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Furthermore, additional polyadenylation signals may produce transcript isoforms with several combinations of miRNA binding sites, which adds even more complexity [ 39].
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The PACAP specific binding sites which were not shared VIP were termed type I, while the binding sites shared with both PACAP and VIP were termed Type II.
To generate a list of unambiguous CTCF negative RAD21 binding sites we removed these sites, leaving 667 reassessed CTCF independent RAD21 binding sites, which we define as motif and CTCF-independent RAD21 binding sites (MCIB).
This transcription factor binding site search identified multiple putative krüppel-like transcription factor binding sites which are indicated in Figure 5A.
Furthermore, we showed that our model performed better on predicting multiple TF binding sites than single TF binding sites, which fits well to the cis-module concept.
The sequence of this binding site does not resemble any known ATP binding sites, which have much higher binding affinities.
Sum1 binds a DNA binding site which resembles, and partly overlaps, the binding site of Ndt80 [ 23], [ 18].
At present, we filter HT-generated data and only add, for instance ChIP sites that have an identified binding site which occurs within the expected upstream regions close to promoters.
An added incentive for these studies was provided by the observation that the IL-6 gene promoter contains an NF-κB binding site which plays a major role in regulating LPS-induced IL-6 transcription [ 55- 57].
Among many other binding sites lost in the –673 construct were an E-box, a STAT binding site which forms a sequence model (Genomatix modelInspector) together with an ets binding site, and a Myc associated zinc finger binding site (MAZF).
There exist two Cys and one Met residues on protein binding site, which are potential stabilizing residues of peptide binding.
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