Table 2 of
Otteson, Mol Vis 2005;
11:986-995.Table 2 of
Otteson, Mol Vis 2005;
11:986-995.
Table 2. Phylogenetic comparison of crx exon-intron splice boundaries
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].
Exon Intron
size size
Species Exon Acceptor splice site (bp) Donor splice site (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
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