Evolutionary conservations of cis-elements of human core promoters.

(A) The typical structure of a core promoter and consensus sequences of cis-elements. The most likely positions in nts relative to the TSS (+1) are given for core promoter cis-elements. (B–D) Mean PhastCons scores of cis-elements of global major TSSs, cis-elements of global minor TSSs, and pseudoelements for INR (B), BRE (C), and TATA (D). In (B)–(D), the mean PhastCons score is significantly different (P < 0.05, Mann–Whitney U test) between any pair of the three bins. Error bars show the standard error. Degenerate nucleotide symbols used are as follows. N: A, G, C, or T; H: A, T, or C; W: A or T; R: A or G; Y: C or T; M: A or C; K: G or T; S: G or C. Data are available at https://github.com/ZhixuanXu/Nonadaptive-alternative-TSSs. BRE, TFIIB recognition element; DPE, downstream promoter element; INR, initiator; nt, nucleotide; TATA, TATA box; TSS, transcription start site.