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LOC113664106 CFTR intron 2 DNase I hypersensitive site [ Homo sapiens (human) ]

Gene ID: 113664106, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113664106
Gene description
CFTR intron 2 DNase I hypersensitive site
Gene type
biological region
Feature type(s)
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
DHS2
Summary
This genomic region represents a DNase I hypersensitive site, DHS2 or 296 + 4.4 kb (intron 2) DHS, located in an intron of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. This DHS is cell-type-restricted and has been observed in Caco2 colon carcinoma cells and MCF7 breast epithelial cells. This region may form looping interactions with the CFTR promoter within a larger topologically associating domain (TAD) that extends both upstream and downstream of the locus. [provided by RefSeq, Nov 2018]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (117508463..117509063)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (118823794..118824394)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (117148517..117149117)

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 promoter region Neighboring gene CFTR intron 1 enhancer 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 CFTR gene and regulation of its expression. McCarthy VA, et al. Pediatr Pulmonol, 2005 Jul. PMID 15806593
  2. Genomic approaches for the discovery of CFTR regulatory elements. Ott CJ, et al. Transcription, 2011 Jan-Feb. PMID 21326906, Free PMC Article
  3. 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
  4. Multiple potential intragenic regulatory elements in the CFTR gene. Smith DJ, et al. Genomics, 2000 Feb 15. PMID 10708521
  5. Evaluation of potential regulatory elements identified as DNase I hypersensitive sites in the CFTR gene. Phylactides M, et al. Eur J Biochem, 2002 Jan. PMID 11856314

See all (8) 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

  • 296 + 4.4 kb CFTR DNase I hypersensitive site

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_062452.1 

    Range
    101..701
    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
    117508463..117509063
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    118823794..118824394
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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