Hello, If you know the consensus sequence of your kinase domain you can use BLAT to find regions of high similarity in your genome of choice.
For example, I grabbed the consensus sequence for Pkinase from Pfam: DLFNFCS--RRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPDNFLMGIGRHCnkclespvgkrkrsmtvstsqdpsfsglnqlFLIDFGLAKKYrdnrtrqHIPYREDKNLTGTARYASINAHL-GIEQSRRDDMESLGYVLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVL ... and pasted it into the blat sequence box here: http://genome.ucsc.edu/cgi-bin/hgBlat ... and BLAT found 10 hits, most of them on annotated genes, but a couple in places annotated as introns. I hope this answers your question. If you have further questions, please respond to this list. Brian On Wed, Feb 2, 2011 at 1:26 PM, <[email protected]> wrote: > > > Hi, > > > > What tool do you use to find out the exons the correspond to the kinase > domain of a kinase? > > > > Thanks > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
