Figure 2

A 1.7 Mb region around the human SHOX2 gene. (a) Ancora genome browser main view. SHOX2, a homeobox gene implicated in limb development [47], is embedded in an array of HCNEs detected by comparison with mouse and zebrafish genomes. Overlaid density plots show densities of HCNEs detected at similarity thresholds of 95% (yellow), 98% (orange) and 100% (red) in the mouse comparison and similarity thresholds of 70%, 80% and 90% in the zebrafish comparison, over a 50 column sliding window. Note that the density of the most strongly conserved HCNEs (red) peaks around SHOX2. Synteny blocks are based on net alignments with the zebrafish genome [18]; boxes indicate aligned segments, connecting lines indicate gaps and labels indicate alignment orientation and position in the zebrafish genome assembly. The centrally shown synteny block encompasses SHOX2, RSRC1 (a gene of unknown function) and the array of HCNEs conserved in zebrafish. (b) Conservation profiles for the same region in the UCSC Genome Browser [21]. Comparison between (a) and (b) demonstrates qualitatively different information provided by the HCNE density plots in (a).