I guess you need to select ALL results instead of 10 in the preview seciton.
On 16/03/2011 17:31, Ana Luisa Toribio wrote:
Many thanks for your reply, Syed. Very much appreciated.
However, there is still a point. My input is a list of 11 transcript ids
and the results are only for only two of them. How can this be possible?
What am I missing?
I would appreciate your feedback, if possible. I need to get this
information in a very large scale.
Best Regards,
Ana
-----Original Message-----
From: Syed Haider [mailto:[email protected]]
Sent: 16 March 2011 16:04
To: Ana Luisa Toribio
Cc: [email protected]
Subject: Re: [BioMart Users] 3'UTR start
Hi Ana,
the results that you see are correct, you just have to include more
information for the interpretation.
If you need 3'UTR coordinates, please see the "genomic coding start/end"
as well as "Exon Chr Start (bp)" and "Exon Chr Start (bp)".
Basically, the "Genomic Coding Start/end" are the chromosomal
coordinates and follows the same coordinates as of Exon Chr Start/End
coordinates EXCEPT that for an EXON that partially contains UTR sequence
(5 prime or 3 prime). So in your example, the genomic coding start/end
would be the same as of Exon Chr Start/End EXCEPT for the last exon
where the genomic coding end is smaller than Exon Chr end as the rest of
the exon contains 3UTR sequence.
Also, where there is no 3'UTR/5'UTR start/end at all for a transcript,
that means zero length UTR sequence. Note that you might see in some
cases multiple entries for 3'UTR/5'UTR start/end which means that the
UTR sequence spans multiple exons. For this, you might want to look at
the "Exon Rank in Transcript" attribute as well.
HTH,
Syed
On 16/03/2011 15:36, Ana Luisa Toribio wrote:
Hi again,
I forgot to mention that in some cases, for the same transcript. I
retrieve more than one "genomic coding end".
See below. For these results, I entered a list of 11 transcripts
belonging to different genes.
Best regards,
Ana
[cid:[email protected]]
From: Ana Luisa Toribio
Sent: 16 March 2011 15:31
To: '[email protected]'
Subject: 3'UTR start
Hi,
I would need to extract some information of gene structure. It is a
long list of genes so I thought that Biomart would be useful.
However, I see that some of the attributes I want, don't retrieve
anything for the majority of the genes. i.e. 3'UTR start.
Basically, one of the major data I would need to extract is the
position of the stop codon (end of the genomic coding sequence) for a
list of transcripts.
Could you give me any feedback, please?
Best regards,
ANa
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Ana Luisa TORIBIO
The Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge.
CB10 1SA
UK
Tel: +44 (0) 1223 494742
E-mail: [email protected]<mailto:[email protected]>
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