Group II intron encoded ORF structure

The ORF of group II introns consists of an RT with seven domains common to all reverse transcriptases, domain X, domain D and the En domain. Within the RT domain, domain 0 is conserved only among non-LTR and retron reverse transcriptases (but not retroviral RTs, for example). Domain 2a is weakly conserved between RTs of group II introns and non-LTR RTs. Domain X is probably analogous to the "thumb" motif of other polymerases, but is not conserved in sequence (as expected because the thumb domain is always poorly conserved). The D domain is not conserved in sequence among different introns, but has been defined functionally as a DNA binding region for the Ll.ltrB intron. The En domain has a nuclease domain and contributes the nuclease activity for antisense strand cleavage during retrohoming.