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Nucleic Acids Res. 2013 Jan;41(Database issue):D188-94. doi: 10.1093/nar/gks1165. Epub 2012 Nov 27.

CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization.

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Department of Microbiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA.


CTCF is a highly conserved transcriptional regulator protein that performs diverse functions such as regulating gene expression and organizing the 3D structure of the genome. Here, we describe recent updates to a database of CTCF-binding sites, CTCFBSDB (, which now contains almost 15 million CTCF-binding sequences in 10 species. Since the original publication of the database, studies of the 3D structure of the genome, such as those provided by Hi-C experiments, have suggested that CTCF plays an important role in mediating intra- and inter-chromosomal interactions. To reflect this important progress, we have integrated CTCF-binding sites with genomic topological domains defined using Hi-C data. Additionally, the updated database includes new features enabled by new CTCF-binding site data, including binding site occupancy and the ability to visualize overlapping CTCF-binding sites determined in separate experiments.

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