 
> 
> <image.png>
> 
> Regards,
> 
> -- 
> G.
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140428/c8838d07/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: screenshot1.png
Type: image/png
Size: 221998 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140428/c8838d07/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: screenshot2.png
Type: image/png
Size: 214614 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140428/c8838d07/attachment-0001.png>