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LOC127403698 OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:124082573-124083571 [ Homo sapiens (human) ]

Gene ID: 127403698, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127403698
Gene description
OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:124082573-124083571
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 region was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac histone modification. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC127403698 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (124746880..124747878)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (125263360..125264358)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1170 Neighboring gene uncharacterized LOC107986448 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:123644150-123645142 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_80867 Neighboring gene uncharacterized LOC105379155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16277 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:123777990-123778496 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:123804163-123805004 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:123832600-123833191 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:123833192-123833782 Neighboring gene NANOG hESC enhancer GRCh37_chr5:123837876-123838461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23009 Neighboring gene NANOG hESC enhancer GRCh37_chr5:123890213-123891101 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:123935182-123935396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23011 Neighboring gene Sharpr-MPRA regulatory region 9682 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:123984206-123984714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23012 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:123995996-123996689 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:123998129-123998646 Neighboring gene zinc finger protein 608 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:124044787-124045526 Neighboring gene NANOG hESC enhancer GRCh37_chr5:124068918-124069490 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:124073123-124073732 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:124074341-124074948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23013 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:124077846-124078540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23015 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:124079931-124080624 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:124083572-124084570 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:124086863-124087461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16279 Neighboring gene uncharacterized LOC105379156 Neighboring gene ribosomal protein L28 pseudogene 3

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 23017

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_105647.1 

    Range
    101..1099
    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
    124746880..124747878
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    125263360..125264358
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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