Hello Konstantin, Most of the tables underlying our gene prediction tracks define the 5' or 3' UTRs as the regions between the transcription and coding start sites and between the coding and transcription end sites, respectively. Thus to calculate the coordinates of the UTRs you simply take the pairs of coordinates:
1. txStart -> cdsStart (5' UTR for + strand genes) 2. cdsEnd -> txEnd (3' UTR for + strand genes) Where txStart, txEnd, cdsStart, and cdsEnd are all fields in the refGene table. If your gene of interest is on the minus strand then 2. defines the 5' UTR and 1. defines the 3' UTR. 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]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Konstantin Halachev wrote: > Hi there, > > I extracted the "3' UTR exons" from the refseq genes for mm9 to Galaxy > and I want to know what exactly is the definition of a 3' UTR exon you > are using in the table? > > Best Regards, > Konstantin > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
