Figure 4. Conserved non coding elements (CNEs) in lamprey's Hha and Hhb.

A is a search of CNEs in PmHha and LfHhb gene sequences, confined with the Latimeria Shh enhancers ar-A, ar-B, and ar-C. Both genes show conserved peaks in the putative enhancer regions. A' is a close-up on ar-C. B is a search of CNEs in intron2 using LfHhb as baseline, showing high conservation between lamprey Hhs, and dispersion of ar-C sub-elements throughout the Latimeria sequence. C is a direct visualization of the underlying nucleotide alignments between coelacanth, lampreys and rat Shh/Hh at the level of C1. Note that the motif conservation extends on the 5′ side in lamprey genes, and is particularly shifted in the case of Hha. Analyses were performed with the global alignment algorithm MLAGAN and visualized with VISTA plot, with Calc Window and Min Cons Width of 20 bp respectively, and 70% Cons Identity. In the baselines, purple boxes indicate the exon positions, while the blue, red, and yellow ovals are the positions of ar-A, ar-B and ar-C, respectively. Conservation peaks representing putative CNEs appear in pink.