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LOC122889050 OCT4-NANOG hESC enhancer GRCh37_chr3:19308542-19309065 [ Homo sapiens (human) ]

Gene ID: 122889050, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889050
Gene description
OCT4-NANOG hESC enhancer GRCh37_chr3:19308542-19309065
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 genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive and primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC122889050 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (19267050..19267573)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (19271151..19271674)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (19308569..19308863)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986066 Neighboring gene uncharacterized LOC105376978 Neighboring gene uncharacterized LOC105376981 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:19114887-19115448 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:19115449-19116010 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:19116011-19116572 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:19167677-19168876 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:19188257-19188850 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:19188851-19189444 Neighboring gene potassium voltage-gated channel subfamily H member 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:19275326-19275842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:19275843-19276358 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:19375136-19375636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14130 Neighboring gene microRNA 4791 Neighboring gene uncharacterized LOC105376982 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:19491994-19493193

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. 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
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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 372

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_077182.2 

    Range
    101..624
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    19267050..19267573
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    19271151..19271674
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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