Figure 6.

Significant change in element length and substitution rate in overlapping CNEs upstream of unc4.1.1 and unc4.1.2. (a) CNEs (filled blue boxes) were identified around each Fugu co-ortholog unc4.1.1 (A1, top) and unc4.1.2 (A2, bottom) (gene exons are shown in the coding sequence (CDS) track as filled red boxes). The scale at the top represents positions along the Fugu sequence used in the multiple alignment. Two CNEs, highlighted in pink boxes, one upstream of Fugu unc4.1.1 (CRCNEAC00031954 [53], referred to as CNE_A1) and one upstream of unc4.1.2 (CRCNEAC00032205 [53], referred to as CNE_A2) are conserved to part of the same sequence in human upstream of UNC4.1. The overlap region is 126 bp in length and encompasses all of the CNE_A2 but only 35% of CNE_A1 (which is 360 bp long), indicating a significant loss of element length in CNE_A2. (b) A relative rate test of the Fugu CNEs across the overlapping region using human as the outgroup reveals a highly significant number of independent substitutions (26) in CNE_A2 with no independent substitutions in CNE_A1 (p < 0.001). This suggests CNE_A1 is likely to have retained the ancestral function while CNE_A2 may have evolved to have a different function.