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LOC122817720 OCT4-NANOG hESC enhancer GRCh37_chr2:105621477-105622097 [ Homo sapiens (human) ]

Gene ID: 122817720, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122817720
Gene description
OCT4-NANOG hESC enhancer GRCh37_chr2:105621477-105622097
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC122817720 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (105005019..105005639)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (105466317..105466937)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (105621477..105622097)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:105470177-105470766 Neighboring gene uncharacterized LOC124908045 Neighboring gene Sharpr-MPRA regulatory region 193 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:105488734-105489459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11836 Neighboring gene POU class 3 homeobox 3 Neighboring gene long intergenic non-protein coding RNA 1159 Neighboring gene VISTA enhancer hs990 Neighboring gene MRPS9 antisense RNA 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:105585853-105587052 Neighboring gene Sharpr-MPRA regulatory region 1600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16309 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16311 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:105654567-105655509 Neighboring gene mitochondrial ribosomal protein S9 Neighboring gene VISTA enhancer hs868 Neighboring gene uncharacterized LOC105373527 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:105719958-105720819 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:105720820-105721680 Neighboring gene MRPS9 antisense RNA 1

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. 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

  • Sharpr-MPRA regulatory region 856

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_076992.2 

    Range
    101..721
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    105005019..105005639
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    105466317..105466937
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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