<html><body><div style="font-family: times new roman, new york, times, serif; font-size: 14pt; color: #000000"><div><span style="color: rgb(51, 102, 255);">Hello Matthieu,</span><br></div><div><br></div><hr id="zwchr"><div style="color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;" data-mce-style="color: #000; font-weight: normal; font-style: normal; text-decoration: none; font-family: Helvetica,Arial,sans-serif; font-size: 12pt;"><b>De: </b>"Matthieu Muffato" <muffato@ebi.ac.uk><br><b>À: </b>"Ensembl developers list" <dev@ensembl.org><br><b>Envoyé: </b>Mercredi 18 Mars 2015 19:55:42<br><b>Objet: </b>Re: [ensembl-dev] ApoC3 is missing<br><div><br></div>Dear Sébastien,<br><div><br></div>It looks like ApoC3 has not been annotated by the Ensembl pipeline. You <br>can have a look at the region with most of the evidence switched on: <br>http://www.ensembl.org/Gallus_gallus/Share/6ce226669bc7414392cd55e837dc1982178952913 <br>(it is the same location as on the NCBI browser)<br><div><br></div>Some ESTs and cDNAs mapping there, and there even is a Genscan <br>prediction, but no proteins are aligned to this locus. </div><div style="color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;" data-mce-style="color: #000; font-weight: normal; font-style: normal; text-decoration: none; font-family: Helvetica,Arial,sans-serif; font-size: 12pt;"><span style="color: rgb(0, 0, 255);">Yes, it is very strange because Apoc3 protein seems to exists :</span><br></div><div style="color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;" data-mce-style="color: #000; font-weight: normal; font-style: normal; text-decoration: none; font-family: Helvetica,Arial,sans-serif; font-size: 12pt;"><span style="color: rgb(0, 0, 255);"><a href="http://www.ncbi.nlm.nih.gov/protein/NP_001289056.1"><span style="color: rgb(0, 0, 255);">http://www.ncbi.nlm.nih.gov/protein/NP_001289056.1</span></a></span></div><div style="color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;" data-mce-style="color: #000; font-weight: normal; font-style: normal; text-decoration: none; font-family: Helvetica,Arial,sans-serif; font-size: 12pt;"><br></div><div style="color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;" data-mce-style="color: #000; font-weight: normal; font-style: normal; text-decoration: none; font-family: Helvetica,Arial,sans-serif; font-size: 12pt;">This could be the <br>reason why the Genescan gene model was not retained by the Ensembl <br>pipeline. Perhaps a genebuilder can shed some light on the situation ?</div><div style="color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;" data-mce-style="color: #000; font-weight: normal; font-style: normal; text-decoration: none; font-family: Helvetica,Arial,sans-serif; font-size: 12pt;"><span style="color: rgb(51, 102, 255);">Excuse my naive question but how can I do a genebuilder ?</span><br><div><span style="color: #3366ff;" data-mce-style="color: #3366ff;">Thanks,<br></span></div><div><span style="color: #3366ff;" data-mce-style="color: #3366ff;">Sébastien<br></span></div><div><span style="color: #3366ff;" data-mce-style="color: #3366ff;"><br></span></div></div><div style="color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;" data-mce-style="color: #000; font-weight: normal; font-style: normal; text-decoration: none; font-family: Helvetica,Arial,sans-serif; font-size: 12pt;"><br></div><div style="color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;" data-mce-style="color: #000; font-weight: normal; font-style: normal; text-decoration: none; font-family: Helvetica,Arial,sans-serif; font-size: 12pt;">On 18/03/15 17:50, p.pierre419@laposte.net wrote:<br>> Good morning,<br>><br>> I am working on phylogeny beetween species and more particulary<br>> gain/loss genes between homo sapiens and gallus gallus.<br>><br>> So, using "Gene tree" (via Ensembl!) --> "view fully expanded tree", we<br>> can note that none gallus gallus gene for ApoC3 is present :<br>> http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?collapse=none;db=core;g=ENSG00000110245;r=11:116829706-116833072<br>><br>> while ApoC3 exists in map viewer for gallus gallus :<br>> http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9031&chr=24&MAPS=genes-r&cmd=focus&fill=40&query=uid%28-1586510584%29&QSTR=apoc3<br>><br>> My question is :<br>> Is it possible to know, from Gene tree or Ensembl! site web, that ApoC3<br>> is present in gallus gallus and may be others species ?<br>><br>> Thanks,<br>> Sébastien<br>><br><div><br></div>-- <br>Matthieu Muffato, Ph.D.<br>Ensembl Compara Project Leader<br>European Bioinformatics Institute (EMBL-EBI)<br>European Molecular Biology Laboratory<br>Wellcome Trust Genome Campus, Hinxton<br>Cambridge, CB10 1SD, United Kingdom<br>Room A3-145<br>Phone + 44 (0) 1223 49 4631<br>Fax + 44 (0) 1223 49 4468<br><div><br></div>_______________________________________________<br>Dev mailing list Dev@ensembl.org<br>Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev<br>Ensembl Blog: http://www.ensembl.info/<br></div><div><br></div></div></body></html>