Secondary structure model for group I introns. Generic secondary structure representations for group I introns highlighting the locations of intron-encoded proteins. (a) The blue lines indicate regions where ORFs that encode homing endonucleases are entirely located in loops. (b) In some group I introns, the endonuclease ORFs extend and overlap with intron core sequences. In both panels, stem regions are represented by solid black lines and single-stranded loop regions are represented by grey curved lines. Exon sequences are represented by black boxes. The ten pairing regions (P1 to P10) are also indicated. The solid green arrowheads indicate the intron-exon junctions (5′ and 3′ splicing sites). The positions of the internal guide sequence (IGS) and the so called P, Q, R and S sequence elements are indicated by thick orange lines. The guanosine-5’-triphosphate (GTP) binding pocket within the P7 helix is indicated by an asterisk.