Fig. 7

Hypomethylated clade of IAPLTR2a2 is characterized by the presence of Maz- and Ubp1-binding motifs. The nucleotide sequences of the R region of the LTR (see top for a schematic view of the LTR sub-regions) of IAPLTR2a2 copies belonging to the methylated and hypomethylated clades were aligned by Clustal X [37]. Maz-binding motifs are highlighted in red. Ubp1-binding sites are indicated by a blue box. CpG sites are indicated by a black box. Members of the hypomethylated clade carry multiple Maz and Ubp1 sites, whereas almost all members of the hypermethylated clade carry none. Sequence Logo representation of the binding motifs is shown at the bottom