Splicing occurs in two transesterification steps. In the first step, a bulged adenosine in domain 6 attacks the 5’ splice site, resulting in cleavage of the 5’ exon and formation of a lariat intermediate. The 5’ exon is held into place after cleavage by the IBS1-EBS1 and IBS2-EBS2 pairings. In the second step, the 5’ and 3’ exons are ligated together and the intron is released as a lariat. To the detail drawn, this reaction is identical to splicing of nuclear pre-mRNA introns, supporting the idea that group II introns were ancestors of spliceosomal introns.

Splicing reaction

Structure showing IBS-EBS pairings and bulged "A" utilized during splicing reaction

Maturase-assisted splicing reaction

       Although some group II introns self-splice in vitro, splicing in vivo requires the additional assistance of protein. The most important splicing factor is the intron-encoded RT. The RT binds to unspliced intron RNA at a high affinity binding site in domain 4A, and makes secondary contacts in domains 1, 2 and 6. Together, the protein-RNA interactions result in conformational changes in the intron that result in self-splicing. After splicing, the RT remains tightly bound to spliced intron, and this RNP particle is the active moiety in subsequent mobility reactions.