Figure 6

Localization of putative p53 sites with selected spacer lengths in the Alu elements. The scheme summarizes the data presented in Figures 5 and S4 (Additional File 4). The consensus sequences of 11 Alu subfamilies were downloaded from Repbase Update [74–76] and aligned using the ClustalW module in BioEdit [77]. Top: The consensus sequences of the Boxes A, B and A' [78] are aligned with the Alu sequences. The CNNG core motifs shown in color indicate predominant positions in the Alu elements where the p53 sites were found. For each Alu subfamily, the distances between the CNNG cores in the consensus sequence are directly related to the predominant spacer lengths observed in the p53 sites residing in the corresponding Alu repeat (Figures 5 and Additional File 4: Figure S4). In the case of AluY subfamily, most of the p53 sites are located around position 215 and have spacer S = 2 (Additional File 4: Figure S4-I). The color code corresponds to the spacer length: red for S = 0, blue for S = 3, green for S = 8 and yellow for S = 14 bp.