I need to know about this as because at certain temperature I am getting a very intense band in genomic DNA for a particular set of primers, whereas at that specific temperature it is not happening in cDNA.
Though i dont know what are your primer sequences, but what i assume is that your primers are raised either from exon-intron junction or entirely from intron. So that you can amplify your genomic DNA. Since cDNA contains only exons u are not able to attach your primers. I suggest you to blast your primer sequences against the genome and also the coding sequence to know from where your primers are made.