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LOC113219436 greater CFTR locus negative regulatory element NR1 [ Homo sapiens (human) ]

Gene ID: 113219436, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113219436
Gene description
greater CFTR locus negative regulatory element NR1
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This nonconserved genomic region, which is located in the greater CFTR locus on chromosome 7, represents a silencer that was shown to strongly repress an SV40 promoter coupled to the HS2 beta-globin enhancer in transfected K562 erythroleukemia and 293T embryonic kidney cells. A subregion was also validated as a repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone), while the same subregion functioned as an enhancer by Sharpr-MPRA in K562 cells (group: K562 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC113219436 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (116420583..116421548)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (117735593..117736560)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (116060637..116061602)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724434 Neighboring gene uncharacterized LOC105375463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26531 Neighboring gene Sharpr-MPRA regulatory region 1934 Neighboring gene uncharacterized LOC124900233 Neighboring gene VISTA enhancer hs2071 Neighboring gene uncharacterized LOC107986838 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:116082532-116083731 Neighboring gene greater CFTR locus negative regulatory element CR2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:116138807-116139308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18556 Neighboring gene Sharpr-MPRA regulatory region 4219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26534 Neighboring gene Sharpr-MPRA regulatory region 9016 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18557 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18558 Neighboring gene caveolin 2 Neighboring gene Sharpr-MPRA regulatory region 15503 Neighboring gene caveolin 1

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. 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
  2. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  3. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article

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

  • Sharpr-MPRA regulatory region 12966
  • greater CFTR locus silencer NR1

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_061703.1 

    Range
    101..1066
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    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
    116420583..116421548
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    117735593..117736560
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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