U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC127403489 OCT4-NANOG hESC enhancer GRCh37_chr5:106903957-106904492 [ Homo sapiens (human) ]

Gene ID: 127403489, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC127403489
Gene description
OCT4-NANOG hESC enhancer GRCh37_chr5:106903957-106904492
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 includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors. 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC127403489 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 (107568203..107568791)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (108071097..108071685)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (106903904..106904492)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene proteasome 26S subunit, ATPase 1 pseudogene 5 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:106620899-106622098 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:106737319-106737856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22862 Neighboring gene ephrin A5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:106801251-106801752 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:106808214-106808968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22863 Neighboring gene NANOG hESC enhancer GRCh37_chr5:106834891-106835392 Neighboring gene Sharpr-MPRA regulatory region 8638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16212 Neighboring gene NANOG hESC enhancer GRCh37_chr5:106855351-106855852 Neighboring gene uncharacterized LOC124901038 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:106906417-106907128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22867 Neighboring gene Sharpr-MPRA regulatory region 13332 Neighboring gene VISTA enhancer hs1734 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:106924851-106925777 Neighboring gene Sharpr-MPRA regulatory region 6875 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:106946073-106947272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22868 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16214 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16215 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:107008991-107009490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16216 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:107031758-107032266 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:107060476-107061675 Neighboring gene ubiquitin specific peptidase 7 (herpes virus-associated) pseudogene Neighboring gene RNA, 7SL, cytoplasmic 782, pseudogene

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. 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

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 Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 22865

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_105438.2 

    Range
    101..689
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    107568203..107568791
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    108071097..108071685
    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