Hi Da Li, The Ensembl Genes track has annotations for these genes on the mitochondrial chromosome. Navigate to the mitochondrial chromosome by entering "chrM" in the position/search box. Then, scroll to the "Genes and Gene Prediction Tracks" and change the Ensembl Genes track to "pack" or "full."
The 12S mitochondrial rRNA gene is ENST00000389680, a.k.a. J01415.24, at chrM:648-1,601. The tRNAGlu(UUC) gene is ENST00000387459, a.k.a. J01415.21, at chrM:14,674-14,742. (The gene names for chrM in this track are not obvious; I found these by first getting position information from http://en.wikipedia.org/wiki/Chromosome_MT_(human)#Genes.) One thing you should be aware of is that UCSC uses a slightly different mitochondrial chromosome than Ensembl. This is described on the hg19 description page (http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=hg19): "Note on chrM Since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion sequence (represented as "chrM" in the Genome Browser) has been replaced in GenBank with the record NC_012920. We have not replaced the original sequence, NC_001807, in the hg19 Genome Browser. We plan to use the Revised Cambridge Reference Sequence (rCRS) in the next human assembly release." The two mitochondrial sequences differ by a few bases. We are in the process of updating the Ensembl Genes track for chrM on hg19 so that their annotations (which are given for NC_012920) appear in the correct corresponding locations on NC_001807 in our browser. The updated track is currently on our preview server, http://genome-preview.ucsc.edu/. You will be able to tell when the track has been updated on the regular site by looking at the "data last updated" line that is visible when you click on an item in the track. I hope this information is helpful. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 3/30/12 6:15 AM, li Da wrote: > > > Dear Sir or Madam: > > But I do know how to > find the standard sequence of mitochondrial tRNA and rRNA, such as > mitochondrial > tRNAGlu(UUC) and 12S mitochondrial rRNA. I do not know whether the UCSC have > thisfeature. > > I shall be eagerly > waiting for your mail. > > > Da Li > Chinamedical university > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
