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All the members of this superfamily have conserved nucleotide, phosphate and magnesium binding sequences but the Rab sequences can be distinguish by their C-terminal prenylation site and five Rab-specific regions (RabF) [ 53].
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This new set no longer corresponds to the original ChIP identified binding sequences, but shares the same nucleotide frequencies and therefore can be used as a negative control set.
When the positions of the bipartite motifs within the binding sequences are depicted, the motifs are usually located in the middle of the binding sequences, but some are not centrally located in the long binding sequences (Fig. 4C, Supplementary Table S3).
De novo motif analysis identified DR4-type REs as the most highly enriched binding sequence, but only 6.3% of the LXR peaks contained such a DR4-type RE.
a, c, e The consensus binding sequences according to the binding intensities observed on the Q9 protein-binding microarray.
Furthermore, the miR-10a binding sequences in the BCL6 3′-UTR were highly conserved across species.
Moreover, the miR-203 binding sequences in the Slug 3′-UTR are highly conserved across species.
Furthermore, two of the three miR-29b binding sequences in the CDK6 3′-UTR are highly conserved across species.
Furthermore, the miR-495 binding sequences in the 3′-UTR of JAM-A mRNA are highly conserved across species.
We chose the other sites based on potential SOX9 binding sequences within the peaks of hybridization.
To obtain a large number of binding sequences, we concatenated the selected binding sequences to increase the sequencing throughput following [ 19].
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