<html><body><div style="font-family: times new roman, new york, times, serif; font-size: 14pt; color: #000000"><div><span style="color: rgb(0, 0, 255);">Precisions</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;"><b>De: </b>"p pierre419" <p.pierre419@laposte.net><br><b>À: </b>"Ensembl developers list" <dev@ensembl.org><br><b>Envoyé: </b>Jeudi 19 Mars 2015 15:43:33<br><b>Objet: </b>Re: [ensembl-dev] ApoC3 is missing<br><div><br></div><div style="font-family: times new roman, new york, times, serif; font-size: 14pt; color: #000000"><div>Hello Rishi,<br></div><div><br></div><div>Thanks a lot for your clarification.<br></div><div><br></div><div>I also tried (via your link blast tool of Ensembl! - I did not know ... it is very useful to blast simultanously on many species !) to blast on gallus using the three different parameters (normal, near match and distant homologies) without find any hit.<br></div><div><br></div><div>I also used discontiguous megablast (NCBI) from nucleotide sequence, without relevant hit. </div><div><br></div><div>I have 2 questions :<br></div><div><br></div><div>Do you know if it is the same <span class="help">BLAST algorithm</span> that "distant homologies" blast ?<br></div><div><br></div><div>To be annotated by the Ensembl pipeline and displayed on the ensembl! gene tree, does a protein must be at a specific level of evidence as "protein coding" (i.e. not displayed if only "predicted" without biochemical evidences).<br></div><div><span style="color: rgb(51, 102, 255);">But even with these indications, Gallus ApoC3 should be taken into account in "Gene tree" : indeed, its RefSeq status is "validated" and its gene type is "protein coding" :</span><br></div><div><a href="http://www.ncbi.nlm.nih.gov/gene/100859721">http://www.ncbi.nlm.nih.gov/gene/100859721</a></div><div><br></div><div><span style="color: rgb(51, 102, 255);">Why ApoC3 is missing in Gene tree in these conditions ?</span><br></div><div>I would like understand,<br></div><div>Thanks,<br></div><div>Sébastien<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;"><b>De: </b>"Rishi Nag" <rishi@ebi.ac.uk><br><b>À: </b>dev@ensembl.org<br><b>Envoyé: </b>Jeudi 19 Mars 2015 11:57:32<br><b>Objet: </b>Re: [ensembl-dev] ApoC3 is missing<br><div><br></div><br>Hi Sebastien<br><div><br></div>I tried to BLAST the ApoC3 human protein to the Galgal4 genome and had no successful results. There is RNASeq data as well aligning as well as the <br>cDNA /EST but without the protein support there wouldn't be an Ensembl gene model at the location.<br><div><br></div>You can use the Blast tools to see where the sequence aligns to other species,<br>http://www.ensembl.org/Multi/Tools/Blast?db=core<br><div><br></div>Regards<br><div><br></div>Rishi<br><div><br></div><br>On 18/03/2015 18:55, Matthieu Muffato wrote:<br>> Dear Sébastien,<br>><br>> It looks like ApoC3 has not been annotated by the Ensembl pipeline. You can have a look at the region with most of the evidence switched on:<br>> http://www.ensembl.org/Gallus_gallus/Share/6ce226669bc7414392cd55e837dc1982178952913 (it is the same location as on the NCBI browser)<br>><br>> Some ESTs and cDNAs mapping there, and there even is a Genscan prediction, but no proteins are aligned to this locus. This could be the reason why the<br>> Genescan gene model was not retained by the Ensembl pipeline. Perhaps a genebuilder can shed some light on the situation ?<br>><br>> Matthieu<br>><br>> 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>><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></div><div><br></div></div></body></html>