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LOC108491823 CTTNBP2 intron enhancer-blocking element 7-1-1 [ Homo sapiens (human) ]

Gene ID: 108491823, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108491823
Gene description
CTTNBP2 intron enhancer-blocking element 7-1-1
Gene type
biological region
Feature type(s)
regulatory: DNase_I_hypersensitive_site, enhancer_blocking_element
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+48.9kb
Summary
This genomic region is located in an intron of the CTTNBP2 (cortactin binding protein 2) gene on chromosome 7, and is also located approximately 48 kb from the 3' end of the CFTR (cystic fibrosis transmembrane conductance regulator) gene. It was identified as a putative enhancer-blocking chromatin insulator based on CTCF association and DNase I hypersensitivity in multiple cell types by ChIP-seq and genome-wide chromatin accessibility assays. A DNase I hypersensitive site, DHS+48.9kb, was also detected by the DNase-chip procedure. This region was validated as a functional enhancer-blocking element based on its ability to block activation of a gamma-globin promoter by the beta-globin HS2 enhancer when positioned between the enhancer and promoter in a lentiviral reporter assay in K562 erythroleukemia cells. This region has also been shown to associate with Rad21, a cohesin complex subunit that is known to interact with CTCF, and it can form looping interactions with the CFTR promoter and the -80.1 kb and -20.9 kb CFTR regulatory elements. [provided by RefSeq, Oct 2018]
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Genomic context

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See LOC108491823 in Genome Data Viewer
Location:
7q31
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (117715346..117716425)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (119030737..119031823)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (117355400..117356479)

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 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 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 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. Identification and characterization of enhancer-blocking insulators to reduce retroviral vector genotoxicity. Groth AC, et al. PLoS One, 2013. PMID 24098520, Free PMC Article
  2. Widespread plasticity in CTCF occupancy linked to DNA methylation. Wang H, et al. Genome Res, 2012 Sep. PMID 22955980, 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. Perinuclear positioning of the inactive human cystic fibrosis gene depends on CTCF, A-type lamins and an active histone deacetylase. Muck JS, et al. J Cell Biochem, 2012 Aug. PMID 22422629
  5. Chromatin Dynamics in the Regulation of CFTR Expression. Gosalia N, et al. Genes (Basel), 2015 Jul 13. PMID 26184320, Free PMC Article

See all (11) 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 +48.9 kb DNase I hypersensitive site
  • chromatin insulator 7-1-1

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_051342.1 

    Range
    101..1180
    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
    117715346..117716425
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    119030737..119031823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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