Question

You characterize the sequence of a full-length cDNA and the corresponding genomic DNA for a particular intron-containing gene from mouse cells. When you align them to each other using a computer program, the exons of the cDNA align perfectly in some regions with pieces of the genomic DNA, whereas other exons appear to have a small number of specific nucleotide differences compared to the genomic DNA. Assume this genomic DNA and cDNA come from the same individual, and there are no sequencing mistakes. What might account for these differences?

Answer 1

There can be two explanations for the given question-

1) There is a possibility of alternative splicing where during exon joining there can be shuffling of some exons. This may result in nucleotide mismatch of genome with cDNA.

2) Another possibility of miss match may arise if the RNA polymerase makes any mistake during mRNA synthesis.