3´ RACE-PCR of cDNA ends yielded a piece of 2 different genes? - (Jun/24/2014 )
Hello, I wonder if anyone could help me on this situation.
I have the bp information of the cDNA sequence for the first 14 exons of one gene. Then I designed specific primers and amplified its 3´cDNA end with RACE-PCR. I surprised that the sequencing result showed that the first 97 bp of the sequence is similar to the exon 14 of the target gene, but the other 240 bp + poly (A)n is 100 % homology to other gene.
The difficulty is that I could not get repeat results because the mRNA (expression) is very low, and it contains high % GC. I only got truncate sequence with the same 97 bp of exon 14, but the 3’ ends are varied and shorten.
Is it possible that the PCR will amplify and jouned the cDNA ends of one gene with another gene ?
Yes, it is, unfortunately. These are called chimeras, and are a problem. I'm not an expert, but you could seek information using that keyword. I would check at the Seqanswers web forum.
Thank you very much