The amino acid alignment between human and mouse sequences shows 55% identity.
The mouse sequence shows additional glycosylation sites at position 270 and 776.
In addition, the comparison of human and mouse genome sequences showed that the segmental duplications are highly related to chromosomal breakpoints in the inversion areas [48].
Sequence alignment of mammalian CDT2 and INTS7 intergenic region derived from human, chimpanzee, canine, feline, bovine, mouse, and rat sequences showed that the two genes had head-to-head orientation with high sequence identity (Fig. 1A, sequence identity marked by asterisks).
Alignment of human and mouse HCN2 sequences shows that these residues are conserved among species and suggests that the regulation of channel activity by phosphorylation might also be conserved.
Comparison of the mouse and human peptide sequences showed 91% identity (Fig. 2).
In the most extreme cases, 17/47 (36%, containing on average 2.2 expression domains in zebrafish and 1.9 in mouse per CNE) of these sequences showed dramatically different patterns (divergence of expression for 75% or more anatomical domains).
Outside the forebrain, the mouse and elephant shark URE2 sequences showed more similarities in their activities compared to zebrafish URE2: both CmURE2 and MmURE2 could target expression to the dorsal root ganglia in primary transgenic embryos (CmURE2-lacZ, n = 1/5; Additional File 3) or in two independent transgenic lines (MmURE2-lacZ, Figure 5A and 19).
Note that the homologous regions based on the new measurement often comprise the best mouse BLAST hits and the best MegaBLAST hits when using the corresponding human regions as queries against the mouse sequences, which shows that the homologous regions are most likely orthologous [ 14].
