<div dir="ltr">Hello<div style>I am Taruna Kewalya student of B.Tech. Bioinformatics doing a research work over gene-transcript-protein relations, I am referring rest API 1.3.2 and with your help I retrieved many valuable data. While studying about exons I understood the chromosomes coordinate concept which you have send me in the last reply. Now I am facing a problem of getting accurate length of exons. <a href="http://beta.rest.ensembl.org/feature/id/ENSG00000146648?feature=exon;content-type=text/xml">http://beta.rest.ensembl.org/feature/id/ENSG00000146648?feature=exon;content-type=text/xml</a> in this we are given start and end coordinates of genomic DNA referring exons, but in online result we are shown that for a particular transcript just like ENST00000275493</div>
has 28 exons whereas the chromosome coordinates say that there are 264 positions for exons. So please let me know how to relate both the number of exons with each other as they shown a big variation.<div style>Thanking you</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jun 27, 2013 at 7:32 AM, Taruna Kewalya <span dir="ltr"><<a href="mailto:kewalyataruna@gmail.com" target="_blank">kewalyataruna@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5"><div dir="ltr"><br><br><div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Emily Pritchard</b> <span dir="ltr"><<a href="mailto:emily@ebi.ac.uk" target="_blank">emily@ebi.ac.uk</a>></span><br>
Date: Mon, Jun 24, 2013 at 6:43 PM<br>Subject: Re: [ensembl-dev] Fwd: Queries regarding API<br>To: <a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><br><br><br>
<div bgcolor="#FFFFFF" text="#000000">
Hi Taruna<br>
<br>
The REST link you've used asks for all the exons in a gene. The
script returns these in a per-transcript manner, which means that
some exons will appear more than once as they appear in more than
one transcript.<br>
<br>
Let's take a look at the first line of the output:<br>
{"ID":"ENSE00001633131","feature_type":"exon","Parent":"ENST00000455089","ensembl_phase":"-1","end":55087058,"seq_region_name":"7","ensembl_end_phase":"1","strand":1,"constitutive":"0","rank":"1","start":55086714},<br>
<br>
This firstly gives me the exon ID, then tells me that it is an exon.
The parent is the ID of the transcript that this exon is found in.
The start and end coordinates refer to the genomic position of the
exon, with the seq_region_name referring to the chromosome number,
and strand indicating if it's on the positive (1) or negative (-1)
strand. The phases refer to the position of the start and end of the
exon in the codons. The rank is the position of the exon in the
transcript.<br>
<br>
These are complete exons of the cDNA. Some of the them will include
the UTRs of the transcripts and some will be of non-coding
transcripts.<br>
<br>
Hope this helps<br>
<br>
Emily<br>
Ensembl helpdesk<div><div><br>
<br>
<div>On 24/06/2013 13:20, Taruna Kewalya
wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div>
<div dir="ltr"><br>
<br>
<div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Taruna Kewalya</b> <span dir="ltr"><<a href="mailto:kewalyataruna@gmail.com" target="_blank">kewalyataruna@gmail.com</a>></span><br>
Date: Thu, Jun 20, 2013 at 11:33 AM<br>
Subject: Queries regarding API<br>
To: <a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>,
<a href="mailto:ktaylor@ebi.ac.uk" target="_blank">ktaylor@ebi.ac.uk</a><br>
<br>
<br>
<div dir="ltr">Hello
<div>
I am Taruna Kewalya, student of Bioinformatics doing a
research work on gene and transcript. Thank you for your
reply it helped me in finding the details properly but now
I am stuck with a new problem. I have downloaded the Rest
API 1.3.2 link <a href="http://beta.rest.ensembl.org/feature/id/ENSG00000146648?feature=exon;content-type=application/json" target="_blank">http://beta.rest.ensembl.org/feature/id/ENSG00000146648?feature=exon;content-type=application/json</a> </div>
<div>this shares a common parent id. So please let me know
what is it relating to? The transcript belongs to cdna or
cds or genomic and please let me know what this parent id
refers to? And please also let me know how to understand
the starting and ending position of exons in a Fasta
sequence.</div>
<div>Thanking you</div>
</div>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
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<pre cols="72">--
Dr Emily Pritchard
Ensembl Outreach Officer
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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