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Here, we identified region II IV as the binding site for human BiP-luminal domain protein interaction.
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To analyze DEGs, we assembled a dictionary of binding sites for human TFs and unconventional DNA-binding proteins (uDBPs) [33].
DNA methylation presents distinct binding sites for human transcription factors.
Known binding sites for human TFs were parsed from several public databases in January 2006.
It is possible that the observations are an artifact and the identified putative transcription factor binding sites are not real binding sites for human genes.
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Some of the conserved ELMs, like the SH3 ligand sites on NEF, have been experimentally verified as binding sites for human proteins [ 28].
As another example, if a user is interested in the mRNA binding sites for human phosphatase and tensin homolog (PTEN), the user enters or selects " PTEN" in the search box for humans in the "binding target search" module.
Sequences containing binding sites for human Sp1 (mostly footprints), were obtained from the TRANSFAC database (July 2007 release), mapped on the human genome, extracted with genome flanking sequences, and realigned using the SeSiMCMC Gibbs sampler [ 55] (see Additional file 6 for details).
We determined that rs5848 is located in the 3′-UTR of GRN within a predicted binding site for the human specific miRNA miR-659.
The rs5848 single base change (c.*78C>T) is located 78 nucleotides downstream of the translation termination codon in the 3′-UTR of the GRN transcript in a predicted binding site for the human specific miRNA miR-659 (Supplementary Material, Table S4).
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