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LOC123493277 OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:21614040-21614968 [ Homo sapiens (human) ]

Gene ID: 123493277, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123493277
Gene description
OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:21614040-21614968
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 and is marked by the H3K27ac and H3K4me1 histone modifications. 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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC123493277 in Genome Data Viewer
Location:
5p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (21613931..21614859)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (21721145..21722073)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (21614040..21614968)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900950 Neighboring gene uncharacterized LOC124900951 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:21325279-21325852 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:21471616-21472269 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:21481591-21482218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:21482219-21482846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:21484729-21485355 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:21485356-21485982 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:21485983-21486609 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:21494970-21495648 Neighboring gene uncharacterized LOC124900949 Neighboring gene GUSB pseudogene 1 Neighboring gene uncharacterized LOC105374685 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:21813195-21813389 Neighboring gene uncharacterized LOC105374683 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:21823845-21825044 Neighboring gene cadherin 12 Neighboring gene small nucleolar RNA, H/ACA box 105A Neighboring gene heat shock protein family D (Hsp60) member 1 pseudogene 1

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 8629

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_077701.2 

    Range
    101..1029
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    21613931..21614859
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107297.1 Reference GRCh38.p14 PATCHES

    Range
    263071..263999
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    21721145..21722073
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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