Fig. 2

Details of a sequence alignment: prediction of acceptor sites and blocks on human and dog. Two multiple alignments are shown here, providing more details about the predictions illustrated in Fig. 1: the alignments of the loci encoding exons C and BC, and exons H and GH. Uppercases indicate nucleotides involved in known exons, and lowercases indicate intronic nucleotides never observed yet to belong to an exon. For example, in human and mouse genes, the longer exon BC is known (uppercase). In the dog gene however, only the shorter exon C is known and the upstream nucleotides have been observed as intronic so far (lowercase). Note that the exon C is not known in human (it does not occur in any human transcript, see Fig. 1a). The splicing sites are indicated in bold, and predicted splicing sites are underlined. For example, a motif “AG” in human has been aligned with the known acceptor “AG” of exon C in mouse, thereby yielding a predicted orthologous splicing site in human (underlined bold “AG”). This motif is now identified as an acceptor site of exon C in human. Additionally, a motif “ag” in dog has been aligned with the known “ag” acceptor of exon BC in mouse, yielding a predicted orthologous splicing site in dog (underlined bold “ag”). The nucleotides of the predicted exons are shown in red. For example, a motif “cag” in dog has been aligned with the sequence “CAG” of the known block ‘B’ in mouse, yielding a predicted block (red “cag”). As a result, shorter exons C and H can exist in human (only longer exons BC and GH were known). In dog two new exons can exist, H (only GH was known) and BC (only C was known)