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These transcription factors are compiled in Tables 1 and 2. Complete lists of significantly overrepresented transcription factor binding sites are provided in the supplementary Table S1.
The binding sites are provided in the TRANSFAC database [ 2].
Structural and functional information on mechanisms of interaction between TFs and their binding sites are provided by experimental techniques, which are costly and time-consuming.
Information concerning the putative binding sites are provided in Additional file 6. MiRs can regulate many target genes and modulate multiple pathways at the same time.
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For small clusters of high sequence similarity and single strains, up to 8 times more discriminating binding sites were provided by the 23S rRNA.
No input files corresponding to RNAMotif search results or to promoter/transcription binding sites were provided to sRNAPredict.
Direct evidence for the potent signalling and targeting function of the CIN85 binding sites is provided by the ability of the T-cell adaptor SLP76 to respond to BCR activation when equipped with the PXXXPR motifs.
For each full-length LTR retrotransposon, superfamily, putative lineage, overall length, identity percentage between both LTR sequences, target site duplication (TSD), polypurine tract (PPT) and tRNA binding site are provided, as well as the sequences of the element and of its LTRs.
Further support for the proposed binding site was provided by MD simulations with the R-enantiomer of AR-C155858 which is more than two orders of magnitude less potent at inhibiting MCT1 in the Jurkat cell line (AstraZeneca, unpublished data).
One way to circumvent this problem has been implemented with antibody systems, where contribution to the binding site is provided by two different polypeptides (light and heavy chains).
AFL has a higher preference toward long-chain substrates whose binding site is provided by a hydrophobic tunnel in the C-terminal domain.
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