Hello Qiwen, You can output the UTRs in BED format using the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables). Once you've selected your assembly of interest select:
group: Genes and Gene Prediction Tracks track: UCSC Genes table: knownGene region: you can retrieve data for the whole genome or for a specified region output format: BED - browser extensible data Then click "get output". This will take you to a menu where you can specify 5' or 3' UTR output. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 1/10/12 5:56 PM, Qiwen Hu wrote: > Hi, > > Thank your for bring us such so many useful tools. Our current work needs > to analyze the alternative splicing effect in 3 and 5 prime UTR region in > human and mouse genome. I have downloaded your gtf and gff file of human > genome but I found there is no annotation of UTR region, so I am wondering > if I can get those annotation in UCSC website ? > Thank you very much, > > Best regards, _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
