I am having the following problem. I work with a fusion gene and need to do a QPCR. I found a couple of papers with primers I can use but have no idea how people manage to design those primers and what is the product length etc.
therefore I would like to ask you guys if anyone is aware of how to design qpcr primers for a fusion gene. Also, it needs to pick up different isoforms of the two fusion partners.
Please let me know if you have some thoughts on that, some ideas of software or website.
So far, I tried NCBI primer design, primer 3 and thinks like that but they all need input sequence of the gene. I can find out the sequences for each of the fusion partner, I can find the 20nt sequence where they fuse together, but I need automated way to screen for where exactly this sequence overlapps with the 5′ and 3′ partner.
sorry for the long post, I hope you got an idea of my problem and could advise.