Hi Praveen, You can get more information for any of our tracks by clicking on the blue track name, by clicking on the thin grey mini-button directly to the left of the track, or by clicking on track item and scrolling down to the "Description" section.
The Ensembl track is built by an automated pipeline that relies in part on proteins from closely-related species. Read more about it at their site: http://www.ensembl.org/info/docs/genebuild/genome_annotation.html. To find evidence that a TREM2 mRNA has been sequenced in rabbit, I would look in the RefSeq Genes track, the Rabbit mRNAs track, and the Rabbit ESTs track. The RefSeq Genes track is a curated gene set produced by NCBI (see http://www.ncbi.nlm.nih.gov/RefSeq/), and it is generally more conservative than Ensembl. The mRNA and EST tracks contain rabbit-specific submissions to GenBank. Unfortunately, there are not currently *any* items in any of these tracks in the TREM2 region on rabbit. (These tracks are updated nightly, so if if there were rabbit-specific mRNAs or ESTs deposited into GenBank, you would be able to see them here.) I only see evidence of the TREM2 gene in the various tracks that align TREM2 mRNAs or proteins from other species: Non-Rabbit RefSeq Genes, TransMap, Human Proteins, and Non-Rabbit mRNAs. I hope this helps explain what you are seeing in the Genome Browser. -- Brooke Rhead UCSC Genome Bioinformatics Group On 5/26/12 6:51 AM, Ballabh, Praveen wrote: > > Thanks, Brooke. I am aware of TREM 2 gene sequence on Ensemble browser. We have designed primer based on this sequence and tried to amplify TREM2 gene (exon of the codiing sequence) using rabbit tissue (cDNA).Unfortunately, we failed to ampify even a single exon. We want to know the source of the sequence reported in Ensembl as well as in UCSC. Did anyone directly report TREM2 gene sequence in rabbit? I look forward to your help. > Best regards, > Praveen > > -----Original Message----- > From: Brooke Rhead [mailto:rh...@soe.ucsc.edu] > Sent: Friday, May 25, 2012 8:46 PM > To: Ballabh, Praveen > Cc: 'genome@soe.ucsc.edu' > Subject: Re: [Genome] Rabbit TREM2 gene sequence > > Hi Praveen, > > You can get sequence for the rabbit TREM2 gene like so: > > Enter "TREM2" in the position/search box on the rabbit genome browser > (http://genome.ucsc.edu/cgi-bin/hgTracks?org=Rabbit&db=oryCun2). You > will see multiple tracks listed with a match for "TREM2." Click on one > of them to get to the general vicinity of the gene. > > There gene tracks here that I might expect to see annotations for rabbit > in are the RefSeq Genes and Ensembl Genes tracks. RefSeq does not have > an annotation here, but Ensembl does. > > Turn on the Ensembl Genes track to "pack" or "full." Click on the gene > (ENSOCUT00000007265). The next page will have links to the predicted > protein, the predicted mRNA, and the genomic sequence. > > If you have further questions, please contact us again at > genome@soe.ucsc.edu. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 5/25/12 3:22 PM, Ballabh, Praveen wrote: >> Thanks Vanessa. I am interested in obtaining TREM2 gene sequence for >> our work in rabbit model. I will be grateful if you can help us in >> providing rabbit TREM2 sequece. Regards, Praveen >> >> ________________________________ From: Vanessa Kirkup Swing >> [mailto:vane...@soe.ucsc.edu] Sent: Friday, May 25, 2012 6:18 PM To: >> Ballabh, Praveen Subject: Re: >> >> Hi, >> >> Would you mind re-sending your email to >> genome@soe.ucsc.edu<mailto:genome@soe.ucsc.edu>? I will still be >> able to answer (or help answer) your question, but it will go into >> our tracking system, our whole team will be able to contribute, and >> other users will be able to benefit from the discussion when >> searching our archives. Thanks! >> >> Vanessa Kirkup Swing UCSC Genome Bioinformatics Group >> >> On Fri, May 25, 2012 at 3:01 PM, Ballabh, >> Praveen<praveen_ball...@nymc.edu<mailto:praveen_ball...@nymc.edu>> >> wrote: Dear Antonio: I am interested in obtaining TREM2 gene sequence >> for our work in rabbit model. I will be grateful if you can help us >> in providing us with rabbit TREM2 sequece. I look forward to your >> favor. Best regards, Praveen >> >> Praveen Ballabh, MD Professor of Pediatrics, Cell Biology and >> Anatomy Regional Neonatal Center, Maria Fareri Children's Hospital >> New York Medical College Valhalla, NY 10595 Phone >> 914-594-4036<tel:914-594-4036> >> >> >> >> _______________________________________________ Genome maillist - >> Genome@soe.ucsc.edu >> https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - Genome@soe.ucsc.edu https://lists.soe.ucsc.edu/mailman/listinfo/genome
