Dot plot of the human 3'RR-2 against 4 species. The comparison of the human regulatory region against the homologous sequences of Ailuropoda melanoleuca (panda), Canis familiaris (dog), Mus musculus (mouse) and Oryctolagus cuniculus (rabbit) shows the conservation of the enhancer positions and the high similarity in the sequence spanning from the alpha gene to the other extreme enhancer HS4. In the mouse the two copies of the enhancer HS3 A and B have in the neighbor region also the 20 bp repeat. In the mouse palindrome (light blue frame) are shown by the black segments with inverted orientation three copies of a region that is in two copies in humans. The wider extension of the palindrome in mouse includes the two HS3 enhancers on the boundaries. The same structures are conserved along the homologues 3'RR in these species and the palindrome is present in the cluster of all species as evidenced by the pale blue rectangle with the central region represented by the HS1.2 enhancer. The black lines depict the internal repeats present in more than one copy. The lines when parallel to the major diagonal have the same orientation, when are perpendicular have inverted orientation, as in the palindrome sequence.
D'Addabbo et al. BMC Evolutionary Biology 2011 11:71 doi:10.1186/1471-2148-11-71