Hello Richard,
The UTR exon is not aligned because the cross-species RefGene tracks are aligned using protein-translated blat, which often will not align UTR. TransMap uses a different approach to cross-species alignment and will do a better job of aligning UTR. Here is the details page for transmap, so you can read more about how it works: http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr12&g=transMap I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group ----- "Richard O'Brien" <[email protected]> wrote: > Dear Sir/Madam, > > I noticed an error with the display of the human GEM gene > (NM_181702) > when viewed in the mouse July 2007 genome browser: > > http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=115&revCmplDisp=0&hgsid=1449 > 70113&hgt.right2=%3E%3E+&position=chr4%3A11630546-11632651&hgtgroup_map_clos > e=0&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_phenoAllele_close=0 > &hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close > =0 > > The human gene has a 5' non-coding exon that is not displayed. > > When the human GEM gene is viewed in the human March 2006 browser > the > non-coding exon is displayed correctly. > > Regards, Richard O'Brien > > Professor > Room 8415 MRB IV > Dept. Molecular Physiology & Biophysics > Vanderbilt University Medical School > Nashville > TN 37232 > Tel 615-936-1503 > Fax 615-322-7236 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
