Hello, Non-coding genes can be identified in the RefSeq Genes and UCSC Genes tracks. There are tRNA repeat sequences includes as a datat type in the Repeat Masker track. This is likely not what your are looking for, but please review the Repeat masker documentation to decide for yourself.
For RefSeq Genes, these can be identified by looking in the primary table, refGene, with transcripts with name like NR_*. Alternatively, any transcript that meets the criteria of this sql query would be none coding: select name from refGene where exonEnds = cdsStart and exonEnds = cdsEnd; For USCS Genes, the track controls allow for the display of non-coding genes. In addition, any transcript that meets the criteria of this sql query would be none coding: select count(*) from knownGene where exonStarts = cdsStart and exonStarts = cdsEnd; If you need the transcript RNA sequence, the table browser can provide this. Adapt the queries above to the "filter" function and output as sequence. http://genome.ucsc.edu/FAQ/FAQformat#format9 http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://genome.ucsc.edu/FAQ/FAQdownloads#download29 Thank you, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Guruprasad Ananda" <[email protected]> wrote: > From: "Guruprasad Ananda" <[email protected]> > To: [email protected] > Cc: "Brian Dynlacht" <[email protected]> > Sent: Wednesday, January 27, 2010 2:38:16 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Fwd: Retrieving genomic coordinates for non-coding RNAs > > Dear UCSC team, > > I'm Guru Ananda from Galaxy team, and I'm forwarding an email from one > of our users regarding retrieval of mouse non-coding RNAs and tRNAs. > Can you please point him to the right track/table to use on the genome > browser? > > Thanks, > Guru > Galaxy team. > > Begin forwarded message: > > > From: "Dynlacht, Brian" <[email protected]> > > Date: January 27, 2010 5:32:57 PM EST > > To: "[email protected]" <[email protected]> > > Subject: Retrieving genomic coordinates for non-coding RNAs > > > > Hello, > > Recently, my colleague Yuval Kluger contacted you about retrieving > non-coding RNAs from the UCSC genome browser. We are especially > interested in ncRNAs and tRNAs, etc. > > Unfortunately, neither of us could figure out what to do next based > on your email below. I am trying to retrieve genome coordinates from > the MOUSE genome. I'd like to start with tRNAS but eventually get to > all know non-coding RNAs. > > Is there any way that you can tell me how to get a direct list of > genomic positions for the mouse genome for this purpose? > > Thanks so much. > > Brian Dynlacht > > Professor > > NYU School of Medicine > > > > > > Hi Yuval, > > > > You should be able to retrieve RNA co-ordinates using the interface > to UCSC genome browser under 'Get data' section on Galaxy. For > information on which tracks and tables to choose, please refer these > links which contain answers to this topic from UCSC mailing list: > > http://www.soe.ucsc.edu/pipermail/genome/2007-August/014299.html > > http://www.soe.ucsc.edu/pipermail/genome/2007-May/013491.html > > http://www.soe.ucsc.edu/pipermail/genome/2006-April/010436.html > > > > Thanks for using Galaxy, > > Guru > > Galaxy team. > > > > > > ------------------------------------------------------------ > > This email message, including any attachments, is for the sole use > of the intended recipient(s) and may contain information that is > proprietary, confidential, and exempt from disclosure under applicable > law. Any unauthorized review, use, disclosure, or distribution is > prohibited. If you have received this email in error please notify the > sender by return email and delete the original message. Please note, > the recipient should check this email and any attachments for the > presence of viruses. The organization accepts no liability for any > damage caused by any virus transmitted by this email. > > ================================= > > > > > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
