Many thanks. Ana -----Original Message----- From: Ana Luisa Toribio Sent: 16 March 2011 17:31 To: 'Syed Haider' Cc: '[email protected]' Subject: RE: [BioMart Users] 3'UTR start
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 > > > _______________________________________________ > > 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]> > Website: http://www.sanger.ac.uk<http://www.sanger.ac.uk/> > ______________________________________________ > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
