Figure 3

Example of the "CONDOR View" graphical browser for CNEs in the vicinity of the SOX21 gene in Fugu. Letters indicate the following features. (A) Title bar shows the reference trans-dev gene and the current baseline organism. (B) Option allowing users to change the baseline organism co-ordinate system to which CNEs are mapped on the graphic. (C) Clickable graphic/image map representing all CNEs across the baseline sequence. Top bar represents the length of the sequence in kilobases (here ~66 Kb). The CDS track shows gene structures (exons indicated as red boxes) with the end arrow indicating the strand direction of the gene. The four organism tracks represent the organism sequences used in the initial MLAGAN/SLAGAN alignments. CNEs are positioned according to the baseline co-ordinate system and drawn as boxes with lengths relative to their size in bps. CNEs are 'bumped' onto lower lines if located too close to another CNE for them to be differentiated on a single line. While all CNEs are mapped to the baseline sequence, boxes are drawn in the other organisms if they are conserved to that CNE in the MLAGAN alignment. Moving the mouse over a specific CNE in one of the organism tracks brings up summary data on that CNE in a table below the browser (E). If the CNE has functional annotation (as shown) a composite schematic of GFP expression is displayed underneath. Clicking on the image map opens up a new web page with detailed information on the CNE. (D) Users can zoom in or out of the image map to get a clearer view of specific sets of CNEs (useful in larger regions).