Figure 2.

Pipmaker [61] dot plot of Abp-containing regions for the mm2 and mm8 assemblies of the mouse (C57BL6/J) genome sequence. Transposable element sequences have been masked in order to emphasize this region's coding sequences. Two grey shaded regions represent gaps in the earlier mm2 assembly. The second of these can be now seen, in mm8, to harbour a large number of Abp genes that were absent from mm2. Predicted genes and pseudogenes are indicated as filled and unfilled triangles, respectively. Abpa paralogues are shown in blue and Abpbg paralogues are shown in red. The original paralogues described by Emes et al. [8] are faded while the new paralogues we describe here are in bright colors. Ribosomal protein L23a pseudogenes on the forward and reverse strands are shown as '+' and '-' symbols, respectively, and are numbered at bottom. The five Mus musculus Abpa clades, each predicted to have originated from a single gene in the last common ancestor with Mus pahari, are indicated by rectangles out-lined in black on the bar beneath the paralogue symbols. Each of the five rectangles is annotated with the Abpa-Abpbg gene pairs (namely 1–2, 3–23, 24, 25, and 26–27) that arose from these single common ancestors and, where appropriate, the identity line in the pip plot is also shaded the appropriate color. More recent, Mus lineage-specific, duplications are represented by smaller colored rectangles embedded within the outlined rectangles.