Figure 1.

Sequence similarity between Drosophila melanogaster (D. mel) and D. pseudoobscura (D. pse) for the Sox21b (CG32139) gene. Top panel: sliding-window BLAST profile. We stepped through D. melanogaster Sox21b gene in 15 bp increments, and at each position BLASTed a 31 bp segment against the D. pseudoobscura ortholog. Each line represents a BLAST hit with a score above 45, the endpoints show the position of the hit in each genome, and the color of the line represents the orientation of the hit (black = same sequence orientation in each genome, red = different orientations in each genome). Central panel: structure of the Sox21b gene in D. melanogaster. Filled boxes represent exons, and open boxes represent untranslated regions (UTRs). Bottom panel: VISTA plot. The appropriate region of the D. melanogaster-D. pseudoobscura genome alignment was downloaded from the VISTA Browser [44]. We stepped through the alignment in 5 bp increments, and for each 501 bp window calculated the percentage of identical nucleotides between the sequences. The plot is shown relative to the D. melanogaster sequence, and represents a smoothed curve through the data using the ksmooth function in the statistical programming language R [49]. Areas under the curve are painted if they show >70% nucleotide conservation (dark blue = within an exon, light blue = within a UTR, pink = intronic and >100 bp in size).