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LOC111674463 CFTR promoter region [ Homo sapiens (human) ]

Gene ID: 111674463, updated on 17-Sep-2024

Summary

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Gene symbol
LOC111674463
Gene description
CFTR promoter region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif, sequence_alteration
protein_bind
regulatory: DNase_I_hypersensitive_site, enhancer, promoter, 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
DHS-200; DHS-900; DHS-1600; DHS-3.4kb
Summary
This region represents the promoter and proximal regulatory regions of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. It includes multiple DNase I hypersensitive sites (DHSs), and enhancer, silencer and transcriptional cis-regulatory elements. An enhancer corresponding to DHS-3.4kb shows cooperative activity with the -35 kb and intron 23 CFTR enhancers. The core promoter is regulated by cyclic AMP and protein kinase A, which stimulate binding of cAMP responsive element binding protein 1 (CREB1), activating transcription factors (ATF1 and ATF2), and CCAAT/enhancer binding protein (C/EBP). Positive regulation by interleukin 1 beta (IL-1beta) is mediated by binding of nuclear factor kappa B (NF-kB). Other known transcription factors include cut like homeobox 1 (CUX1 or CDP/cut), which negatively regulates promoter activity, nuclear transcription factor Y (NF-Y), YY1 transcription factor, serum response factor (SRF), and the transcription factors SP1 and USF2 (upstream transcription factor 2), which cooperate in CFTR promoter activation. Naturally-occurring polymorphisms in this sequence may affect transcription factor binding sites and influence promoter activity. This region participates in long-range interactions with enhancers located within a larger topologically associating domain (TAD) that extends both upstream and downstream of the locus. These long-range interactions suggest complex regulation of expression of this promoter in different cell types. [provided by RefSeq, Nov 2018]
Orthologs
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Genomic context

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See LOC111674463 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (117476071..117480094)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (118791407..118795430)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (117116125..117120148)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene CFTR -35 kb upstream enhancer Neighboring gene uncharacterized LOC105375468 Neighboring gene ANKRD49 pseudogene 4 Neighboring gene DNase I hypersensitive site -20.9 kb upstream of CFTR Neighboring gene greater CFTR locus negative regulatory element NR9 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

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The promoter of the human cystic fibrosis transmembrane conductance regulator gene directing SV40 T antigen expression induces malignant proliferation of ependymal cells in transgenic mice. Perraud F, et al. Oncogene, 1992 May. PMID 1373882
  2. NF-kappa B mediates up-regulation of CFTR gene expression in Calu-3 cells by interleukin-1beta. Brouillard F, et al. J Biol Chem, 2001 Mar 23. PMID 11114294
  3. A naturally occurring sequence variation that creates a YY1 element is associated with increased cystic fibrosis transmembrane conductance regulator gene expression. Romey MC, et al. J Biol Chem, 2000 Feb 4. PMID 10652351
  4. Modulation of CFTR gene expression in HT-29 cells by extracellular hyperosmolarity. Baudouin-Legros M, et al. Am J Physiol Cell Physiol, 2000 Jan. PMID 10644511
  5. First putative sequence alterations in the minimal CFTR promoter region. Romey MC, et al. J Med Genet, 1999 Mar. PMID 10204861, Free PMC Article

See all (66) 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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Homology

Other Names

  • CFTR -3.4 kb enhancer
  • CFTR promoter-proximal regulatory region

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_056120.2 

    Range
    101..4124
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    117476071..117480094
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    118791407..118795430
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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