[ensembl-dev] Exon order in header

Tue Apr 29 12:06:04 BST 2014

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 waiting moderator approval due to size limit).

G.

On 29 April 2014 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: Inline images 1]
>
> 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
>>
>>
>> _______________________________________________
>> 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.
>

-- 
G.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140429/5da46949/attachment.html>
-------------- 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/20140429/5da46949/attachment.png>
-------------- 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/20140429/5da46949/attachment-0001.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 136753 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140429/5da46949/attachment-0002.png>