U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123497935 OCT4-NANOG hESC enhancer GRCh37_chr5:90634700-90635294 [ Homo sapiens (human) ]

Gene ID: 123497935, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC123497935
Gene description
OCT4-NANOG hESC enhancer GRCh37_chr5:90634700-90635294
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Jan 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (91338883..91339477)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (91822758..91823352)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (90634869..90635163)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22785 Neighboring gene RNA, U4 small nuclear 90, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:90575335-90576276 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:90576277-90577218 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:90607093-90608292 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:90609644-90610843 Neighboring gene lung cancer associated transcript 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:90627976-90628476 Neighboring gene ribosomal protein S18 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16171 Neighboring gene arrestin domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16172 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:90679204-90679721 Neighboring gene ARRDC3 antisense RNA 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • Sharpr-MPRA regulatory region 9063

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_077788.2 

    Range
    101..695
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    91338883..91339477
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    91822758..91823352
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases