Editing was inferred from alignment of cDNAs to human genomic DNA. (A) Schematic illustration of exons 2 to 4 of the non-coding gene NR_024561. Exons are depicted as blue boxes. The Alu-exon, derived from AluJo (marked AEx; shown by purple box), is in an antisense orientation and is shown in the middle. The intronic, sense-orientation Alu sequence (AluS) is 731 base-pairs downstream of the exonized Alu. Sense and antisense Alus are expected to form double-stranded RNA, thus allowing RNA editing. RNA editing changes an AA dinucleotide into a functional AG 3′ splice site (lower panel). RNA editing also occurs in three positions in the Alu-derived exon (E1, E2, and E3). (B) Predicted folding of the sense and antisense Alu sequences (upper and lower lines, respectively). Adenosines that undergo editing are marked by red. Splice sites utilized for Alu exonization are marked as 5′ss and 3′ss on the alignment. (C) Alignment of this region from four species: human, gorilla, orangutan, and rhesus. The 5′ splice site, 3′ splice site, and the three editing positions are marked in yellow.