Hello Stefanie, Presumably the 6000 genes you found were those for which cdsStart=cdsEnd. These are noncoding entries but not specifically those subsets you mention. You can find out more about how the UCSC genes set is created on the UCSC genes description page:
http://genome.ucsc.edu/cgi-bin/hgGene?hgg_do_kgMethod=1 Another way to locate noncoding genes would be to consult the kgTxInfo table. This table is what is used for display of the "Gene Model Information" that is shown near the bottom of the page when you click on a UCSC Gene. You can find out more about it here: http://genome.ucsc.edu/cgi-bin/hgGene?hgg_do_txInfoDescription=1 If you are interested in tRNA/snoRNA/mirRNA entries you may find one of these tracks useful: RNA Genes: http://genome.ucsc.edu/cgi-bin/hgTrackUi?&c=chrX&g=rnaGene sno/miRNA: http://genome.ucsc.edu/cgi-bin/hgTrackUi?&c=chrX&g=wgRna tRNA Genes: http://genome.ucsc.edu/cgi-bin/hgTrackUi?&c=chrX&g=tRNAs Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 10/6/10 9:15 AM, Stefanie Gerstberger wrote: > Hi, > I was checking the UCSC known gene files for tRNA/snoRNA/mirRNA and could not > find any. Is it correct that the UCSC known genes contains only mRNA > transcripts? There is a discrepancy of ~27000 total canonical UCSC genes and > ~21000 UCSC protein coding genes. Are the missing 6000 genes genes which have > lengths and characteristics of mRNAs/long noncoding RNAs but have not been > shown > to be expressed as protein? > > Thanks a lot, > Stefanie > > > > > > > --------------------------------------------------- > Stefanie Gerstberger > graduate student in Chemical Biology > Tri-Institutional Program > Cornell University, > Rockefeller University, > Memorial Sloan Kettering Cancer Center > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
