The sequence quality of reference genome databases is essential for the accurate definition of regulatory DNA segments as candidate human specific regulatory sequences (HSRS). It is unclear how database improvements would affect the validity of the HSRS definition. Here, sequence conservation analysis of 15,371 candidate HSRS was carried out using the most recent releases of reference genomes databases of humans and nonhuman primates (NHP) defining the conservation threshold as the minimum ratio of bases that must remap of 1.00. This analysis revealed that 2,262 of 2,739 (82.6%) sequences of human accelerated regions lack evidence of human-specific mutations and appear highly conserved in humans and NHP. Similarly, the majority (404 of 524; 77.1%) of human accelerated DNase hypersensitive sites represents highly conserved in humans and NHP regulatory sequences lacking evidence of human-specific mutations. Present analysis revealed a major database refinements effect on the validity of HSRS definition and suggests that human-specific phenotypes may evolve as a results of integration into human-specific genomic regulatory networks of both conserved in NHP and human-specific genomic regulatory elements.