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LOC127404449 OCT4-NANOG hESC enhancer GRCh37_chr5:158384828-158385690 [ Homo sapiens (human) ]

Gene ID: 127404449, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127404449
Gene description
OCT4-NANOG hESC enhancer GRCh37_chr5:158384828-158385690
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 and primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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 LOC127404449 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 (158957820..158958682)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (159486619..159487481)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (158384828..158385690)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2227 Neighboring gene uncharacterized LOC124901122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23533 Neighboring gene Sharpr-MPRA regulatory region 1261 Neighboring gene VISTA enhancer hs1208 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:158067088-158067611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23535 Neighboring gene NANOG hESC enhancer GRCh37_chr5:158124779-158125433 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:158139245-158139745 Neighboring gene VISTA enhancer hs813 Neighboring gene NANOG hESC enhancer GRCh37_chr5:158164501-158165077 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16566 Neighboring gene EBF transcription factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23536 Neighboring gene VISTA enhancer hs230 Neighboring gene NANOG hESC enhancer GRCh37_chr5:158378905-158379562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23537 Neighboring gene NANOG hESC enhancer GRCh37_chr5:158403034-158403551 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16567 Neighboring gene VISTA enhancer hs1022 Neighboring gene VISTA enhancer hs1117 Neighboring gene VISTA enhancer hs1123 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:158522773-158523666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:158524561-158525454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16568 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:158527204-158527832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:158527833-158528459 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:158531040-158531945 Neighboring gene uncharacterized LOC107986467 Neighboring gene long intergenic non-protein coding RNA 2202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23540 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:158588140-158589339 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:158634672-158635327 Neighboring gene uncharacterized LOC107986468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23544 Neighboring gene ring finger protein 145

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 23538
  • ATAC-STARR-seq lymphoblastoid active region 23539

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_106398.1 

    Range
    101..963
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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
    158957820..158958682
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    159486619..159487481
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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