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LOC127138825 hESC enhancers GRCh37_chrX:1324089-1324592, GRCh37_chrY:1274255-1275102 and GRCh37_chrY:1273405-1274254 [ Homo sapiens (human) ]

Gene ID: 127138825, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127138825
Gene description
hESC enhancers GRCh37_chrX:1324089-1324592, GRCh37_chrY:1274255-1275102 and GRCh37_chrY:1273405-1274254
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 is found within pseudoautosomal region 1 (PAR1) of chromosomes X and Y, where each chromosome contains the same DNA region. Three subregions were validated as active enhancers by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells. All subregions associate with the NANOG transcription factor, one subregion additionally associates with OCT4, and two subregions are marked by the H3K4me1 histone modification. [provided by RefSeq, Oct 2022]
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Genomic context

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See LOC127138825 in Genome Data Viewer
Location:
X;Y
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (1204512..1206209)
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (1204512..1206209)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (1050326..1052023)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (1064535..1066232)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (1323405..1325102)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (1273405..1275102)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene repetin pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:1252013-1252514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:1252515-1253014 Neighboring gene 60S ribosomal protein L6-like Neighboring gene cytokine receptor like factor 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chrX:1367406-1367922 and GRCh37_chrY:1317424-1317933 Neighboring gene NANOG hESC enhancer GRCh37_chrY:1330085-1330594 Neighboring gene colony stimulating factor 2 receptor subunit alpha Neighboring gene uncharacterized LOC124905238 Neighboring gene microRNA 3690 Neighboring gene RNA, 5S ribosomal pseudogene 498

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene repetin pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:1252013-1252514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:1252515-1253014 Neighboring gene 60S ribosomal protein L6-like Neighboring gene cytokine receptor like factor 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chrX:1367406-1367922 and GRCh37_chrY:1317424-1317933 Neighboring gene NANOG hESC enhancer GRCh37_chrY:1330085-1330594 Neighboring gene colony stimulating factor 2 receptor subunit alpha Neighboring gene uncharacterized LOC124905238 Neighboring gene microRNA 3690 Neighboring gene RNA, 5S ribosomal pseudogene 498

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. 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

  • NANOG hESC enhancer GRCh37_chrX:1324089-1324592
  • NANOG-H3K4me1 hESC enhancer GRCh37_chrY:1273405-1274254
  • OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrY:1274255-1275102

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_088496.1 

    Range
    101..1798
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    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    1204512..1206209
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    1204512..1206209
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    1050326..1052023
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    1064535..1066232
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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