Brian, Once other source that may of of interest: Todd Lowe's lab ahs mouse tRNA data: http://lowelab.ucsc.edu/GtRNAdb/Mmusc/Mmusc-by-locus.html
This could be used directly or converted into a Custom track, http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "Brian Dynlacht\"\"Guruprasad Ananda" <[email protected]> > Cc: "Guruprasad Ananda" <[email protected]>, [email protected] > Sent: Friday, January 29, 2010 10:11:27 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Fwd: Retrieving genomic coordinates for non-coding RNAs > > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
