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Within each species, we defined the tissue-specificity of regulatory regions by comparing the regulatory calls made within each of the tissues separately (Definitions of regulatory regions (Fig. (Fig.1c1c and Table S4)). Two regulatory regions were considered active across tissues if either overlapped another regulatory region of the same regulatory activity with at least 50% of its length. i.e., a tissue-shared active enhancer was considered tissue-shared only if it overlapped an active enhancer in another tissue (Additional file 1: Figure S5). All other combinations were considered intra-species dynamic (Intra-species dynamic regulatory signatures (Fig. (Fig.4a4a and S5)) and not included in any analyses or figures unless explicitly stated. A gene or transcript was considered expressed in a tissue according to the method outlined in RNA-seq mapping and normalization (Fig. (Fig.1d1d and Table S5).

Figure 2b shows the sum across all ten species for the intersections between tissue activity using an UpSetR plot version 1.4.0 [88], while Additional file 1: Figure S6A shows the data only for mouse. For all further analyses regulatory regions and gene expression were considered tissue-specific if they were only active in a single tissue and tissue-shared if active in two or more tissues (Additional file 1: Figure S5).

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