Group II intron DNA sequence and RNA structure. (A) Genomic structure of a group II intron. The 2- to 3-kb sequence consists of RNA and protein portions. The intron RNA domains are depicted in red and demarcated with Roman numerals. Domains I to IVa are at the 5′ end of the intron, while domains IVb to VI are at the 3′ end. The IEP sequence is nested within the RNA’s sequence and the domains are denoted by differently shaded blue boxes. The IEP contains a reverse transcriptase domain (RT) with motifs 0 to 7, a maturase domain (X, sometimes called X/thumb), a DNA-binding domain (D), and an endonuclease domain (En). Exons are shown in green. (B) Secondary structure of the unspliced RNA transcript. The intron RNA (red) folds into a structure of six domains, with the ORF encoded in a large loop of domain IV. The 5′ and 3′ exons are the green vertical lines at the bottom. Watson-Crick pairing interactions that are important for exon recognition are IBS1-EBS1, IBS2-EBS2, and δ-δ′ (for IIA introns), which are shown with teal, orange, and brown shadings, respectively, and connected with black lines. For IIB and IIC introns, the 3′ exon is recognized instead through an IBS3-EBS3 pairing (not shown). The ε-ε′, λ-λ′, and γ-γ′ interactions are also indicated, because they have potential parallels in the spliceosome (Figure 5); other known tertiary interactions are omitted for simplicity. Both the RNA and DNA structures depicted correspond to the L. lactis ltrB intron. EBS, exon-binding site; IBS, intron-binding site; ORF, open reading frame.