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. Author manuscript; available in PMC: 2010 Nov 15.
Published in final edited form as: Nature. 2008 Apr 10;453(7194):534–538. doi: 10.1038/nature06904

Figure 2. Gene–pseudogene interactions produce endogenous siRNAs.

Figure 2

a, Endo-siRNAs unambiguously mapped to the functional Ppp4r1 mRNA are plotted in blue, above the mRNA (individual exons indicated as thick arrows). The extent of the open reading frame (ORF) is indicated. Endo-siRNAs from the Ppp4r1 pseudogene are shown in red below the pseudogene. Arrows indicate two segments of Ppp4r1 homology. siRNAs plotted above each line are sense oriented, with respect to the functional mRNA, and those below are antisense. Shown below is an enlargement of one section of the mRNA with individual antisense siRNAs aligned. A dash indicates a match; an asterisk indicates a mismatch. The heights of the bars indicate the number of siRNAs starting at each position. b, Endogenous siRNAs homologous to Ran-GAP are shown below a schematic of the genomic inverted repeat structure from which they arise (the ~800-base loop is not depicted). Those shown above and below the x axis come from the upper or lower arm of the hairpin, respectively. No siRNAs were sequenced from the ~800-base loop that separates the two stem arms. c, siRNAs antisense to Ppp4r1 counted and plotted by the number of mismatches to the functional mRNA.