Hi Nadine, You can obtain the splice sites for the refSeq genes using the Table Browser. Below are instructions to obtain the hg19 splice sites. For mm9 and mm8, change the clade, genome, and assembly and follow these same instructions (for mm9 select Mammal, Mouse & July 2007; for mm8 select Mammal, Mouse & Feb. 2006).
Click "Table" in the blue bar at the top of the page and make the following selections: clade: Mammal genome: Human assembly: Feb. 2009 group: Genes and Gene Prediction Tracks track: RefSeq Genes table: refGene region: genome output format: selected fields from primary and related tables output file: if you would rather have the results saved to a file instead of displaying in the browser window, enter the name you would like the output file to have (e.g. hg19SpliceSites), otherwise, leave blank file type returned: plain text Click "get output." Select the fields you wish to see in your results. I would suggest selecting at least the following fields from refGene: name, chrom, strand, exonStarts, and exonEnds (these last two contain the splice site data that you inquired about). Please don't hesitate to contact the mail list again if you require further assistance. Katrina Learned UCSC Genome Bioinformatics Group Albrecht, Nadine wrote: > I need the acceptor and donor splice sites for the refSeq gene identifiers of > the UCSC genome tables hg19, mm9 and mm8 or for the chromosomal sequences of > the different assemblies. > > Does a file exist with this kind of information on the UCSC genome browser? > > Thank you in advance, > > Nadine Albrecht > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
