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LOC127404194 OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:145453205-145454157 [ Homo sapiens (human) ]

Gene ID: 127404194, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127404194
Gene description
OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:145453205-145454157
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 naive human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K4me1 histone modification. This locus also includes a subregion containing a Neanderthal adaptively introgressed genetic variant. That subregion was validated as an enhancer by MPRAs in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 5:145453934 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC127404194 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (146073642..146074594)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (146607930..146608880)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (145453205..145454157)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986458 Neighboring gene SH3 domain containing ring finger 2 Neighboring gene apolipoprotein O like pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_80983 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:145405605-145406400 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:145406401-145407194 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:145407216-145408415 Neighboring gene uncharacterized LOC107986459 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:145428236-145428736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23358 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:145452250-145453204 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81045 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81119 Neighboring gene PLAC8 like 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:145481092-145481650 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81180 Neighboring gene MPRA-validated peak5518 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81226 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81266 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81335 Neighboring gene leucyl-tRNA synthetase 1 Neighboring gene ribosomal protein L35a pseudogene 16

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. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Jagoda E, et al. Mol Biol Evol, 2022 Jan 7. PMID 34662402, 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

  • Neanderthal introgressed variant-containing enhancer experimental_81014

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_106143.1 

    Range
    101..1053
    Download
    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
    146073642..146074594
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    146607930..146608880
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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