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LOC121331322 OCT4-NANOG hESC enhancer GRCh37_chr9:19457239-19457834 [ Homo sapiens (human) ]

Gene ID: 121331322, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121331322
Gene description
OCT4-NANOG hESC enhancer GRCh37_chr9:19457239-19457834
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors. A subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). 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, May 2023]
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Genomic context

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See LOC121331322 in Genome Data Viewer
Location:
9p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (19457241..19457879)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (19469978..19470616)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (19457239..19457877)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr9:19407977-19408834 and GRCh37_chr9:19408835-19409690 Neighboring gene NADH:ubiquinone oxidoreductase subunit A5 pseudogene 3 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:19446057-19447256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:19460877-19461378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19795 Neighboring gene uncharacterized LOC105375988 Neighboring gene microtubule associated protein 1 light chain 3 beta pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:19492981-19493504 Neighboring gene alkaline ceramidase 2 Neighboring gene solute carrier family 24 member 2

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. 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
  3. 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

  • ATAC-STARR-seq lymphoblastoid active region 28223
  • Sharpr-MPRA regulatory region 13319

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_074346.3 

    Range
    101..739
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    19457241..19457879
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    19469978..19470616
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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