General Introduction

Group II introns are a unique class of catalytic RNAs (ribozymes) that are capable of self-splicing. Under certain in vitro conditions, many group II intron RNAs catalyze their own excision from precursor RNAs, with concomitant ligation of their flanking exons. The reaction occurs without any protein cofactors in vitro; however, in vivo and under near-physiological conditions in vitro, the reaction requires the assistance of protein, usually by an intron-encoded protein (IEP). The splicing mechanism utilized by group II introns is essentially identical to that of eukaryotic nuclear pre-mRNA introns. This along with other similarities has led to the widespread belief that group II introns were the evolutionary ancestors of spliceosomal introns.

In addition to their self-splicing properties, many group II introns encode a multifunctional protein (IEP) that has reverse transcriptase (RT) activity. This protein allows the introns to act as retroelements and move throughout their genomes via an RNA intermediate. Group II introns have two modes of mobility, retrohoming and retrotransposition. For retrohoming, group II introns recognize and insert into specific DNA target sites (homing sites; ~20-30 bp), often at high frequency. For retrotransposition, the introns insert at low frequencies into ectopic sites that to some extent resemble the homing site in sequence.

Group II introns were originally identified and studied in organellar genomes, where many of the introns lack the IEP. However, the advent of genome sequencing revealed many of the introns in bacterial genomes, and their numbers continue to grow as new genomes and metagenome samples are sequenced. Even now, most group II introns are not annotated correctly in newly sequenced genomes. A major goal of this website is to be a reference for correct identification and cataloguing of group II introns. All bacterial introns listed in the main page are full-length and appear to be functional, based on intron RNA and IEP characteristics. The database names the full-length introns, and provides information on their boundaries, host genes, and secondary structures. In addition, the website now provides tools for analysis that may be useful to researchers who encounter group II introns in DNA sequences.