[i] Elements without protein similarity were declared phylogenetically conserved noncoding elements (PCNEs). Merging any overlapping PCNEs creates nonredundant PCNE segments, which are used to calculate the total genomic area covered by PCNEs.

[ii] ^aConserved elements were detected using our gene-family-based method.

[iii] ^bAmphioxus and fugu lack genomic UTR predictions.