PAX6 is an evolutionarily conserved transcription factor that plays a critical role in vertebrate and invertebrate eye formation. Heterozygous null mutations in the PAX6 gene result in aniridia in humans and a distinct small eye syndrome in rodents. Vertebrates primarily express two alternatively spliced isoforms of Pax6 that differ by the presence or absence of exon 5a (e5A) that encodes an additional 14 aa residues within the paired domain. The e5a-containing isoform, PAX6(5a), is specific to and conserved in vertebrates. To determine the role of PAX6(5a), we have generated mice that lack e5a of the Pax6 gene. Unlike Pax6 null mice that exhibit anopthalmia with central nervous system defects and lethality, 5a isoform-null mice have iris hypoplasia and defects in the cornea, lens, and retina. Although invertebrates have structures that respond to light intensity and act to restrict light exposure of the eyes, a significant and distinct feature of the vertebrate eye is its ability to regulate the amount of incoming light through contractile pupils. This feature of the eye not only allows vertebrates to see in various light conditions but also enhances image resolution. The requirement of the 5a isoform in iris formation suggests that the evolution of this isoform contributed to advanced features of the vertebrate eye. P AX6 is an essential and evolutionarily conserved transcription factor for eye formation (1-3). Heterozygous null mutations in the PAX6 gene result in distinct phenotypes in humans (aniridia) and rodents (small eye) (4, 5). Aniridia is a severe panocular disease that is characterized by lack of proper iris development, associated with cataracts, optic nerve hypoplasia, and glaucoma. Small eye syndrome is distinguished from aniridia by reduced eye size, cataracts, and poor lens development. Homozygous mutations in the PAX6 gene result in severe brain abnormalities, microencephaly, early postnatal death, and the absence of the eyes and nose in both humans (4) and rodents (5, 6).The Pax6 locus encodes two products caused by alternative splicing of exon 5a (e5a) that adds an additional 14 aa residues within the paired domain (7,8). The e5a-containing isoform, PAX6(5a), is specific to and conserved in vertebrates (9). Pax6 is expressed in the developing eye, nose, pancreas, and central nervous system (7, 10-13). PAX6 is a protein of 422 aa residues, and PAX6(5a) is 14 aa longer and exhibits unique DNA-binding properties (14). Structural analysis of PAX6 identified two DNA-binding domains (a paired domain at the amino terminus and a paired-like homeodomain located centrally), a glycine-rich region that links the two DNA-binding domains, and a transactivation domain at the carboxyl terminus. The paired domain of PAX6 is a bipartite DNA-binding motif and is believed to have two independent amino-terminal and carboxyl-terminal subdomains (15, 16). The paired domain can bind DNA alone or cooperatively by interacting with other DNA-binding domains, such as the homeodomain (17). Unlike other paired domains th...