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Hi Taruna,<br>
<br>
With the rest API, you are retrieving all the exons for a gene, in
this case ENSG00000146648.<br>
<br>
That gene has in turn 11 transcripts, ENST00000275493 is one of
them.<br>
<br>
So with the rest API, you will get all exons for all 11 transcripts.<br>
But you can see that, from the 154 lines the rest API returns, 28
are for transcript ENST00000275493, the others are for the other
transcripts.<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 27/06/13 08:35, Taruna Kewalya
wrote:<br>
</div>
<blockquote
cite="mid:CAAFwbv3xvCEPjMcoH_vbiA0kGM_bw62FXLL_GKEYQe6faEeEZg@mail.gmail.com"
type="cite">
<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
moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:dev@ensembl.org"
target="_blank">dev@ensembl.org</a>, <a
moz-do-not-send="true"
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 moz-do-not-send="true"
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>
<br>
</div>
</div>
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<span><font color="#888888"> <br>
<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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