Figure 1. The pre-mRNA splicing reaction and snRNA interactions in the spliceosomes. (a) Diagram of the two-step spliceosomal splicing reaction described in the text. (b) RNA–RNA interactions in the major, U2-dependent spliceosome. (Left) The initial interactions of the pre-mRNA with U1 and U2 snRNPs. (Right) The interactions in the mature spliceosome. Hatched bars indicate regions that interact by base-pairing. The adenosine residue at the branch site is circled. (c) RNA–RNA interactions in the minor, U12-dependent spliceosome.

Figure 2. Pictograms of the major U2-dependent intron class consensus splice site signals. Approximately 20000 5¢ and 3¢ splice sites from annotated GenBank files were extracted and aligned as described in Burge et al. 1999. In these pictograms, the size of a letter corresponds to the frequency with which that base is present at each position in a compilation of splice sites. (a) Major class 5¢ splice site consensus sequence. The position labeled 1 is the first nucleotide of the intron and the position labeled –1 is the last nucleotide of the upstream exon. (b) Major class branch site consensus. A small database of experimentally confirmed branch sites (Nelson and Green, 1989) was used to generate this pictogram. The position labeled 1 is the branch site residue. (c) Major class 3¢ splice site consensus. The position labeled –1 is the last nucleotide of the intron and the position labeled 1 is the first nucleotide of the downstream exon.

Figure 3. Pictograms of the minor U12-dependent intron class consensus splice site signals. Because the consensus sequences differ between the GU–AG and AU–AC subclasses of U12-dependent introns, these are presented separately. The GU–AG subclass consensus was derived from 160 examples, while the AU–AG subclass consensus was derived from 30 examples. (a) Minor class GU 5¢ splice site consensus sequence. The position labeled 1 is the first nucleotide of the intron and the position labeled –1 is the last nucleotide of the upstream exon. (b) Minor class GU–AG branch site consensus sequence. The position labeled 1 is the branch site residue. (c) Minor class AG 3¢ splice site consensus. The position labeled –1 is the last nucleotide of the intron and the position labeled 1 is the first nucleotide of the downstream exon. (d) Minor class AU 5¢ splice site consensus sequence. (e) Minor class AU–AC branch site consensus sequence. (f) Minor class AC 3¢ splice site consensus sequence.