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. 2022 Jun 24;13:875939. doi: 10.3389/fgene.2022.875939

TABLE 3.

Top 10 miRNA binding regions identified in TP53 and RB1 genes.

Binding regions in TP53
miRNA Site position a LogitProb b Region ΔGhybrid c ΔGtotal d Site access e Site consv f Site location g
miR-93-5p 1,166–1,174 0.864 CDS −15.900 −15.316 0.714 0.959 0.820
miR-93-5p 1,166–1,186 0.848 CDS −18.400 −18.018 0.805 0.981 0.820
let-7a-5p 1829–1850 0.835 3′UTR h −21.500 −12.736 0.631 0.001 0.357
let-7a-5p 1,161–1,177 0.831 CDS −20.100 −19.630 0.767 0.900 0.816
let-7a-5p 1,161–1,179 0.808 CDS −22.300 −21.904 0.783 0.910 0.816
miR-205-5p 1,025–1,031 0.787 CDS −17.500 −10.665 0.602 0.997 0.701
miR-22-3p 534–570 0.762 CDS i −21.100 2.9490 0.448 0.963 0.285
miR-31-5p 1,158–1,177 0.755 CDS −21.800 -16.974 0.667 0.912 0.813
miR-205-5p 835–848 0.755 CDS −23.700 -13.153 0.442 0.907 0.540
miR-223-3p 859–870 0.727 CDS −16.200 -6.7460 0.421 0.803 0.560
Binding regions in RB1
let-7a-5p 2,506–2,517 0.953 CDS i −18.100 −16.708 0.823 0.999 0.840
miR-130a-3p 2,529–2,537 0.917 CDS −17.100 −11.446 0.708 1.000 0.848
miR-31-5p 4,704–4,721 0.912 3′UTR −20.100 −17.244 0.651 1.000 0.963
let-7a-5p 4,686–4,712 0.911 3′UTR −22.100 −17.127 0.608 0.999 0.953
miR-31-5p 4,704–4,719 0.899 3′UTR −18.700 −16.076 0.627 1.000 0.963
miR-31-5p 4,704–4,717 0.898 3′UTR −17.200 −14.545 0.672 1.000 0.963
let-7a-5p 4,686–4,719 0.896 3′UTR −20.700 −14.420 0.573 1.000 0.953
miR-130a-3p 2,529–2,534 0.892 CDS −15.900 −10.778 0.646 1.000 0.848
miR-142-3p 2002–2026 0.883 CDS −18.500 −12.601 0.692 0.847 0.659
let-7a-5p 562–571 0.878 CDS −15.500 −14.118 0.846 0.957 0.142
a

Start and end position of the target region (site) predicted to be bound by miRNA.

b

Probability of the site being an miRNA binding site as predicted by our nonlinear logistic model.

c

A measure of stability for miRNA:target hybrid as computed by RNAhybrid.

d

A measure of the total energy change of the hybridization.

e

A measure of structural accessibility as computed by the average probability of a nucleotide being single-stranded (i.e., unpaired) for the nucleotides in the predicted binding site.

f

Conservation score by the PhastCons program for the binding site.

g

Relative starting location of the predicted binding site along the length of the sequence (e.g., for 3ʹ′ UTR, 0 indicates the 5ʹ′ end of the UTR, and one corresponds to the 3ʹ′ end).

h

“seed” region in 3′UTR (“seed” position: 1843–1849, binding: 8mer).

i

“seed” region in CDS (“seed” position: 564–570, binding: 8mer).