Using phylogenetic footprinting to detect conserved TFBSs. This schematic diagram shows a hypothetical human gene aligned with its orthologs from three other mammals. Cross-species sequence comparison reveals conserved TFBSs in each sequence. Sequence motifs of the same shape (colored in green) represent binding-sites of the same class of transcription factors. TFBS1 and TFBS4 are conserved in all four mammals; TFBS3 represents a newly acquired, primate-specific binding site. TFBS2 and TFBS2' represent orthologous regulatory sites that have diverged significantly between the primate and rodent lineages. Blue rectangles represent TATA boxes.
Zhang and Gerstein Journal of Biology 2003 2:11 doi:10.1186/1475-4924-2-11