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Figure 5 | BMC Genomics

Figure 5

From: Duplication and positive selection among hominin-specific PRAME genes

Figure 5

Scatter plot of the lowest neutral rate estimates (either K S calculated from exon, or K I for intron, alignments) for human PRAME genes and either their human paralogues (indicated in red) or their chimpanzee orthologues (indicated in black). Circles represent averages of intronic rate (K I ) estimates, whereas squares represent averages of exonic rate (K S ) estimates. The horizontal axis represents genomic location within a 0.74 Mb region of human chromosome 1 (see Figure 1). Two recent segmental duplications (Homo_7–12 and 15–20, and Homo_19–25 and 26–32; see text) are highlighted in blue and pink, respectively. The dark line represents the median K S value (3.58 × 10-3) for human paralogues. The grey band identifies 25–75% of this median value (second and third quartiles). The blue line represents the median K S (0.011) for human-chimpanzee coding sequence [30, 31]. The exonic K S value for Homo_12 vs Homo_15 is not shown due to incongruencies in K S -derived phylogenetic trees (see text). Homo-Pan rate estimates are missing when the most-closely related sequences, that are available, are relatively divergent K I or K S > 0.1. These missing values are likely to reflect the incompleteness of the current chimpanzee genome assembly. Homo-Homo rate estimates are missing for 4 genes (Homo_1, 3, 5 and 13) which appear not to have duplicated recently (K I or K S > 0.1).

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