Both investigations revealed a highly conserved miRNA binding site and strong evolutionary selection on miRNA binding sites in rice.
Most data points lie above the diagonal line, indicating that the association between protein binding sites and breakpoints is stronger far from genes than near genes (p = 3.43⋅10-98).
Here, we test if there are differences between conservation-based methods and PWM scanning on weak and strong binding sites and find the difference in performance to be greater on the stronger binding sites.
The hst-3.2 (tm3006 ) deletion allele results in a protein that lacks more than two thirds of the sulfotransferase domain, including part of the 3′-PAPS (phosphoadenosyl-phosphosulfate) and the substrate binding sites and is a predicted strong loss of function allele.
For example, the presence of binding sites and active sites imposes a strong constraint on the variability of sequences that is difficult to separate from the purely structural one.
To investigate whether recombination, another neutral evolutionary force, plays any role in the observed correlations, we simulated recombination using two methods, namely between genes and between binding sites, and found that neither had strong effect on the accumulation of TFBS (Additional file 1).
Phylogibbs predicts strong Mad binding sites and few Brk binding sites in the proximal constructs.
At three levels of gene organization--amino acids, promoter Su(H) binding sites, and 3' UTR domains--there is strong conservation among the orthologs from different species but little hierarchical signal among the paralogous copies.
These include basement membrane formation of hemidesmosomes and laminin-binding sites and a strong polarity [ 18- 21].
We examined the variation in sequences of binding sites and have been able to show good conservation of strong binding sites among the organisms we have investigated.
