[ensembl-dev] Exon order in header

Tue Apr 29 13:40:04 BST 2014

Dear Genomeo,

I agree with you, changing the Exon order in biomart would make things more intuitive but the exon order is automatically decided by the biomart software during the biomart build, I am afraid this is something we can't change.

Regarding the "Constitutive Exon" attribute, I am afraid biomart will only print "1" in the sequence header if the exon is constitutive (there will be no 0 in the header if the Exon is not constitutive). The constitutive Exon attribute in biomart will show you Exons that are present in all the Transcripts of a given gene.

I am not sure which Ensembl Exon ID is Exon1:
1) If Exon1 is ENSE00002313642 (first Exon in the Exon rank) then I am afraid it is not a constitutive exon as it is only present in the Transcript ENST00000536043 (please see attached screenshot1)
2) If Exon1 is (First Exon in the biomart output) ENSE00001254406 then I am afraid it not a constitutive exon either as it is present in the following Transcripts ENST00000361669, ENST00000439827, ENST00000536043, ENST00000394720 (please see attached screenshot2).

Hope this helps,
Thomas
On 29 Apr 2014, at 11:59, Genomeo Dev <genomeodev at gmail.com> wrote:

> Thanks for the reply.
> 
> For the exon IDs in the header, it might be more intuitive to print them in the order of the exon rank so that it would be directly observable which exons are spliced out (as the respective exon ranks will appear in numerical order).
> 
> This is what I get when I try to get the Constitutive Exon field in the header. Although Exon 1 is constitutive for GRM3, there is no attribute for that in the header:
> 
> <image.png>
> 
> G.
> 
> On 28 April 2014 13:50, Thomas Maurel <maurel at ebi.ac.uk> wrote:
> 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
>  
> <screenshot1.png><screenshot2.png>
> 
> _______________________________________________
> 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/
> 
> 
> 
> 
> -- 
> 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/20140429/c5913750/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: screenshot1.png
Type: image/png
Size: 220727 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140429/c5913750/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: screenshot2.png
Type: image/png
Size: 202697 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140429/c5913750/attachment-0001.png>