On Dec 15, 2011, at 3:33 PM, Steve Heitner wrote: > 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. > Hi Steve
I confess I still don't know how to interpret the browser & table results. I just downloaded the table knownToEnsembl from the browser. Here's a snippet: uc012gtn.1 ENSMUST00000170783 uc009pmv.1 ENSMUST00000170783 uc009pmw.1 ENSMUST00000170783 uc009pmx.1 ENSMUST00000170783 uc009pmy.1 ENSMUST00000170783 uc009pmz.1 ENSMUST00000170783 uc009pna.1 ENSMUST00000170783 uc009pnb.1 ENSMUST00000170783 uc009pnc.1 ENSMUST00000170783 uc009pnd.1 ENSMUST00000170783 uc009pne.1 ENSMUST00000170783 ENSMUST0000017083 appears to be the same transcript as uc012gto.1 in the browser, a couple of short exons on either end of a much longer intron, a transcript for Cyp19a1. (It is on the downloaded list, but not this snippet). uc012gtn is annotated as a partial Cyp19a1 transcript which appears to have a common exon with uc012gto.1. The rest are the very sort ncRNAs in the intron of uc012gto.1. How should I interpret equality of these transcripts in the knownToEnsembl table? Is it just an overlap of the loci, i.e., no functional equivalence should be inferred? Thanks Mike > --- > Steve Heitner > UCSC Genome Bioinformatics Group > > -----Original Message----- > From: [email protected] [mailto:genome- > [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 > 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
