Interpro domains) among genes differentially expressed in females in at least one of the six planned contrasts. (PDF) Table S19 Ability to detect significant differences between flies carrying the ultraconserved region CG15121–CG1689 in its disrupted or intact form across some of the experiments performed. (PDF) Table S20 Number of tRNA, rRNA, and snoRNA genes in the ultraconserved region CG15121–CG16894 with potential to mediate NAHR events. (PDF) References 1. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, et al. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316: 1484–1488. 2. Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, et al. (2010) The developmental transcriptome of Drosophila melanogaster. Nature. 3. Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, et al. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787–1797. 4. 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