Introns with coding sequences
In fungal mitochondria, for some genes, it was shown that introns may code for RNA maturases or endonucleases which take part in RNA processing, and DNA recombination respectively (see Expression of Gene : Protein Synthesis 3. RNA Processing (RNA Splicing, RNA Editing and Ribozymes) for more details).
Two hypotheses for origin of mRNA introns - 'early intron' and 'late intron'
Although introns are generally absent in protein-coding genes of bacteria, archaebacteria and some lower eukaryotes, class II type of self splicing introns have recently been reported even in bacteria. Such a distribution of introns has been used for a study of the role of introns in the evolution of genes or alternatively for a study of the origin of introns themselves. There are two different hypotheses available in this connection, (i) According to 'early- intron hypothesis, (also called "exon theory of genes" by Walter Gebert, 1987), ancestral exons existed as independent genetic units or microgenes and their association with introns helped generation of diversity in genes through trans-splicing and exon shuffling.
Efforts are being made to combine the two above hypotheses using strong features of both to formulate a new intermediate hypothesis.