Figure 1

Promoter subfamily homology in V1R gene blocks. A. PipMaker plots [26] of V1R gene blocks showing a representative example from each promoter subfamily (subfamily is denoted in the gene name; for example, V1r b 8 is a representative from the B subfamily). Each gene block shown was extracted from percent-identity-plots (PIPs) of self alignments of V1R loci (50–100% identity on vertical axis). Thus, the blocks shown exhibit homology at each position in the block to other V1R genes of the same promoter subfamily (i.e., at a particular position, multiple plots that cross that position indicate that multiple V1Rs in the promoter subfamily are homologous at that position). Homology to the upstream (orange), coding (red), and downstream (yellow) regions is indicated by shading. B. Gene block conservation scores are shown for the same representative set of V1R blocks shown in A. For each position in a gene block, the conservation score is a value between 0 and 1 (see Methods for definition of conservation scores). Coding regions (red), conservation peaks (green), and other regions of the block (blue) are shaded. Dark yellow background shading represents mean block conservation in non-repeat upstream block sequences; the light yellow band represents 0.5 standard deviations above the mean conservation score value. Grey stripes denote RepeatMasked positions. In both panels, homology to transcription start sites (TSS's) for each block is highlighted purple; for the V1rj2 block, an empirically determined TSS (pink), as well as homology to the TSS for V1rk1 (purple), are shown. Homologous TSS positions are derived from alignments of promoter subfamilies (see Methods). Each horizontal tick mark represents 1 kb.