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Fig. 3 | Genome Biology

Fig. 3

From: Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences

Fig. 3

Conserved elements in the CHASERR lncRNA. a Human CHASERR gene structure is shown with motifs conserved in at least four species color-coded by their depth of conservation. The region of the last exon is magnified, and the motifs discussed in the text are highlighted. b Sequence logos of the sequences flanking the two most conserved motifs, with the shared AARAUGR motif shaded. c Top: mouse Chaserr locus with the positions of the primer pairs used for qRT-PCR, and the regions targeted by the GapmeRs (the same ones as used in [28]) and ASOs highlighted. Bottom: qRT-PCR with primers targeting Chaserr (shown on top) or Chd2 exons in N2a cells treated with the indicated reagents, n = 4 for ASO treatments and n = 5 for GapmeRs. d Volcano plot for comparison of MS intensities between pulldown with the WT sequence of the Chaserr last exon and the last exon where the conserved elements were mutated (Additional File 1: Fig. S3A). e qRT-PCR using primers targeting the indicated regions following IP with the indicated antibody, n = 4. Top right: Western blot using anti-DHX36 antibody on the indicated sample

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