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LOC111828515 OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:197268447-197269042 [ Homo sapiens (human) ]

Gene ID: 111828515, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111828515
Gene description
OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:197268447-197269042
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 and is marked by the H3K4me1 histone modification. A subregion was also validated as an enhancer 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 Activating non-DNase unmatched - State 16:ElonW, transcriptional elongation, weaker H3K36me3) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). Another overlapping subregion displayed weak repressive activity by Sharpr-MPRA in both HepG2 cells (group: HepG2 Repressive non-DNase unmatched - State 16:ElonW) and K562 cells (group: K562 Repressive non-DNase unmatched - State 4:PromP). [provided by RefSeq, Oct 2022]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (197541576..197542172)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (200274220..200274816)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (197268649..197269043)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374309 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:197205169-197206368 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:197216831-197217376 and GRCh37_chr3:197217377-197217922 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:197229162-197229325 Neighboring gene Sharpr-MPRA regulatory region 5776 Neighboring gene long intergenic non-protein coding RNA 2012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:197238623-197239160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:197247683-197248388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:197248389-197249094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:197250741-197251240 Neighboring gene 3-hydroxybutyrate dehydrogenase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:197269043-197269636 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21111 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197303211-197303712 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:197306909-197307455 Neighboring gene ribosomal protein L36 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15088 Neighboring gene SDHA pseudogene 4

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 4170
  • Sharpr-MPRA regulatory region 8020
  • Sharpr-MPRA regulatory regions 4170 and 8020

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_056243.2 

    Range
    101..697
    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
    197541576..197542172
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187534.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    16711..17307 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    200274220..200274816
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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