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LOC123956156 OCT4-NANOG hESC enhancer GRCh37_chr7:66705704-66706246 [ Homo sapiens (human) ]

Gene ID: 123956156, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956156
Gene description
OCT4-NANOG hESC enhancer GRCh37_chr7:66705704-66706246
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 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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 16:ElonW, transcriptional elongation, weaker H3K36me3). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC123956156 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 (67240717..67241259)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (68460415..68460957)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (66705929..66706223)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene tRNA-yW synthesizing protein 1 homolog Neighboring gene uncharacterized LOC124901666 Neighboring gene Sharpr-MPRA regulatory region 9636 Neighboring gene MPRA-validated peak6550 silencer Neighboring gene uncharacterized LOC124901665 Neighboring gene speedy/RINGO cell cycle regulator family member E21 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26092 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18220 Neighboring gene PMS1 homolog 2, mismatch repair system component pseudogene 4 Neighboring gene STAG3 cohesin complex component like 4 (pseudogene)

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 9158

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_078350.2 

    Range
    101..643
    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
    67240717..67241259
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    68460415..68460957
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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