Figure 6

Genome-specific flexibility in less-conserved sequences revealed by exchanging input reference DNAs. By swapping the input reference DNA for one of the aligning regions in another genome and reinitiating the EvoPrint analysis, one can identify species-specific changes in the spacing between conserved sequences. A) EvoPrint analysis of the human CASZ1 gene identified two highly conserved MCSs within its second intron that are separated by 441 bp. Shown is a relaxed EvoPrint that was generated with ceBLAT alignments of the human sequence to: chimpanzee, rhesus, mouse, rat, dog, cat, horse, cow, hedgehog, elephant, armadillo, opossum, chicken, X. tropicalis, Fugu, Tetraodon, Medaka, stickleback, and zebrafish genomes. Uppercase black-colored bases are present in all orthologs or found in all but one of the aligning regions. B) Shown is a relaxed EvoPrint obtained when the human input reference sequence, used to generate the EvoPrint shown in (A), is exchanged for the highest scoring aligning region in the zebrafish genome. The zebrafish CASZ1 relaxed EvoPrint reveals that the intervening genomic region between the two highly conserved MCSs in the zebrafish orthologue is 7,061 bp longer than that found in the human genome.