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LOC123575642 OCT4-NANOG-H3K4me1 hESC enhancers GRCh37_chr6:829333-829880 and GRCh37_chr6:829881-830426 [ Homo sapiens (human) ]

Gene ID: 123575642, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575642
Gene description
OCT4-NANOG-H3K4me1 hESC enhancers GRCh37_chr6:829333-829880 and GRCh37_chr6:829881-830426
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. Two subregions were validated as active enhancers by ChIP-STARR-seq in naive and primed human embryonic stem cells, where both are associated with the OCT4 and NANOG transcription factors and are marked by the H3K4me1 histone modification. An overlapping subregion was also validated as a functional repressive element by Sharpr-MPRA (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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (829333..830426)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (686424..687517)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (829609..829903)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene exocyst complex component 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23858 Neighboring gene MARK2 pseudogene 18 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:692466-693352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:694782-695290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:701331-701850 Neighboring gene MPRA-validated peak5620 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16818 Neighboring gene uncharacterized LOC105374873 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:839153-839702 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:862355-863554 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:867961-868143 Neighboring gene uncharacterized LOC101927691 Neighboring gene uncharacterized LOC124901236

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

  • OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:829333-829880
  • OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:829881-830426
  • Sharpr-MPRA regulatory region 881

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_077901.2 

    Range
    101..1194
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    829333..830426
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    686424..687517
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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