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    LOC108281137 MED14-independent group 3 enhancer GRCh37_chr17:57831571-57832770 [ Homo sapiens (human) ]

    Gene ID: 108281137, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC108281137
    Gene description
    MED14-independent group 3 enhancer GRCh37_chr17:57831571-57832770
    Gene type
    biological region
    Feature type(s)
    misc_feature: CAGE_cluster
    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 element is located in an intron of the VMP1 (vacuole membrane protein 1) gene. 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, 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 defined as a low expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE), and was validated as a functional enhancer by reporter assays in HepG2 cells. [provided by RefSeq, Aug 2022]
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    Genomic context

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    Location:
    17q23.1
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (59754210..59755409)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (60622978..60624179)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (57831614..57832456)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8782 Neighboring gene clathrin heavy chain Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:57760547-57761746 Neighboring gene Sharpr-MPRA regulatory region 12460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57780642-57781146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57781147-57781650 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57784605-57785260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:57794547-57795046 Neighboring gene peptidyl-tRNA hydrolase 2 Neighboring gene vacuole membrane protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57845677-57846178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57860713-57861526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12516 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57911971-57912470 Neighboring gene VISTA enhancer hs1656 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:57917673-57918402 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:57919688-57919882 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57923900-57924888 Neighboring gene RNA, U6 small nuclear 450, pseudogene Neighboring gene microRNA 21

    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. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article
    2. 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

    • VMP1 intron CAGE-defined low expression enhancer
    • VMP1 intron low CAGE FANTOM5 enhancer

    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_051088.2 

      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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      59754210..59755409
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      60622978..60624179
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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