Hi Yingfeng, If you BLAT the sequence from NR_000137, you will find that this region is an inverted repeat. Details for each nnRNA can be retrieved using the Table Browser. Click on "Tables" on the blue bar on the top of the main page and make the following selections:
clade: Mammal genome: Human assembly: hg19 group: Genes and Gene Prediction Tracks track: RefSeqGenes table: refGene region: genome filter: click 'create' then in the 'name DOES match' field type: NR_* output format: select fields from primary and related tables output file: if you would rather have the results saved to a file instead of displaying in the browser window, enter the name you would like the output file to have, otherwise, leave blank file type returned: plain text Click "get output". From here, select the appropriate fields then click "get output". I hope this helps. Feel free to contact us again at [email protected] if you have further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 3/15/2012 9:10 AM, Yingfeng Wang wrote: > Hello, > > I meet a problem in genome browser when I use RefSeq Genes track. > > Here are the first three ncRNA genes I got in a Celegans segment ( > WS220/ce10, chrI:12140001-12340000 ), > > #filter: refGene.name like 'NR\_%' > #bin name chrom strand txStart txEnd cdsStart cdsEnd > exonCount exonStarts exonEnds score name2 > cdsStartStat cdsEndStat exonFrames > 677 NR_000137 chrI + 12144973 12145160 > 12145160 12145160 1 12144973, 12145160, > 0 unk unk -1, > 677 NR_000138 chrI + 12144973 12145160 > 12145160 12145160 1 12144973, 12145160, > 0 unk unk -1, > 677 NR_000137 chrI - 12149569 12149756 > 12149756 12149756 1 12149569, 12149756, > 0 unk unk -1, > > > All three have the same bin; the 1st and 2nd genes are on the same > region with different names; the 1st and 3rd genes have the same name > but on the different regions. > > Could you please explain a little about it? > > By the way, could you please let me know how to retrieve the > description of each ncRNA gene on this track, e.g., the type of a > ncRNA gene? > > Thank you very much! > > Yingfeng > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
