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    LOC111501788 MED14-independent group 3 enhancer GRCh37_chr3:5390480-5391679 [ Homo sapiens (human) ]

    Gene ID: 111501788, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC111501788
    Gene description
    MED14-independent group 3 enhancer GRCh37_chr3:5390480-5391679
    Gene type
    biological region
    Feature type(s)
    regulatory: enhancer, transcriptional_cis_regulatory_region
    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 predicted to be a cell type-specific enhancer based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It 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. This sequence 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 a functional enhancer by high-throughput massively parallel reporter assays (MPRAs) in both liver carcinoma HepG2 cells and erythroleukemia K562 cells. The subregion contains a motif for the NFE2L2 activator, and mutation of the motif results in reduced enhancer activity. [provided by RefSeq, Aug 2022]
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    Genomic context

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    See LOC111501788 in Genome Data Viewer
    Location:
    3p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (5348795..5349994)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (5342500..5343699)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (5391100..5391244)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 553, pseudogene Neighboring gene microRNA 4790 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:5306534-5306699 Neighboring gene UPF0764 protein C16orf89-like Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:5371861-5373060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19387 Neighboring gene uncharacterized LOC105376936 Neighboring gene mitochondrial ribosomal protein S35 pseudogene 1

    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. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Kheradpour P, et al. Genome Res, 2013 May. PMID 23512712, Free PMC Article
    2. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, et al. Nature, 2011 May 5. PMID 21441907, Free PMC Article
    3. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, 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

    • NFE2L2 activator MPRA enhancer 18
    • NFE2L2 motif-containing MPRA enhancer 18
    • massively parallel reporter assay enhancer 18

    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_055945.2 

      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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      5348795..5349994
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      5342500..5343699
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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