In my lab there are primers for specific cDNA and I would like to know if they are useful to amplify a genomic region
If they are complimentary to the specific sequence you want to amplify, they can be used perfectly.
Ok, I will try to give you a better explanation.
In my lab there are some primers for amplifying this cDNA of Vitis Vinifera (Grapewine): Actin (GenBank accession EC969944). Can I use these primers to amplify the same gene (only exons) but starting from genomic DNA and not cDNA?
I just realise one thing now, while working with cDNA, you don't have introns because its processed mRNA, and with the these primers (if they were used to PCR full length cDNA) you will eventually clone the whole gene including the introns.
If the primers fall in the same exon, yes they can work perfectly but if the primers amplify two or more exons then you will amplify a bigger region which also contains introns as well
Yes you can as long as the primers are not exon spanning (matching sequence of the boundaries of 2 exons). You will amplify the the exons and introns that lie within your primers instead of amplifying just the CDS sequence.
Ok, thanks to everyone! how can I compare the sequence of actin (GenBank accession EC969944) to the vitis vinifera genome to analyze if the region amplified by my primer covers one more exons?
Not clear what you mean; but I assume you can use BLAT at UCSC (or blast) to compare the cDNA you have with the genomic DNA. If the match is not contiguous then you can go back to the browser and see where the exons are. Hope this helps.
Hi Vincenzo,
you can also check your template/primer combination with a primer design tool, like the NCBI PrimerBlast (http://www.ncbi.nlm.nih.gov/tools/primer-blast/). This will also show you the exon/intron structure of your product, if there is some.
Thank you Elena, which parameters should I indicate in Primer Blast?
Thank you Wubin, but in your database there is not the vitis vinifera genome!
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