Figure 1.

Cross-species comparisons of the β-globin gene promoter. (a) Analysis of the human promoter without phylogenetic filtering generates numerous predictions, most of which are biologically irrelevant. (b) Comparison with the chicken promoter fails to detect conserved sites (screened with the artificially low conservation cutoff of 25%). (c) Comparison with the mouse promoter sequence identifies conserved sites, including a documented GATA-binding site [49] (boxed). (d) Comparison with the cow promoter identifies more conserved sites. (e) Comparison to the Macaque monkey (Macaca cynomolgus) promoter results in a plot similar to the single sequence analysis. Unless indicated, all plots were generated using all available matrices from vertebrates, with 70% conservation cutoff, 50 base-pair window size and 85% transcription factor score threshold settings. The y axis in all graphs specifies the percentage of identical nucleotides within a sliding window of fixed length (using the default of 50 base-pairs). The x axis refers to the nucleotide position in the human sequence at which the window initiates.

Lenhard et al. Journal of Biology 2003 2:13   doi:10.1186/1475-4924-2-13