Genes were counted in more than one promoter category if they had had different types of core promoter predictions for different alternative start sites. Percentages are relative to the number of classified genes.

^aProtein-coding genes annotated with GO term GO:0006355 (regulation of transcription, DNA-dependent).

^bProtein-coding genes annotated with GO term GO:0007275 (multicellular organismal development).

^cProtein-coding genes overlapping a 40-kb region where at least 1% (400 bp) of the sequence is covered by HCNEs.