Predicted secondary structure of the

Copyright information:

Taken from "Group II intron in has an unusual 3′ extension and splices 56 nucleotides downstream of the predicted site"

Nucleic Acids Research 2007;35(5):1612-1623.

Published online 14 Feb 2007

PMCID:PMC1865049.

© 2007 The Author(s).

I4 group II intron from ATCC 10987. Exon nucleotides are in lowercase. Roman numerals (I to VI) indicate the six typical functional RNA domains and their subdomains are designated by combinations of letters, numbers and superscripts according to the nomenclature of (). The extra 56-nt 3′ segment harbored by .I4 is boxed in grey. Sites corresponding to consensus positions involved in tertiary interactions (,) are indicated by pairs of Greek letters or EBS/IBS (exon binding sites and intron binding sites). Sites of tertiary base-pairing interactions are boxed or circled in red with arrows indicating the orientation of complementarity. Sites implicated in other tertiary contacts are boxed or circled in blue. The IBS3–EBS3 and γ–γ′ base-pair interactions involved in 3′ splice-site selection are indicated by black dotted lines. The δ′ nucleotide was set at the expected location (C:350) according to (), however it is not complementary to the δ site, while nucleotide A:349 is. ORF, intron-encoded multifunctional open reading frame. Numbering of residues does not include the ORF. A–U, G–C and G–U base pairs are linked by blue, red and green dots, respectively.