The large spread of coverage, from our highest resolution, most conservative set of bases implicated in GENCODE protein coding gene exons (2.9%) or specific protein DNA binding (8.5%) to the broadest, most general set of marks covering the genome (approximately 80%) -- with many gradations in between -- presents a spectrum of elements with different functional properties discovered by ENCODE. 99% of the known bases in the genome are within 1.7 kbp of any ENCODE element, whereas 95% of bases are within 8 kb of a bound TF motif or DNaseI footprint. Interestingly, even using the most conservative estimates, the fraction of bases likely to be involved in direct gene regulation, even though incomplete, is significantly higher than that ascribed to protein coding exons (1.2%), raising the possibility that more information in the human genome may be important for gene regulation than for biochemical function. Many of the regulatory elements are not constrained across mammalian evolution, which to date has been one of the most reliable indication of an important biochemical event for the organism. Thus, our data provide orthologous indicators for suggesting possible functional elements.
