Figure 3

VISTA plot of an MLAGAN alignment of orthologous regions surrounding two pax2 co-orthologs in Fugu (Fr) and Pax2 in chicken (Gg), rat (Rn) and human. The baseline is 268 kb of human sequence. Conservation between human and each sequence is shown as a peak. Peaks that represent conservation in a non-coding region of at least 65% over 40 bp are shaded pink with coding exons shaded purple and peaks located within untranslated regions shaded light-blue. All CNEs conserved in at least one of the Fugu co-orthologs are color-coded. CNEs in both Fugu co-orthologs that overlap the same region in human are shaded yellow while CNEs that are 'distinct' (or conserved solely) in pax2.1 are shaded red and CNEs distinct to pax2.2 are shaded green. Peaks marked with a double-headed arrow are conserved in Fugu in the opposite orientation (and therefore do not show up in the VISTA plot). A number of the CNEs around PAX2 are also duplicated CNEs (dCNEs) that are located elsewhere in the genome in the vicinity of PAX2 paralogs. CNEs marked with an orange box have another dCNE family member in the vicinity of PAX5 and the CNE marked with a blue box has a dCNE family member conserved upstream of PAX8.