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The consensus sequence recognized by PPAR/RXR heterodimers, contains an imperfect direct repeat of two nuclear receptor binding motifs separated by a single nucleotide.
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A typical CCCH protein usually contains two tandem CCCH-type zinc-binding motifs separated by 18 amino acids [14].
The superfamily is characterized by two CxxC motifs separated by approximately 17 amino acid residues.
The small Cu+ binding motifs are separated by a flexible linker and bridge the FRET pair Cerulean (donor) and Citrine (acceptor).
The active form of HNF4α is a homodimer which recognizes a direct repeat (DR) of the AGGTCA motif separated by 1 nucleotide (DR1) as a binding site.
In this study, we identified the PhoP-binding consensus sequence as a direct repeat of a 7 bp motif separated by a 4 bp spacer by using a method of systematic evolution of ligands by exponential enrichment (SELEX).
With a selected cutoff for sequence similarity, all the binding motifs were separated into several groups.
Many simple motif extraction algorithms have been proposed primarily for extracting the transcription factor binding sites, where each motif consists of a unique binding site [ 4- 10] or two binding sites separated by a fixed number of gaps [ 11- 13].
These sites are designated binding motif 1 (BM1), and binding motif 2 (BM2), and are separated by between 11 32 amino acids in Arabidopsis [ 8].
The TAP-tag consists of Protein A and a calmodulin-binding peptide separated by the recognition motif for the TEV (tobacco etch virus) protease.
Significant synergistic transcriptional factors in down-regulated genes from Day 1 to Day 2. The Motif column shows the consensus binding site sequence for the transcriptional factor where two motifs are separated by an underscore.
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