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Fig. 1 Characterization of the zebrafish mmp9 gene. (A) Sequence Analysis. Full-length nucleotide sequence and deduced protein sequence (bold) of zebrafish mmp9 with residue numbers indicated. The conserved domains of the encoded Mmp9 protein were analysed with the Conserved Domain program at the GenBank website (www.ncbi.nlm.nih.gov). These include a matrix metalloprotease catalytic domain (red), a zinc catalytic domain (blue), three fibronectin domains (green), and a hemopexin-like domain (pink). (B) Phylogenetic tree of matrix metalloproteinases. Radial phylogenetic tree constructed using TreeView (Page, 1996) based on a sequence alignment produced with ClustalX (Heringa, 1999). Bootstrap values shown were calculated from 100 predicted trees. The following sequences from GenBank were used: Dr Mmp9, (this study NP_998288); Bt Mmp2, NP_777170; Bt Mmp9, CAA55127; Cc Mmp9, BAB39390; Dr Mmp2, AAP74482; Gg Mmp2, NP_989751; Gg Mmp9, AAG47650; Hs MMP2, AAH02576; Hs MMP9, CAC10459; Hs MMP-12, P39900; Mm Mmp2, NP_032636; Mm Mmp9, BAB23442; Ol Mmp2 BAA85769; Ol Mmp9, BAA85770; Om Mmp2 BAA78479; Om Mmp9, CAC85923; Po Mmp9, BAB68366; Rn Mmp9, AAA90911; Xl Mmp9, AAD41624. Abbreviations: Bt, Bos taurus (cow); Cc, Cyprinus carpio (carp); Dr, Danio rerio (zebrafish); Gg, Gallus gallus (chicken); Hs, Homo sapiens (human); Mm, Mus musculus (mouse); Ol, Oryzias latipes (medaka fish); Om, Oncorhynchus mykiss (rainbow trout); Po, Paralichthys olivaceus (Japanese flounder); Rn, Rattus norvegicus (Norway rat); Xl, Xenopus laevis (African clawed frog). Scale bar indicates 0.1 nucleotide substitutions per site.
Reprinted from Gene expression patterns : GEP, 7(1-2), Yoong, S., O'connell, B., Soanes, A., Crowhurst, M.O., Lieschke, G.J., and Ward, A.C., Characterization of the zebrafish matrix metalloproteinase 9 gene and its developmental expression pattern, 39-46, Copyright (2007) with permission from Elsevier. Full text @ Gene Expr. Patterns