U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC111674466 DNase I hypersensitive site -20.9 kb upstream of CFTR [ Homo sapiens (human) ]

Gene ID: 111674466, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC111674466
Gene description
DNase I hypersensitive site -20.9 kb upstream of CFTR
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
protein_bind
regulatory: DNase_I_hypersensitive_site, enhancer_blocking_element, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DHS-20.5kb; DHS-20.9kb
Summary
This genomic region represents a DNase I hypersensitive site, DHS-20.9kb, located approximately 20 kb upstream of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. It contains enhancer-blocking elements that bind the CCCTC-binding factor (CTCF) and POU class 2 homeobox 1 (Pou2f1/Oct1) transcription factor. It also associates with the cohesin complex subunit Rad21, and with the transcription factors FOXA1/A2 and HNF1, where recruitment of HNF1 requires FOXA factor presence. This region is a structural element involved in active locus 3D structure, where it can physically interact with the CFTR promoter and other CFTR regulatory elements, including the intron 19 and +48.9 kb elements, and those interactions depend on CTCF and Rad21 presence. Deletion of this region by CRISPR/Cas9 editing results in a redistribution of architectural proteins at other CFTR regulatory sites, mainly at the -80.9 kb, intron 1 and +48.9 kb sites, whereby an active locus 3D structure is maintained. [provided by RefSeq, Nov 2018]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (117458800..117459399)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (118774134..118774733)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (117098854..117099453)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene greater CFTR locus negative regulatory element CR18 Neighboring gene DNase I hypersensitive site -80 kb upstream of CFTR Neighboring gene ankyrin repeat, SAM and basic leucine zipper domain containing 1 Neighboring gene CFTR -44 kb upstream enhancer Neighboring gene CFTR -35 kb upstream enhancer Neighboring gene uncharacterized LOC105375468 Neighboring gene ANKRD49 pseudogene 4 Neighboring gene greater CFTR locus negative regulatory element NR9 Neighboring gene CFTR promoter region Neighboring gene CFTR intron 1 enhancer Neighboring gene CFTR intron 2 DNase I hypersensitive site Neighboring gene CFTR intron 3 DNase I hypersensitive site Neighboring gene CF transmembrane conductance regulator Neighboring gene greater CFTR locus negative regulatory element CR19 Neighboring gene greater CFTR locus negative regulatory element CR20 Neighboring gene CFTR antisense RNA 1 Neighboring gene DNase I hypersensitive sites in intron 10ab of CFTR Neighboring gene DNase I hypersensitive site in intron 10c of CFTR Neighboring gene CFTR intron 11 enhancer Neighboring gene DNase I hypersensitive sites in introns 16 and 17a of CFTR Neighboring gene CFTR intron 18a DNase I hypersensitive site Neighboring gene DNase I hypersensitive site in intron 18 of CFTR Neighboring gene CFTR intron 18b DNase I hypersensitive site Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:117270281-117271480 Neighboring gene CFTR intron 19 DNase I hypersensitive site Neighboring gene CFTR intron 20 enhancer Neighboring gene CFTR intron 21 enhancer Neighboring gene CFTR intron 23 enhancer Neighboring gene DNase I hypersensitive region 5.4 to 7.4 kb downstream of CFTR Neighboring gene DNase I hypersensitive region 15.6 kb downstream of CFTR Neighboring gene CFTR +21.5 kb DNase I hypersensitive site Neighboring gene CFTR +36.6 kb downstream enhancer Neighboring gene greater CFTR locus negative regulatory element NR11 Neighboring gene CTTNBP2 intron enhancer-blocking element 7-1-1 Neighboring gene uncharacterized LOC105375469 Neighboring gene cortactin binding protein 2

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. The sheep genome contributes to localization of control elements in a human gene with complex regulatory mechanisms. Mouchel N, et al. Genomics, 2001 Aug. PMID 11549312
  2. Analysis of a DNase I hypersensitive site located -20.9 kb upstream of the CFTR gene. Nuthall HN, et al. Eur J Biochem, 1999 Dec. PMID 10561583
  3. In vivo analysis of DNase I hypersensitive sites in the human CFTR gene. Moulin DS, et al. Mol Med, 1999 Apr. PMID 10448643, Free PMC Article
  4. Characterization of DNASE I hypersensitive sites in the 120kb 5' to the CFTR gene. Smith AN, et al. Biochem Biophys Res Commun, 1995 Jun 6. PMID 7540005
  5. The role of CTCF in coordinating the expression of single gene loci. Gillen AE, et al. Biochem Cell Biol, 2011 Oct. PMID 21916612

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • -20.9 kb CFTR enhancer-blocking element
  • CFTR looping element II

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_056123.2 

    Range
    101..700
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    117458800..117459399
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    118774134..118774733
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases
Research Materials