Comparison of chordate Pax2/5/8 proteins and gene structures. (A) Alignment of the chordate Pax2/5/8 proteins showing the conserved DNA-binding paired-domain (dark blue), the octapeptide motif (dark green), the octapeptide-like motif (light green), and the lysine-arginine (KR) rich region (red). Arrowheads indicate the positions of introns. (B) Exon-intron organization deduced from the comparison of ESTs and genomic regions available in public databases (Ghost: http://ghost.zool.kyoto-u.ac.jp/indexr1.html, JGI: http://genome.jgi-psf.org/ciona4/ciona4.home.html, and NCBI: http://www.ncbi.nlm.nih.gov). Numbers indicate the length of the exons (boxes) in base pairs. The position of the conserved domains shown in (A) is indicated with the same code of colors. Exons containing the putative beginning of the coding sequence are labeled in orange. Exons with low degree of sequence conservation and which are hardly alignable among different organisms are labeled in light blue. Exon regions containing 5' and 3'UTR are labeled in grey. Analysis of EST sequences suggested the presence of multiple splice variants, revealing exons (in pink) that were absent from other EST sequences for the same gene; these alternates include the exon harboring the poorly conserved octapeptide motif from Ciona intestinalis. The arrow indicates the totally conserved position of the intron within the paired domain. For a phylogenetic analysis of the chordate Pax2/5/8 proteins, see Additional file 1. Bfl: Branchiostoma floridae; Cin: Ciona intestinalis; Csa: Ciona savignyi; Dre: Danio rerio; Hro: Halocynthia roretzi; Hsa: Homo sapiens; Odi: Oikopleura dioica; Pma: Phallusia mammillata.