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Although one might predict that genes containing multiple binding sites would show a higher degree of correlation to Oct4, a very cursory analysis of the data reveals that this is in fact not the case.
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The binding sites would not only reveal mRNA targets but would show GQ motif consensus if that's really the in vivo binding site for Aven.
As previously demonstrated for H. armigera, Cry2Ab binding sites in H. punctigera were shown to be shared by Cry2Ae, which explains why an alteration of the shared binding site would lead to cross-resistance between the two Cry2A toxins.
A protein binding site would be an attractive hypothesis.
A defined consensus sequence for the AtoC binding site would greatly facilitate the identification of potential AtoC binding elements.
Using the same amplifying strategy as before the H2-binding site would also be present offering a second binding site.
Adenine, with its two metal binding sites, should show the best affinity, whereas thymine, with no strong metal binding sites, should show little or no affinity.
Perhaps a more plausible cap-binding site would be located in the conserved Ago 5' guide RNA binding pocket.
Before reporting and discussing evolutionary hypotheses based on predicted transcription factor binding sites, we would like to show that these predictions are not random, despite the high rate of incorrect predictions.
The 3D patterns corresponding to the quercetin binding sites are shown in green.
Weak binding sites were shown to contribute significantly to TF binding [23], [34], making a binary demarcation of sites and non-sites more problematic.
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