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LOC113225348 greater CFTR locus negative regulatory element CR27 [ Homo sapiens (human) ]

Gene ID: 113225348, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113225348
Gene description
greater CFTR locus negative regulatory element CR27
Gene type
biological region
Feature type(s)
regulatory: 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
Summary
This conserved genomic region, which is located in an intron of the CTTNBP2 (cortactin binding protein 2) gene in the greater CFTR locus on chromosome 7, can function as both a silencer and an enhancer-blocking element. It was shown to strongly repress an SV40 promoter coupled to the HS2 beta-globin enhancer in transfected K562 and HeLa cells, and it could also modestly repress a gamma-globin promoter coupled to the HS2 enhancer in transfected K562 cells, all when present in the reverse orientation in the reporter construct. When present in the forward orientation, it modestly blocked HS2 enhancer activation of both a gamma-globin promoter in K562 cells and an SV40 promoter in HeLa cells, when positioned between the enhancer and promoter. A CT-motif that is present at one end of this element was shown to be necessary for its silencing function. [provided by RefSeq, Sep 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 (117780838..117781107)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (119096575..119096844)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (117420892..117421161)

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 DNase I hypersensitive site 83.7 kb downstream of CFTR Neighboring gene cortactin binding protein 2 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. Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes. Ellsworth RE, et al. Proc Natl Acad Sci U S A, 2000 Feb 1. PMID 10655503, Free PMC Article
  2. 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
  3. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074

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

  • greater CFTR locus silencer and enhancer-blocking element CR27

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_061723.1 

    Range
    101..370
    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
    117780838..117781107
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    119096575..119096844
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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