Interestingly, the third TFBS following the conservation ranking corresponds to ADF1, which was located within the 5′UTR and is known to bind the same motifs recognized by the E2F1 factor in mice (Hsiao et al., 1994) Despite these results, we cannot discard the possibility that exons are wrongly predicted as promoters in certain situations.
The Foxg1 consensus-binding site is very similar to the Foxa2-binding motif (Additional file 5: Figure S2b), and likely to bind to the same motif [ 56].
Ciolkowski et al. [ 58] reported that Arabidopsis AtWRKY6 and AtWRKY11 bind well to W-boxes that have a G residue directly 5' adjacent to the element, whereas AtWRKY26, AtWRKY38, and AtWRKY43 bind to the same motif if the 5'-residue is a T, C, or A. Furthermore, bacterial challenge changed the binding intensity of proteins to W-boxes [ 9].
Being denied access to the preferred methylated motif, Kaiso instead binds to the same motif in its unmethylated state.
Two regulatory links from two different genomes tend to be similar if the two TFs from these links bind to the same motifs in the TGs, implying that these TFs might regulate the TGs in a similar way.
A critical question is whether Aplip1 also binds to BRP with the same motif as it uses to bind to RBP.
Since NFAT and NF-κB proteins contact identical nucleotides, it is unlikely that both factors can bind at the same time to the same motif.
This HXN (His 124-X-Asn 126) sequence is the same motif that binds l-serine in the ACT domain of E. coli d-phosphoglycerate dehydrogenase (His 344-X-Asn 346).
The same motif was shown to bind exclusively to the Sho1 SH3 domain in yeast, but to multiple non-yeast SH3 domains, indicating that evolution has tweaked the motif-domain interface to reduce deleterious promiscuous binding to other co-localised SH3 domains in the yeast proteome [ 53].
For good measure, the artist adds an oil painting with the same motif.
