Hi Yingfeng, When you click on a (RefSeq) gene, on the details page there are links for RefSeq and Entrez Gene. Both of those will have additional information about the gene. I believe the Entrez link may have the information you're looking for.
Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 3/16/12 5:37 PM, Yingfeng Wang wrote: > Luvina, > > Thank you for your help. > > Could you please help me to know why NR_000137 and NR_000138 are on > the same region? I attach two related records again. As you can see, > these two records are same except names. > > #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, > > In human genome (Hg18), I can find the description I need. It is field > "type" on track "RNA Genes". For example, "snRNA" tells me the gene is > a snRNA gene. But I can't find a similar field in the genome of > C.elegans. Could you please give me some hints? > > Again, thank you very much for your help. > > Yingfeng > > > On Fri, Mar 16, 2012 at 6:31 PM, Luvina Guruvadoo<[email protected]> wrote: >> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
