The long term objective of this research is to understand when and how introns arose and what their evolutionary history has been. One hypothesis proposes that many extant introns are the vestiges of ancient introns used in ancient organisms to shuffle small exonic modules and thereby create larger genes. This introns-early hypothesis predicts that adjacent introns will be in the same phases relative to the reading frame. I will analyze a database of genes containing introns accepted to have arisen recently (genes transferred from organelles to the nucleus). If these genes have symmetric phase correlations it would suggest that introns could show these correlations for reasons other than exon shuffling and that this prediction can not be used to support the ancient exon shuffling hypothesis. The ancient intron shuffling hypothesis also predicts that introns will lie between compact 3D protein modules. I will look in the above database for introns at these positions. If introns prefer these module boundary regions in the non-shuffled genes the module boundary prediction can not be used to support the introns-early hypothesis. Lastly, I will compare intron densities in the non- shuffled database with other nuclear genes. If the intron densities in these two datasets mirror each other in a lineage specific manner this suggests that the original nuclear genes had few introns. Since most human genes contain many introns the potential health benefits of understanding how introns arose and what their evolutionary history and utility have been are enormous. Numerous human diseases have intron-related causes. Understanding how introns propagate could lead to novel gene therapy techniques. Given the elementary nature of introns, understanding them will greatly increase understanding of ourselves.
