Figure 2.

Protein alignment of Whn DNA binding domains. (A) Genomic structure of whn genes. Introns are indicated by thin lines, exons by rectangles. Shading indicates regions encoding the DNA binding domain. Note the highly variable sizes of introns. (B) Alignment of all known Whn DNA binding domains (uppercase letters) and flanking sequences; amino acids are abbreviated in single-letter code. The phase of introns is indicated in brackets. Asterisks indicate that splice junctions were determined by comparison with other whn genes, rather than by comparison of genomic and cDNA sequences. The sequences for mouse (4), rat (4, 8, 15) and fugu (8) have been described earlier. Residues identical in all eight genes are given in the consensus line; some conservative changes are denoted by number: 1, negatively charged amino acid (E, D); 2, positively charged amino acid (K, R). The bottom line indicates the presumed secondary structure characteristics of the Whn winged-helix domain based on the structure of the DNA binding domain of HNF3γ (16). h, helix; s, β-sheet; w, loop (wing). Pairwise comparisons indicate that Whn DNA binding domains from human and amphioxus are 80% identical. Characteristic amino acid signatures are highlighted in different colors. Note that the exon containing the Whn DNA binding domain in amphioxus extends further into the 5′ direction.