Hello Shi, This sequence may seem to align to the positive strand using BLAT, but this is because there are no introns to help with strand assignment and the positive strand is the default. It seems very likely that the strand assignment should be (-).
After running a web BLAT, opening tracks like UCSC Genes, RefSeq, and the mRNA track to "pack" can help you can see that the genes in this region align to the (-) strand. If you flip the genome orientation to the (-) strand (use the "reverse" button), it may help to put the alignment in context. Please let us know if you need more help, Regards, Jen UCSC Genome Browser Support http://genome.ucsc.edu/contacts.html [email protected] [email protected] On 7/9/10 3:12 PM, Shi, Shuqun wrote: > Hello, > Recently, I allign my human sequence with UCSC, it shows the sequence is the > same with forward strand. However, the sequence is the oppsite with the cDNA > orentation (NM_004898). It seems to me that one orentation could be wrong. > Could you please help me? > For you convenience, I send you the sequence as attached. > 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
