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LOC111674473 DNase I hypersensitive sites in intron 10ab of CFTR [ Homo sapiens (human) ]

Gene ID: 111674473, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111674473
Gene description
DNase I hypersensitive sites in intron 10ab of CFTR
Gene type
biological region
Feature type(s)
protein_bind
regulatory: DNase_I_hypersensitive_site, enhancer_blocking_element, silencer, 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
DHS10a; DHS10b; DHS10ab
Summary
This record represents a DNase I hypersensitive region located in an intron of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. It includes two closely located DNase I hypersensitive sites (DHS10a and DHS10b), where hypersensitivity is increased following forskolin activation of CFTR transcription, and is dependent on FOXA1/A2 transcription factor association. Each DHS can bind to the HNF1alpha transcription factor. This region was shown to interact physically with the CFTR promoter. A conserved sub-region, CR21, was shown to function as both a silencer and an enhancer-blocking element in transfected K562 cells. It strongly repressed a gamma-globin promoter coupled to the HS2 beta-globin enhancer, and also modestly repressed an SV40 promoter coupled to the HS2 enhancer, when present in the forward orientation in the reporter construct. The CR21 sub-region could also modestly block HS2 enhancer activation of the SV40 promoter when located between the enhancer and promoter in the reverse orientation in the reporter construct. Two CT-motifs that are present in the CR21 element were shown to contribute to its silencing function. Another sub-region that spans these DHSs could also weakly repress a basal CFTR promoter in reporter assays in transfected Caco2 and MCF-7 cells. In addition, a different sub-region was shown to augment activity of the DHS11 enhancer element located in a downstream CFTR intron in transfected Caco2 cells. [provided by RefSeq, Sep 2018]
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Genomic context

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Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (117572048..117573728)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (118887398..118889078)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (117212102..117213782)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375468 Neighboring gene DNase I hypersensitive site -20.9 kb upstream of CFTR 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 greater CFTR locus negative regulatory element CR19 Neighboring gene CF transmembrane conductance regulator Neighboring gene greater CFTR locus negative regulatory element CR20 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 DNase I hypersensitive site 83.7 kb downstream of CFTR 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

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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 intron 10(ab) DNase I hypersensitive sites
  • greater CFTR locus negative regulatory element CR21
  • greater CFTR locus silencer and enhancer-blocking element CR21

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_056129.2 

    Range
    101..1781
    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
    117572048..117573728
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    118887398..118889078
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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