Splice sites and end of sequence conditions are called signals and ordered signal pairs define the exon/intron intervals in an alternative exon splicing model. Figure 3 shows a portion of the model and two example sets of states aligned to genomic sequence. The model in Figure 3 predicts alternative splicing in internal exons for the three splicing types in Figure 1 plus constitutive exons. The states represent sequence intervals between pairs of signals. The top right example in Figure 3 shows an initial "Upstream Constitutive Intron" state between signal pair (Beg, SD), which marks an intron proximal to a constitutive splice site followed by states for each downstream exon interval: "Internal First Exon of IR" (SD,SD-IR), "Retained Intron" (SD-IR,SA-IR), and "Internal Last Exon of IR" (SA-IR,SD), ending in the "Downstream Constitutive Intron" state (SD,END-INTRONc). The bottom right example in Figure 3 shows "Upstream Alternative Intron" (Beg,MA1), "Multiple Acceptor 1" (MA1,MA2), "Single Donor" (MA2,SD), and "Downstream Constitutive Intron" (SD, END-INTRONC). States not shown in Figure 3 model rarer forms of splicing, including combinations of alternative splicing events and splicing in exons at the end of genes. The complete model is given in the Methods section.