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LOC127404266 NANOG hESC enhancer GRCh37_chr5:149338737-149339340 [ Homo sapiens (human) ]

Gene ID: 127404266, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127404266
Gene description
NANOG hESC enhancer GRCh37_chr5:149338737-149339340
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 was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it associates with the NANOG transcription factor. 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 LOC127404266 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 (149959174..149959777)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (150495720..150496324)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149338737..149339340)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene PPARG coactivator 1 beta Neighboring gene microRNA 378a Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149138890-149139607 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149143045-149143915 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149152433-149153272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23389 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149183799-149184608 Neighboring gene NFE2L2 motif-containing MPRA enhancer 202 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:149195389 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149198738-149199254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23391 Neighboring gene phosphodiesterase 6A Neighboring gene Sharpr-MPRA regulatory region 12732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149318171-149318672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149318673-149319172 Neighboring gene Sharpr-MPRA regulatory region 12514 Neighboring gene MFF pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16504 Neighboring gene solute carrier family 26 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23393 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:149379441-149380229 Neighboring gene tigger transposable element derived 6

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 active region 23392

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_106215.1 

    Range
    101..704
    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
    149959174..149959777
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    150495720..150496324
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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