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LOC113875022 MED14-independent group 3 enhancer GRCh37_chrX:39766731-39767930 [ Homo sapiens (human) ]

Gene ID: 113875022, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113875022
Gene description
MED14-independent group 3 enhancer GRCh37_chrX:39766731-39767930
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. A subregion was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells, where it was defined as a group 3 enhancer that depends on the BRD2, BRD4, P300/CBP and CDK7 cofactors, but it has limited or no dependence on the MED14 core Mediator complex subunit. A subregion was also validated as an enhancer 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 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC113875022 in Genome Data Viewer
Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (39907477..39908781)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (39307706..39309010)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (39767409..39767703)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chrX:39699064-39699252 Neighboring gene microRNA 1587 Neighboring gene Sharpr-MPRA regulatory region 12649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39717183-39717683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39734537-39735038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39735039-39735538 Neighboring gene ribosomal protein S11 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:39756695-39757676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39765114-39765903 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39787967-39788468 Neighboring gene uncharacterized LOC105373180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39788469-39788968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39808059-39808558 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:39813184-39813412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39828711-39829255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39832750-39833500 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:39863451-39863973 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:39865487-39866423 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39867643-39868270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39871294-39872017 Neighboring gene long intergenic non-protein coding RNA 3053

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. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, Free PMC Article
  2. 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
  3. 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:39767339-39768035
  • Sharpr-MPRA regulatory region 3177

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_063210.3 

    Range
    101..1405
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    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    39907477..39908781
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    39307706..39309010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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