Question

Generally speaking, the DNA sequences of introns evolve relatively rapidly, and are not well conserved. Nevertheless, it is still possible that the existence and the location of an intron may have been conserved, that is whether an intron has existed at that exact location in that gene over a long period of evolutionary history. How (specifically) would you go about determining whether or not the existence of a particular intron has been conserved in evolution? Would you focus on the alignment of protein sequences, or DNA sequences, or both, or something else? Why?

Answer 1

For determination of the position of the introns, we have to choose a particular gene and have to align it's DNA sequences from multiple species. Multiple sequence alignment with those DNA sequences will not only give the changes in DNA sequences but also help us to determine the positions of different exons and introns.

In some cases alignment of mRNA sequences of any particular gene may help us to determination of positions of exons and if we map back this Exon positions to the DNA sequences then we may find which are the introns are present in between different exons.

Alignment of protein sequence will not help us to determine the conservative nature of any intron. Because any protein sequence will be complementary to its mRNA sequence and mRNAs can be generated by alternative splicing. In that case many exons may be skipped. So, protein sequence alignment will not help us in any way for determination of conservation of any intron.