TABLE 1.
Predicted binding sites of various microRNAs on PLD mRNA are conserved among species and are energetically favorable
The bold font represents 100% conservation of the PLD mRNA nucleotide sequence. miRNA sequences listed are the seed sequence of each miRNA, which represents the miRNA region that associates with mRNA. Species conservation information was taken from TargetScanHuman. ΔG values were calculated for the human binding pair of the miRNA seed sequence and corresponding PLD mRNA sequence using mform web server software (The RNA Institute, University at Albany). mirSVR scores are as reported in the miRanda-mirSVR database. A negative score denotes a favorable match with scores <−1.0 representing the top 7% of predictions. Data for miR-3619–5p were not yet available on miRanda-mirSVR at time of publication. Weighted context ++ scores were obtained from TargetScanHuman based on the algorithm described in Agarwal et al. (23). Again, a negative score denotes a favorable reaction with greater magnitude indicating higher favorability.
| Species | miR-182 | miR-203 | miR-887 | miR-3619 |
|---|---|---|---|---|
| 3′- … AGAUGGUAACGGUU | 3′- … GUAAAGU | 3′- … GGCAAGUG | 3′- … GGACGACU 3′- … GGACGACU | |
| Human | 5′- … UCUAGG--UUGCCAA … | 5′- … CAUUUCA … | 5′- … CCGUUCAA … | 5′- … 227CCUGCUGC … 5′- … 501CCUGCUGA … |
| Chimp | 5′- … UCUAGG--UUGCCAA … | 5′- … CAUUUCA … | 5′- … CCGUUCAA … | 5′- … 227CCUGCUGC … 5′- … 501CCUGCUGA … |
| Mouse | 5′- … UCCAUACAAGUUGCCAA … | 5′- … CAUUUCA … | 5′- … UGGUUCAU … | 5′- … 227CCUGUCAC … 5′- … 501CCUGCUGA … |
| Rat | 5′ … UCCGGG--UUGCCAAA … | 5′- … CAUUUCA … | 5′- … CGGUUCAC … | 5′- … 227CUUGUCAC … 5′- … 501CCUGCUGA … |
| Pig | 5′- … UCUACA--UUGCCAAA … | 5′- … CAAGCGUUUCA … | 5′- … CAGUUCAA … | 5′- … 227CUCGAUGGAUGC 5′- … 501GCUGCUAC … |
| ΔG (human) | −13.60 | −11.70 | −13.40 | −13.30–19.00 |
| mirSVR score | −0.4703 | −1.2145 | −1.3069 | Not available |
| Weighted context ++ score | −0.07 | −0.08 | −0.66 | −0.08–0.27 |