Hi Paul, NM_033178 maps very well to multiple places on the genome, and each of these places has been assigned a UCSC Gene identifier. Which one is the best? Probably a research question there. The gene looks to be highly duplicated with many pseudogenes. Most of those are mapped to chrUn (chrUn contains clone contigs that can't be confidently placed on a specific chromosome).
Also, in the browser, click on the gene and read the description, as it has some helpful details, e.g.: "This gene is located within a D4Z4 repeat array in the subtelomeric region of chromosome 4q. The D4Z4 repeat is polymorphic in length; a similar D4Z4 repeat array has been identified on chromosome 10." For additional explanation I would suggest reading the Methods section in the UCSC Genes description page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?&c=chr10&g=knownGene <http://genome.ucsc.edu/cgi-bin/hgTrackUi?&c=chr10&g=knownGene> To get protein sequences for these, use the table browser: http://genome.ucsc.edu/cgi-bin/hgTables. (I'm directing you to the RefSeq Genes track for the protein sequence, as that method gets the same protein that is in GenBank.) Select group: Gene and gene prediction tracks track: Ref Seq Genes table: refGene region: genome Paste in your identifier (e.g., NM_033178) output: sequence Click "get output", then, select "protein" and "get output" again. You also might be interested in taking a look at the Gencode V7 pseudogene track in the browser. Please let us know if you have any additional questions: [email protected] <mailto:[email protected]> - Greg Roe UCSC Genome Bioinformatics Group On 8/7/11 9:42 PM, Parul Sagar wrote: > Respected Sir, > > sir i am Parul Sagar, Junior Research Fellow, *Institute of Cytology and > Preventive Oncology*(ICMR). > > I am working on some project and i need some data of *Homo** **sapien*s. I > want to ask one thing, in table *knownToRefSeq *(Group: Gene and Gene > Prediction Track, Track: UCSC Genes, table: knownToRefSeq)* *there is so > many ids for one mRNA_id(NM_), for eg > uc011mgj.1 NM_033178 > uc011mgk.1 NM_033178 > uc011mgl.1 NM_033178 > uc011mgm.1 NM_033178 > uc011mgn.1 NM_033178 > uc011mgo.1 NM_033178 > > so which id(uc_) i should take for mRNA(NM_), and these ids are different in > what way....? > > I need protein sequences for these mRNA also.... > > i'll be very grateful to you.. > > thank you. > > > > Parul Sagar > Junior Research Fellow > *Institute of Cytology and Preventive Oncology*(ICMR) > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
