Hi Hani, The table browser is a good tool to obtain data from from our database. To get to it click on "Tables" from the blue navigation bar.
For all the human non poly A RNA transcripts: Once you get there set the following clade, genome, and assembly to what you are interested in. Then set the following: group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownGene region: genome intersect: Click "create" Set the following: *group:* mRNA and EST Tracks,* track:* Poly(A),* table:* PolyA_DB (polyaDB) and select:* All UCSC Genes records that have no overlap with Poly(A) * * *output format: sequence Click "get output" Select "genomic" Click on "submit" Select the options that you want. Click "get sequence" This will give the UCSC identifier, the coordinates, and the sequence. For human mitochondrial RNA: Once you get there set the following clade, genome, and assembly to what you are interested in. Then set the following: group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownGene region: position chrM:1-16571 output format: sequence click "get output" Select "genomic" Click on "submit" Select the options that you want. Click "get sequence" This will give the UCSC identifier, the coordinates, and the sequence for those located on Chromosome M. Also, there are other RNA tracks that may be of interest to you on the they hg19 browser which are located under the "Genes and Gene Prediction Tracks" grouping sno/miRNA http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgRna tRNA http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=tRNAs Hope this is what you are looking for. If you have further questions please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Hani Choudhry <[email protected]> Date: Thu, Jun 16, 2011 at 6:05 AM Subject: [Genome] Database download To: "[email protected]" <[email protected]> Cc: "[email protected]" <[email protected]> Dear UCSC genome, Could you please help me to find my way to download the following: 1- Database of human non poly A RNA transcripts (gene name, location and sequence)? 2- Database of human mitochondrial RNA produced in mitochondria (gene name, location and sequence)? Thanks for your attention and help. Look forward to your reply. Regards, Hani Choudhry .......................................................................... Hani Choudhry, Genomic Research Lab Wellcome Trust Centre of Human Genetics Nuffield Dept of Clinical Medicine University of Oxford Oxford- UK Lab tel: +44-1865287519 Mobile: +44-7771219664 Email: [email protected]<mailto:[email protected]> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
