Fig. 2. In silico analysis of FoxE3 cis-regulatory elements. (A) Genomic sequence of the human FOXE3 locus (-29.0 to +30.4 kb) aligned with its orthologous mouse, chicken and X. tropicalis sequences using MultiPipMaker. The aligned sequences were downloaded from the VISTA Browser (http://genome.lbl.gov/vista/index.shtml) or from the Xenopus tropicalis v4.1 genome site (http://genome.jgi-psf.org/Xentr4/Xentr4.home.html). A non-coding region conserved from human to Xenopus is boxed with a dotted red line. Black arrows indicate exons of human FOXE3 and its neighboring gene, FOXD2, and their orientations. Coding and untranslated sequences are shaded with light blue and light cyan, respectively. The scale at the bottom of the alignment indicates relative positions in the human FOXE3 locus. (B) The conserved non-coding element of Xenopus FoxE3 (-6159 to -5698) identified by MultiPipMaker is aligned with its orthologous chicken, mouse and human sequences using ClustalW (http://www.ebi.ac.uk/clustalw/). Sequences conserved in at least three species are shaded in gray. Putative transcription factor-binding motifs mapped in conserved sequences are boxed in different colors. The three gray boxes indicate conserved sequences that do not match any known binding motifs.