Dear Dr. Gueguen, A useful tool for extracting exons is the Table Browser. From the main page, click on "Tables" in the blue navigation bar and set the following:
clade: Mammal genome: Human assembly: (select assembly of interest) group: Genes and Gene Prediction Tracks track: UCSC Genes (or whichever track you choose) table: knownGene (if you have selected the UCSC Genes track) region: select "position" and enter "chr14:59600000-70500000" If you are looking for the genomic coordinates of these exons, select "BED" as the output format and click "get output". On the following page, select "Exons plus" (0 bases at each end) and click "get BED". For more information on the BED format, please see http://genome.ucsc.edu/FAQ/FAQformat#format1. If you are looking for the sequence of these exons, select "sequence" as the output format, and click "get output". On the following page, select "genomic" and click "submit". From here, select all exon types, format as desired and click "get sequence". More information on how to use the Table Browser can be found here: http://genome.ucsc.edu/cgi-bin/hgTables#Help I hope this helps. Please contact us again at [email protected] if you have any further questions. Regards, Luvina --- Luvina Guruvadoo UCSC Genome Bioinformatics Group GUEGUEN PAUL wrote: > Hello, > I have a question about a feature of UCSC genome Bowser... > > Is it possible to extract all the exons of genes (exome) in a defined region > (chr14:59,600,000-70,500,000) using UCSC? > > Best regards, P.GUEGUEN > > --- > Dr Paul GUEGUEN > Assistant Hospitalo-Universitaire > CHRU de BREST - Laboratoire d'Hématologie > Bd Tanguy Prigent 29609 BREST Cedex > Tel direct : +33 (0)2 98 34 70 35 > Tel secrétariat : +33 (0)2 98 34 70 33 > Fax : +33 (0)2 98 14 51 48 > Mail : [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
