Figure 4: Conservation of orthologous sequence between human and dog.

a, Histogram of conservation scores, S, for all 50-bp windows across the human genome with at least 20 bases of orthologous sequence aligning to the dog genome, for all aligning sequences (red) and for ancestral repeat sequence only (blue). b, Conservation scores for the subset of windows that also have at least 20 bases of orthologous sequence aligning to the mouse genome. c, Conservation scores of the complementary subset of windows lacking such orthologous sequence in mouse. d, Density of 50-bp windows not overlapping known coding regions, for which P_selection(S) > 95%, based on comparisons between human and dog (HD), human and mouse (HM), or between human, mouse and dog (HMD), and the density of known genes, all in 1-Mb sliding windows across human chromosome 3. e, Enrichment of HCNEs in the immediate neighbourhood of genes encoding developmental regulators in the 204 highly conserved regions. The histogram shows the median number of HCNE bases in the intronic and surrounding intergenic sequence, for the 197 known or putative development regulators (indicated by top of red bar) and for all of the 1,285 genes (blue bar). The histogram is centred at the 5′-end of the gene (marked 0) and each bin corresponds to half of the normalized distance to the flanking consecutive upstream genes (marked -1, -2 and -3) or consecutive downstream genes (1, 2 and 3) as indicated. The sequences surrounding the developmental genes are typically longer, have more HCNE sequence and have a higher density of HNCE sequence than other genes in the regions (see Supplementary Information).