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This result is consistent with the hypothesis that when a transcription factor binding event is conserved, this conservation is a good indictor of a functional regulatory connection [23].
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A previous study comparing CTCF binding in multiple cell types had shown that a large fraction of CTCF binding events are conserved across cell types [ 40].
Interestingly, we found that only one intron 4 retention event (I4R) introducing PTCs downstream of their DNA binding domains is conserved between CCA1 and LHY homologs.
This indicates that even though the binding location of DB00631 fluctuates with different peptides, the overall binding affinity is conserved.
Furthermore, an Rbpjκ binding site is conserved on the promoters of Nrf2 among animal species.
Further analysis of this binding site reveals that the YopJ binding site is conserved in other MKKs.
All positions are not highly conserved; however the hydrophobic nature of the binding site is conserved.
The Norrin Fz4CRD binding interface is conserved between the complex structures.
Second, on HsChr4, a highly conserved CTCF-binding event is found associated with a copy of mammalian repeat MamRep564, which is shared among all placentals but appears to have arisen subsequent to the placental-marsupial split.
The binding site, M3, is conserved in 8 of them.
In the case of pdc2Δ344 the DNA-binding and transactivation site are both intact, whereas in pdc2Δ519 only the DNA-binding site is conserved.
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