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    LOC126863193 MED14-independent group 3 enhancer GRCh37_chrX:4628486-4629685 [ Homo sapiens (human) ]

    Gene ID: 126863193, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC126863193
    Gene description
    MED14-independent group 3 enhancer GRCh37_chrX:4628486-4629685
    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 STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) 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 ChIP-STARR-seq in primed 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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    Location:
    chromosome: X
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (4710445..4711644)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (4254984..4256183)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene RPL24 pseudogene 9 Neighboring gene NANOG hESC enhancer GRCh37_chrX:4139581-4140146 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:4174729-4175230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:4175231-4175730 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:4203631-4203806 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:4300102-4300943 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:4393267-4393845 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:4463784-4464983 Neighboring gene uncharacterized LOC101928201 Neighboring gene NANOG hESC enhancer GRCh37_chrX:4722126-4722632 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:4809466-4809972 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:4872887-4874086 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:4969484-4970683 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:5073162-5073812 Neighboring gene MT-ND6 pseudogene 12 Neighboring gene MT-CYB pseudogene 12

    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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

    General gene information

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    Other Names

    • ATAC-STARR-seq lymphoblastoid active region 29378
    • NANOG hESC enhancer GRCh37_chrX:4628515-4629016

    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_087689.1 

      Range
      101..1300
      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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      4710445..4711644
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      4254984..4256183
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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