Figure 3

An analytical view of the Arabidopsis CCCH gene family. The following parts are shown from left to right. Protein neighbor-joining tree: The unrooted tree, constructed using ClustalX (1.83), summarizes the evolutionary relationship among the 68 members of CCCH families. The neighbor-joining tree was constructed using aligned full-length amino acid sequences. The proteins are named according to their gene name (see Table 2) with the CCCH zinc finger number of each protein. The tree shows the 11 major phylogenetic subfamilies (left column, numbered I to XI and marked with different alternating tones of a gray background to make subfamily identification easier) with high predictive value. The numbers beside the branches represent bootstrap values (≥500) based on 1000 replications that were used to class the major 11 subfamilies. Gene structure: The gene structure is presented by black exon(s) and spaces between the black boxes correspond to introns. The sizes of exons and introns can be estimated using the horizontal lines. Protein structure: Each black box represents the motif in the protein, as indicated in the table on the left side. The conserved motifs outside CCCH motif are highlighted with an arranged number, and the same number referred to the same motif. The length of the motif can be estimated using the scale at top. aa, amino acids.