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LOC117038774 OCT4-NANOG hESC enhancer GRCh37_chr3:129024401-129024985 [ Homo sapiens (human) ]

Gene ID: 117038774, updated on 10-Oct-2023

Summary

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Gene symbol
LOC117038774
Gene description
OCT4-NANOG hESC enhancer GRCh37_chr3:129024401-129024985
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 predicted to be an enhancer based on an activity-by-contact (ABC) model that predicts enhancer-gene connections, where the putative enhancer strength is measured by DNase I hypersensitivity and H3K27 acetylation, and the contact frequency by Hi-C. 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. A subregion was also validated as a positively-acting cis-regulatory element for the H1-10 (H1.10 linker histone, also known as H1FX) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in K562 erythroleukemia cells. [provided by RefSeq, Jan 2023]
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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 (129305558..129306142)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (132050356..132050940)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (129024465..129024965)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374102 Neighboring gene NANOG hESC enhancer GRCh37_chr3:128950251-128950752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20507 Neighboring gene CRISPRi-FlowFISH-validated H1-10 regulatory element 3 Neighboring gene COPI coat complex subunit gamma 1 Neighboring gene microRNA 6826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14719 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20508 Neighboring gene 5-hydroxymethylcytosine binding, ES cell specific Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14723 Neighboring gene H1-10 antisense RNA 1 Neighboring gene H1.10 linker histone Neighboring gene nucleoporin 210 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. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Fulco CP, et al. Nat Genet, 2019 Dec. PMID 31784727, 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

  • CRISPRi-FlowFISH-validated H1-10 regulatory element 4

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_068100.2 

    Range
    101..685
    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
    129305558..129306142
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    132050356..132050940
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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