Figure 1. The chemistry of pre-mRNA splicing. The two steps of splicing are indicated in cartoon form (a), with an expanded view of the branch structure, including the unusual 2¢–5¢ phosphodiester bond (b).

Figure 2. Consensus sequences and base pairing between splicing consensus sequences and small nuclear RNAs (snRNAs). (a) Frequency matrices presenting the 5¢ splice site, 3¢ splice site, and branchpoint consensus sequences. (b) Base pairing between consensus sequences and U-RNAs (U1: 5¢ Splice site; U2: Branch site). The single unpaired nucleotide in the base pairing between U2 snRNA and the branch site is the A at which branch formation occurs. The U snRNA sequences shown are phylogenetically invariant, and the consensus sequences shown are similar in all eukaryotes. However, the sequence of any individual splice site is likely to differ from the sequence shown. As a result, the extent of base pairing is generally less than depicted here. Additional base pairing interactions between snRNAs and the pre-mRNA, or among snRNAs, that occur late in the splicing process are not shown.

Figure 3. Examples of interactions among factors that recognize splicing signals. Appropriate spacing of splice sites across either an intron (a) or an exon (b) facilitates spliceosome assembly. (c) Recognition of an exonic splicing enhancer by an SR protein. (d) Repression of splicing mediated by heterogeneous nuclear RNA proteins (hnRNPs) bound at sites within introns.

Figure 4. Different outcomes of the failure to recognize a specific splicing signal. When a splicing signal (such as the 5¢ splice site at the 3¢ end of exon 2) is defective, one might expect the affected intron to be retained (Alternative A). However, the most commonly observed result is exon-skipping (Alternative B). Another result often observed is splicing at a cryptic 5¢ splice site (Alternative C). These outcomes demonstrate the role of splicing signals other than the splice sites themselves.