Hi Bai Yun, The most recent human assemblies (hg18 Mar. 2006 and hg19 Feb. 2009) have a track called, RepeatMasker, which contains data about the location and sequence of some, but not all, of the human non-coding RNA. Go to the Gateway page (http://genome.ucsc.edu/cgi-bin/hgGateway) and make the following selections: clade: Mammal genome:Human assembly: Mar. 2006 (hg18) or Feb. 2009 (hg19) Click "submit"
Scroll down to the blue bar that says, Variation and Repeats, (you may need to click the "+" on the left to expand the tracks in this section). Under "RepeatMasker" select "full" from the pull down menu and click one of the "refresh" buttons on the page. In the "full" visibility mode, the RepeatMaser track has a line called "RNA" that displays RNA repeats including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA. If you want to extract the location of all the RNA repeats from the RepeatMasker, you can use the Table Browser. Click "Table" in the blue bar at the very top of the page and select the following: group: Variation and Repeats track: RepeatMasker table: rmsk region: genome filter: click the "create" button; next to "repClass" select "does", type "RNA" in the field & click "submit" output format: all fields from selected table Click the "get output" button to see the results. In order to extract the sequence of all the RNA in RepeatMasker, go back to the Table Browser and change "output format:" to "sequence" and click "get output" again. Choose the sequence retrieval options you prefer and then click "get sequence" to see your results. You will find detailed information about chrUn_gl###### on the hg19 gateway page (scroll down to the Assembly Details section and see the "Chromosome name scheme" subsection): http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=135492575&clade=mammal&org=Human&db=hg19 There is some additional information about chrUn in this FAQ: http://genome.ucsc.edu/FAQ/FAQdownloads#download11 I hope you find this information useful. Please don't hesitate to contact the mail list again if you require further assistance. Katrina Learned UCSC Genome Bioinformatics Group 白云 wrote: > Hi! Dear UCSC Technical Support > > Can I introduce my self, my name is Bai Yun, a postdoctor at National > Human Genome Center at Shanghai. Recently, I am interesting in human > non-coding RNA, and really want to download all known sequences of > human non-coding RNA from your ftp. However I don't know which file could > include all known human tRNA, rRNA, scaRNA, CDBox, snRNA, snoRNA, > ncRNA? So can you give me some guidance? > > By the way, when I blat my sequences to your database, I found some > sequences can map to "chrUn_gl#########", can you tell me what does this > means? Thanks a lot, look forward your letter. > > Bai Yun > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
