Structural comparison of group II introns, spliceosomal introns, and snRNAs. (A) Group IIA intron. EBS, exon-binding site; DV, domain V; DVI, domain VI; IBS, intron-binding site. (B) Pairings between U2, U5, and U6 snRNAs and the intron and exons. For both panels, intron sequences and snRNA sequences are shown in red, with exons shown in green. Base pairs are indicated by gray dashes and unpaired nucleotides as black dots. The size of sequences represented by dotted red lines are indicated in nucleotides. For group II introns, selected nucleotide positions critical for splicing are shown, while the sequences shown for snRNAs correspond to the 95% consensus for the U2, U5, and U6 snRNAs sequences present in Rfam . The blue square inset shows an alternative secondary structure model for the ISL of U6, which is less compatible with DV of group II introns but is formed for naked snRNAs. The green square indicates an alternative four-way junction structure, also formed by naked snRNAs. Question marks indicate the interactions found in group II introns for which no equivalent interactions are reported in snRNAs. See text for a full description.