I have a peptide of 20 aa. When I map this peptide to the genome, the first 12 aa map to exon1 in frame 1 and last 8 aa map to exon2 in frame 3. Is it possible?
How confident are you about the genome sequence? It could be incorrect. In addition to the possibility that you have wrong peptide sequence.
The transcriptome was translated into three frames and the obtained peptide was MS/MS analyzed. The genome sequence is correct.