Fig. 3: The AP2x-377 enhancer contains several predicted low-affinity Dfd–Exd binding sites. | Nature Communications

Fig. 3: The AP2x-377 enhancer contains several predicted low-affinity Dfd–Exd binding sites.

From: Specificity of the Hox member Deformed is determined by transcription factor levels and binding site affinities

Fig. 3

a Dfd–Exd binding regions in AP2x-377 predicted by the No Reads Left Behind (NRLB) algorithm. The identified regions are located in the conserved domains 2 and 3. b Alignment of an optimal high-affinity class 2 Dfd–Exd binding site (class 2 DE) with the putative Dfd–Exd binding sites present in AP2x-377. Sites 1–10 were identified in the Dfd–Exd NRLB predicted regions with sites 3 and 4 showing a considerable overlap. Site 11 (highlighted by a box) was not detected by the NRLB algorithm but due to similarities to known characterized low-affinity binding sites12. Nucleotides highlighted in yellow and brown display 80–100% and 60–80% similarity among all sequences aligned, respectively. Non-highlighted nucleotides display <60% similarity among all sequences aligned. c Weblogo frequency plot of the predicted Dfd–Exd binding sites present in AP2x-377. See also Supplementary Fig. 5.

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