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For the transcription factors Msn2/4 and Hac1 neither ScanProsite nor MEME provided useful results, since the binding motifs are very short.
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AP-1 motifs are very often found near binding sites for many types of TFs, including ERα, and AP-1 has been considered by some as a "general" enhancer binding factor [ 18].
We note, however, that transcription factor binding motifs are usually very short and, hence, transcription factor binding look-alike sequences may arise in the genome by chance.
The ion binding motifs are shown.
In Fig. 1D the different binding motifs are illustrated.
The primary sequences of this secondary structure motif are very different, only several nucleotides in the loop and bulge area are critical for binding and other nucleotides are variable.
Characterizing transcription factor binding motifs is a common bioinformatics task.
The binding motifs were obtained from Gene Regulation and PlantCARE [ 63].
DNA binding motifs were predicted by PlantCARE [ 60].
HLA-B58 and HLA-B63 have binding motifs that are very similar to HLA-B57 and are also associated with good immune control of HIV-1 [11] [11].
The residues comprising the conserved iron-binding motifs are indicated with blue arrow and labelled.
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