Hello, Mike. It is not uncommon to find piRNAs in clusters (see http://en.wikipedia.org/wiki/PiRNA). The introns of Cyp19a1 appear to contain one of these clusters. The only unusual thing here is that these transcripts do not exist in Ensembl. We cannot provide an answer as to why that is the case. You might consider contacting Emsembl with that question (http://www.ensembl.org/info/about/contact/index.html).
Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Michael Muratet Sent: Wednesday, December 14, 2011 2:10 PM To: [email protected] Subject: [Genome] 103 isoforms for Cyp19a1? Greetings I am working on trying to match up two sets of expression data, one based on knownGenes and one based on Ensembl. While trying to build a map, I got a curious result for Cyp19a1 that I haven't been able to figure out. There are 103 knownGene transcripts (e.g., uc009ppd.1) that map to Ensembl transcript ENSMUST00000170783. Each of these appears to have its own cluster ID. The Ensembl gene, ENSMUSG00000032274 has two transcripts. Looking on the browser, it looks like ENSMUST00000034811 = uc009pmu.1 and ENSMUST00000170783 = uc012gto.1. Then there are a bunch of small transcripts, e.g., DQ691824/uc009pov.1. Poking around some other databases, these appear to be piRNAs. Is this an artifact because the loci overlap? Thanks Mike Michael Muratet, Ph.D. Senior Scientist HudsonAlpha Institute for Biotechnology [email protected] (256) 327-0473 (p) (256) 327-0966 (f) Room 4005 601 Genome Way Huntsville, Alabama 35806 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
