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We found two upregulated miRNAs (Ptc-miR472 and Ptc-miRn5) that were both predicted to target putative disease resistance proteins in P. trichocarpa (Additional file 5: S5) [ 25].
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miR-125b and miR-939 were strongly induced after LPS treatment, and both were predicted to target TNF-α TNF-α
Because of the sequence homology, we also considered miR-34b* (miR-34b-5p) and miR-200a miR-200a-3p miR-200a-3p miR-200a-3palthough not predicted to target the NOTCH1 3′UTR.
The 3' sequences produced from both antisense duplexes were predicted to target Apetala2 (AP2) gene and other AP2-related genes, which are already well known targets of the miRNA172 family (Additional file 8).
To do this, we first identified expressed miRNAs predicted to target both a pseudogene and its parent gene.
Moreover, these miRNAs are predicted to target both KIT and ETV1, which are key factors in GIST oncogenesis.
In agreement with these findings, we also observed downregulation of miR-324-5p miR-324-5p miR-324-5ppredicted to target both E-cellular and N-cadherin expression [ 11].
MiR-4732-3p was predicted to target both SMAD2 and SMAD4 [ 11], components of the TGF-β pathway instrumental in fine-tuning proliferation for efficient erythropoiesis [ 12].
The Type III cas system contains more than one type of cas gene operon belonging to either Type I or II or the repeat-associated mysterious proteins (RAMP) module operon and are predicted to target both DNA and RNA [ 53].
Eight miRNAs had 222 predicted targets in common; for example, mir-29b was predicted to target 196 of these.
154/223 miRNAs are predicted to target at least one gene while 69/223 have no predicted targets.
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