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LOC113604967 DNase I hypersensitive site 83.7 kb downstream of CFTR [ Homo sapiens (human) ]

Gene ID: 113604967, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113604967
Gene description
DNase I hypersensitive site 83.7 kb downstream of CFTR
Gene type
biological region
Feature type(s)
misc_feature: conserved_region
regulatory: DNase_I_hypersensitive_site
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+83.7kb
Summary
This genomic region, which is located approximately 83 kb from the 3' end of the CFTR (cystic fibrosis transmembrane conductance regulator) gene, and is also within an intron of the CTTNBP2 (cortactin binding protein 2) gene, represents a DNase I hypersensitive site, DHS+83.7kb. This region associates with the transcription factor CTCF, and also with the cohesin components RAD21 and SMC1, where occupancy by those factors requires CTCF presence. A sub-region, CR26, was also identified as a conserved region and putative negative regulatory element, though it did not function as a silencer or an enhancer-blocking element when assayed in transfected K562, HeLa or 293T cells. This region may play a structural role in the active CFTR locus, and it can form minor looping interactions with the -80.1 kb and +48.9 kb CFTR regulatory regions. [provided by RefSeq, Nov 2018]
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Genomic context

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See LOC113604967 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (117750516..117751175)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (119066262..119066921)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (117390570..117391229)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene CF transmembrane conductance regulator Neighboring gene greater CFTR locus negative regulatory element CR20 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 antisense RNA 1 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 ReSE screen-validated silencer GRCh37_chr7:117372591-117372808 Neighboring gene greater CFTR locus negative regulatory element NR12 Neighboring gene cortactin binding protein 2 Neighboring gene greater CFTR locus negative regulatory element CR27 Neighboring gene greater CFTR locus negative regulatory element NR13 Neighboring gene greater CFTR locus negative regulatory element CR28 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:117449968-117450716 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:117450717-117451463 Neighboring gene greater CFTR locus negative regulatory element NR14 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:117499510-117499710 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:117590690-117591889 Neighboring gene greater CFTR locus negative regulatory element NR19 Neighboring gene uncharacterized LOC105375470 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:117830912-117831127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26548 Neighboring gene LSM8 homolog, U6 small nuclear RNA associated

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus. Gosalia N, et al. Nucleic Acids Res, 2014 Sep. PMID 25081205, Free PMC Article
  2. Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Yang R, et al. Nucleic Acids Res, 2016 Apr 20. PMID 26673704, Free PMC Article
  3. A transcription factor network represses CFTR gene expression in airway epithelial cells. Mutolo MJ, et al. Biochem J, 2018 Apr 16. PMID 29572268, Free PMC Article
  4. Screening for Regulatory Variants in 460 kb Encompassing the CFTR Locus in Cystic Fibrosis Patients. Kerschner JL, et al. J Mol Diagn, 2019 Jan. PMID 30296588, Free PMC Article
  5. Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus. Petrykowska HM, et al. Genome Res, 2008 Aug. PMID 18436892, Free PMC Article

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • CFTR locus CTCF site V
  • greater CFTR locus conserved region CR26

NCBI Reference Sequences (RefSeq)

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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_062445.1 

    Range
    101..760
    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
    117750516..117751175
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    119066262..119066921
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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