Ruchir, Try using the Table Browser with the following options:
clade: Mammal; genome: Human; assembly: Mar2006 group: Genes and Gene Prediction Tracks; track: RefSeq Genes: table: refGene. output format: sequence click "get output" select "genomic" On the next page check the box next to "3' UTR exons". You could also specify precisely how many bases up or downstream, if you desired. Finally click "get seequence". The "other refSeq" track is for non human refseq genes. You could find out more on the description page: "This track shows known protein-coding and non-protein-coding genes for organisms other than human, taken from the NCBI RNA reference sequences collection (RefSeq). The data underlying this track are updated daily." I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group ----- "Ruchir - INTL Shah" <[email protected]> wrote: > Hi, > > I have a two part question: > > 1. How do you recommend I go about downloading all 3' UTR sequences > from > a given genome. I'm interested in human, mouse, drosophila, yeast and > pombe genomes. All annotated 3' UTR sequences. I would like to ensure > that I include all refseq genes (not UCSC gene names) > > 2. I had downloaded 3' UTR sequences in the past using the 'tables'. > but > now I see different options under the pull down menus for 'track' and > 'tables'. What is the difference between "Refseq genes" and "other > refseq"? What option should I use if I want to get all refseq genes? > > Thanks in advance, > > Ruchir > > Ruchir Shah, Ph.D. > Sr. Bioinformatics Scientist > Global Health Sector > SRA International Inc. > 2605 Meridian Parkway > Durham, NC 27713 > 919-313-7504 > [email protected] > www.sra.com <http://www.sra.com/> > Enhancing human health around the world, every day. > P Please consider the environment before printing this e-mail > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
