<p>Exons (boxes) are drawn to scale and are labeled according to their homology with mouse sequence. Pairwise similarity (percent identical residues plus conserved amino acid substitutions based on the Blossum40 matrix) of the zebrafish protein to the mouse protein is presented for each exon in parentheses. Full-length values for mouse to zebrafish <i>kitla:</i> 29% identical and 43% similar. Full-length values for mouse to zebrafish <i>kitlb:</i> 20% identical and 50% similar. Although quite diverged in sequence, the zebrafish paralogs display well-conserved intron site locations with themselves and with the mouse ortholog. The best alignment of <i>kitlb</i> reveals that it has lost exon 6, which is alternatively spliced in mouse and human. Exon 5 of <i>kitla</i> has expanded 3′ with a corresponding contraction of exon 6. <i>Kit</i> binding domain contains the residues that interact with <i>Kit</i> as determined from crystal structures of the two mouse proteins [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030017#pgen-0030017-b026" target="_blank">26</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030017#pgen-0030017-b027" target="_blank">27</a>]. The locations of the major cleavage site in mouse exon 6 and the minor cleavage site in mouse exon 7 are indicated. We cannot identify either cleavage site by sequence conservation in either zebrafish gene (see also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030017#pgen-0030017-sd001" target="_blank">Dataset S1</a>). MOs (red bars) were targeted to overlap the ATG start site for <i>kitlb</i> and the exon 3–intron 3 boundary of <i>kitla</i> and <i>kitlb.</i> The splice site MOs resulted in splicing of exon 2 to exon 4 (red lines), resulting in a shorter, in-frame, transcript (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030017#pgen-0030017-g004" target="_blank">Figure 4</a>E and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030017#pgen-0030017-g004" target="_blank">4</a>F).</p
