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LOC112997557 OCT4-NANOG hESC enhancers GRCh37_chr5:129502144-129502824 and GRCh37_chr5:129502825-129503503 [ Homo sapiens (human) ]

Gene ID: 112997557, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112997557
Gene description
OCT4-NANOG hESC enhancers GRCh37_chr5:129502144-129502824 and GRCh37_chr5:129502825-129503503
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 associated with the OCT4 and NANOG transcription factors were validated as active enhancers by ChIP-STARR-seq in human embryonic stem cells. An overlapping subregion was also validated as a functional enhancer 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 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone), with weaker activity in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 24:Quies). [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (130166451..130167810)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (130685297..130686656)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (129502789..129503083)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene chondroitin sulfate synthase 3 Neighboring gene RNA, 5S ribosomal pseudogene 191 Neighboring gene heat shock protein family A (Hsp70) member 8 pseudogene 4 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:129541966-129543165 Neighboring gene NANOG hESC enhancer GRCh37_chr5:129563309-129563853 Neighboring gene uncharacterized LOC105379171 Neighboring gene RNA, U7 small nuclear 53 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

  • OCT4-NANOG hESC enhancer GRCh37_chr5:129502144-129502824
  • OCT4-NANOG hESC enhancer GRCh37_chr5:129502825-129503503
  • Sharpr-MPRA regulatory region 1157

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_061554.2 

    Range
    101..1460
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    130166451..130167810
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    130685297..130686656
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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