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LOC127398942 OCT4-NANOG-H3K27ac hESC enhancers GRCh37_chr3:148803647-148804164 and GRCh37_chr3:148804165-148804682 [ Homo sapiens (human) ]

Gene ID: 127398942, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127398942
Gene description
OCT4-NANOG-H3K27ac hESC enhancers GRCh37_chr3:148803647-148804164 and GRCh37_chr3:148804165-148804682
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 includes two enhancers that were validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where they associate with the OCT4 and NANOG transcription factors and are 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, Jun 2023]
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Genomic context

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See LOC127398942 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (149085860..149086895)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (151836577..151837612)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (148803647..148804682)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14802 Neighboring gene Sharpr-MPRA regulatory region 13788 Neighboring gene ubiquilin 4 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:148726195-148726695 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:148733083-148733712 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:148733713-148734340 Neighboring gene glycogenin 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:148738584-148739234 Neighboring gene helicase like transcription factor Neighboring gene HLTF antisense RNA 1 Neighboring gene mediator complex subunit 28 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:148847467-148847966 Neighboring gene HPS3 biogenesis of lysosomal organelles complex 2 subunit 1 Neighboring gene ceruloplasmin

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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

Variation

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See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 20678
  • OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:148803647-148804164
  • OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:148804165-148804682

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_100908.2 

    Range
    101..1136
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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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    149085860..149086895
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    151836577..151837612
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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