The discovery of a second type of spliceosomal intron in the genomes of many multicellular eukaryotes raised the exciting possibility of comparing the structural and functional features of the two splicing systems with the hope of shedding light on important features of each (Tarn & Steitz, 1997). This hope was amply fulfilled with the discovery of the parallel roles played in the two systems by the respective sets of spliceosomal snRNAs. The initial identification of functions for the previously known U11 and U12 snRNAs (Hall & Padgett, 1994; Tarn & Steitz, 1996b) was magnified by the discovery of the novel U4atac and U6atac snRNAs (Tarn & Steitz, 1996a). The similarities of these latter two snRNAs to the U4 and U6 snRNAs of the major splicing system were apparent and led to detailed comparisons of the features of these RNAs and their interactions (Tarn & Steitz, 1996a). For both the U4/U6 pair and the U4atac/U6atac pair, a similar secondary structure was proposed involving two intermolecular base paired helical regions termed stem I and stem II, separated by an intramolecular stem-loop structure in both U4 and U4atac (Fig. 1A,B). Although the stem II interactions appeared to be very similar in both structures, the stem I interaction in the U4atac/U6atac structure was shorter and differently arranged than in the U4/U6 structure.