Table 2. Phylogenetic comparison of CRX exon-intron splice boundaries.

Species	Exon	Acceptor splice site	Exon size (bp)	Donor splice site	Intron size (bp)
human*	1		>103	TTCTGAAGgtgagcgtc	12392
mouse**	1		>78	TTCCAAAGgtgagtctt	8540
zebrafish	1		>515	ATG(n90)CTACCCAGgtcagttca	731
human	2	tctcttgcagGCCCCCTG	135	ATG(n90)CTACCCAAgtgagtaca	859
mouse	2	tctcttgtagGTGCCCTC	135	ATG(n90)ATACTCAAgtaagtatg	1633
zebrafish	2	gtatgtatagCCACTCCG	152	GAGTTCAGgtgagtcct	583
human	3	cccaccccagGCGCCCCC	152	GGGTTCAGgtggggtgg	1698
mouse	3	ccccgcttagGTGCCCCT	152	GGGTCCAGgtaggatga	953
zebrafish	3	gtttcttcagGTGTGGTT(n586)TGA	1725
human	4	tatcccccagGTTTGGTT(n637)TGA	1829
mouse	4	ctctatctagGTCTGGTT(n637)TGA	2478

Alignment of splice junctions of zebrafish crx with human and mouse CRX reveals conservation of splice acceptors and donor sites located within the coding regions. The identified 5′ UTR in zebrafish crx is contained entirely in exon 1, whereas the 5′ UTR in mouse and human crx is divided into two exons. Despite this difference, the positions of the splice junctions in coding regions are highly conserved. The splice junction between exons 1 and 2 in zebrafish crx is located at the same position, relative to the ATG initiation codon, as the splice junctions between exons 2 and 3 in human and mouse. Splice junctions were identified by aligning cDNA sequences with the corresponding genomes using the BLAT program at the UCSC genome database (UCSC). The human sequence (BC016664) marked with an asterisk (*) is aligned with the human genome May 2004 assembly; the mouse sequence (AK053533) marked with a double asterisk (**) is aligned with the mouse genome October 2003 assembly; zebrafish (AF503443) is aligned with the zebrafish genome June 2004 assembly. There are additional splice-variants unique to human crx [28].