Hi Erica, In the In Silico PCR tool, setting the Target to UCSC Genes searches for alignment of your primers against the sequences of the genes in the UCSC Genes track. For more information about UCSC Genes, you can see the UCSC Genes track description: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene
Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 8/10/11 11:12 AM, Erica Sanchez wrote: > Hello, > > My name is Erica Sanchez. I have used your in silico PCR tool in the past > when designing primers for DNA amplification to check for single product > amplification. Recently, I have been designing RT PCR primers, across exon > boundaries to eliminate amplification of DNA contamination. I understand > that these primers should then NOT produce a product with the in silico PCR > tool when using the "genome assembly" as my target, but I realized that if I > changed the target to "UCSC genes" that the predicted product for amplifying > my cDNA does come up. I am emailing to ask for clarification of what UCSC > genes is referring to. Is this referring to RNA, cDNA, ESTs? I think it > makes sense that this is some king of cDNA library, but an unsure. All of my > RT primer pairs (designed across exon boundaries) are coming up with no > product under genome assembly and with my predicted amplification product > under UCSC genes target. Please provide me with clarification of this target > choice. > > Thank you, > > Erica Sanchez > > *Example of Primers used:* > > ELOVL 2 (gene name) > * F* 5'-CTCAGCTGGTGCAGTTCGTGC-3' * R* 5'- GGC TTT TTT CGG TAT GTC > TGA ACG-3' > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
