A central question in molecular genetics concerns how transcriptional regulatory sequences and de novo genes originate and reach evolutionary fixation. In this study, we utilize the human bicistronic gene SMIM45 as a model to analyze the evolutionary trajectories of gene development. This locus comprises several functional units: three enhancers (one featuring an embedded silencer), an exonic silencer that partially overlaps an ORF, a highly conserved ancestral sequence encoding a 68-aa microprotein, and a human-specific de novo gene encoding a 107-aa protein expressed spatiotemporally in embryonic brain tissues. We identify significant disparities in formation mechanisms; for example, the NANOG hESC enhancer originated simply via two Alu insertions that constitute the regulatory element. In contrast, the exonic silencer (ATAC-STARR-seq lymphoblastoid silent region 13815) originated by a combination of diverse mechanisms, including a "cultivator gene" process of base pair fixation consistent with the Cultivator Model proposed by Li Zhao and coworkers. Consequently, SMIM45 exemplifies novel mechanisms of regulatory element development that occurred over several hundred million years, culminating in the birth of a human-specific de novo 107-aa cistron. The properties of these super-enhancers and super-silencers suggest a complex, intricate regulation of the 107-aa protein in fetal tissues.