Figure 3.

Multiple alignment of a misannotated exon of the cMet gene. According to the MLAGAN alignment, the RefSeq-annotated start position of the exon is not well conserved among the mammals. There is also a large gap (∼250 positions) in the alignment after the first 20 nucleotides of this exon, generated by sequence in cat that has no clear homolog in any of the other species aligned. However, a consensus splice acceptor site and the start position of an Acembly gene prediction exon (exon 9 in Met.f and Met.e, exon 10 in Met.a and Met.h), beginning 54 nucleotides downstream of the RefSeq exon 10, is neatly conserved across all the mammals studied. Additionally, no human ESTs correspond to the RefSeq annotation, whereas all ESTs (as annotated in the UCSC genome browser) align precisely with the Acembly gene prediction exon.