<div dir="ltr">Thanks for the reply.<div><br></div><div>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).</div>
<div><br></div><div>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:</div><div><br></div><div><img src="cid:ii_145ad21350977e73" alt="Inline images 1" width="562" height="180.34768907563026"><br>
</div><div class="gmail_extra"><br></div><div class="gmail_extra">G.<br><br><div class="gmail_quote">On 28 April 2014 13:50, Thomas Maurel <span dir="ltr"><<a href="mailto:maurel@ebi.ac.uk" target="_blank">maurel@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Dear Genomeo,<br><br>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).<br>
<br><div>For this example you will get the following back:<br>>GRM3|ENSG00000198822|ENST00000546348|ENSP00000444064|ENSE00000700691;ENSE00002307238;ENSE00003523712;ENSE00002052628|2;4;3;1|1416<br><br>In this example the Exon rank is the following in the sequence header:<div>
2) ENSE00000700691</div><div>4) ENSE00002307238</div><div>3) ENSE00003523712<br>1) ENSE00002052628</div><div><br></div><div>You can see that the Ranking match the ensembl website: <a href="http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000198822;r=7:86273706-86493917;t=ENST00000546348" target="_blank">http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000198822;r=7:86273706-86493917;t=ENST00000546348</a></div>
<div><br>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.</div><div><br></div><div>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: <a href="http://www.ensembl.org/Help/Glossary?id=471" target="_blank">http://www.ensembl.org/Help/Glossary?id=471</a>).</div>
<div>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?</div><div><br></div><div>The "Structure" section can help you to see if an Exon is constitutive or not (please see last column of the attached screenshot2). </div>
<div><br></div><div>Hope this helps,</div><div>Regards,</div><div>Thomas<div><div class="h5"><br>On 28 Apr 2014, at 12:54, Genomeo Dev <<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>> wrote:<br>
<br></div></div><blockquote type="cite"><div><div class="h5">Hi,<br><br>(1)<br><br>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?<br>
<br>>GRM3|ENSG00000198822|ENST00000546348|ENSP00000444064|1416|2;4;3;1<br>MRRTNHEPEPGCRLTAAAATAVSSSSCQELSVRAPFNPNKDADSIVKFDTFGDGMGRYNV<br>FNFQNVGGKYSYLKVGHWAETLSLDVNSIHWSRNSVPTSQCSDPCAPNEMKNMQPGDVCC<br>WICIPCEPYEYLADEFTCMDCGSGQWPTADLTGCYDLPEDYIRWEDAWAIGPVTIACLGF<br>
MCTCMVVTVFIKHNNTPLVKASGRELCYILLFGVGLSYCMTFFFIAKPSPVICALRRLGL<br>GSSFAICYSALLTKTNCIARIFDGVKNGAQRPKFISPSSQVFICLGLILVQIVMVSVWLI<br>LEAPGTRRYTLAEKRETVILKCNVKDSSMLISLTYDVILVILCTVYAFKTRKCPENFNEA<br>KFIGFTMYTTCIIWLAFLPIFYVTSSDYRVQTTTMCISVSLSGFVVLGCLFAPKVHIILF<br>
QPQKNVVTHRLHLNRFSVSGTGTTYSQSSASTYVPTVCNGREVLDSTTSSL*<br><br><br>(2)<br><br>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.<br>
<br><br></div></div><span><image.png></span><br><br>Regards,<br><br>-- <br>G.<br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
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</blockquote><br><div>--<br>Thomas Maurel<br>Bioinformatician - Ensembl Production Team<br>European Bioinformatics Institute (EMBL-EBI)<br>European Molecular Biology Laboratory<br>Wellcome Trust Genome Campus<br>Hinxton<br>
Cambridge CB10 1SD<br>United Kingdom<br> </div><img height="731" width="1351" src="cid:A6A22211-5CB8-468C-B1FB-73F60796DFA7@windows.ebi.ac.uk"><img height="643" width="1351" src="cid:51B570DB-9171-4FA5-BB7A-F6BAB5D45F15@windows.ebi.ac.uk"></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">G.</div>
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