Figure 6

Distribution of promoter features for intergenic, intronic and host gene promoters. (a) Probability density function (PDF) of the CpG score across intergenic (blue), intronic (red) and host gene (gray) promoters. (b) PDF of the conservation score, calculated from the PhastCons vertebrate UCSC track, across intergenic, intronic and host gene promoters. (c) PDF of the distance between intergenic, intronic and host gene TSSs from miRNA precursors. (d) PDF of transcription start site (TSS) width, shown as log₁₀(width) for clarity, for intergenic, intronic and host gene promoters. (e) PDF of the TATA box affinity values, calculated using TRAP, for intergenic, intronic and host gene promoters. (f) Bar plot showing the fraction of promoters that have a TATA box affinity lower than 0.01, in the range between 0.01 and 0.07 or higher than 0.07 for intergenic, intronic and host gene promoters, as well as for all human promoters and background regions. The two affinity levels of 0.01 and 0.07 correspond to the median and upper quantile affinity values for human promoters, respectively.

bp, base pair; miRNA, microRNA; PDF, probability density function; TSS, transcription start site.