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LOC127827610 OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:55493639-55494166 [ Homo sapiens (human) ]

Gene ID: 127827610, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127827610
Gene description
OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:55493639-55494166
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 and is marked by the H3K27ac histone modification. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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 LOC127827610 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (55026921..55027448)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (49232110..49232637)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (55493639..55494166)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene GTP cyclohydrolase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:55364129-55364629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5774 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5776 Neighboring gene farnesyl diphosphate synthase pseudogene 3 Neighboring gene Sharpr-MPRA regulatory region 2393 Neighboring gene WD repeat and HMG-box DNA binding protein 1 Neighboring gene ribosomal protein SA pseudogene 13 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:55494167-55494693 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:55517727-55518416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5779 Neighboring gene suppressor of cytokine signaling 4 Neighboring gene mitogen-activated protein kinase 1 interacting protein 1 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8424 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:55543983-55545182 Neighboring gene uncharacterized LOC124903318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8425 Neighboring gene Sharpr-MPRA regulatory region 8345

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 silent region 5777

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_129112.1 

    Range
    101..628
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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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    55026921..55027448
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    49232110..49232637
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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