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LOC117135104 TMPRSS2 E3 enhancer [ Homo sapiens (human) ]

Gene ID: 117135104, updated on 10-Oct-2023

Summary

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Gene symbol
LOC117135104
Gene description
TMPRSS2 E3 enhancer
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 locus represents an enhancer located approximately 21 kb upstream of the TMPRSS2 (transmembrane serine protease 2) gene, which functions as an entry gene for human coronaviruses, including SARS-CoV and SARS-CoV-2 (COVID-19 virus). The extended TMPRSS2 5' regulatory region is responsive to androgen receptor (AR), and it drives expression of a TMPRSS2-ERG or TMPRSS2-ETV1 oncogenic fusion gene in androgen-dependent prostate cancers. This subregion functions as a non-AR-responsive enhancer that can activate a heterologous promoter in transfected LNCaP and VCaP prostate cancer cells. [provided by RefSeq, Apr 2020]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is involved in host gene regulation.
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Genomic context

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Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (41529122..41531495)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (39918657..39921032)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (42901049..42903422)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18479 Neighboring gene MX dynamin like GTPase 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:42824122-42825321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42830117-42830618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18481 Neighboring gene transmembrane serine protease 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42851654-42852154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42852155-42852655 Neighboring gene transmembrane protease serine 2 breakpoint cluster recombination region Neighboring gene TMPRSS2 promoter region Neighboring gene TMPRSS2 repressive element NBS1 Neighboring gene TMPRSS2 repressive element NBS2 Neighboring gene TMPRSS2 repressive element NBS4 Neighboring gene TMPRSS2 androgen receptor-responsive -13 kb enhancer Neighboring gene TMPRSS2 -17 kb enhancer Neighboring gene uncharacterized LOC124905021 Neighboring gene TMPRSS2 E4 enhancer Neighboring gene small nucleolar RNA SNORA32 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:42918133-42918311 Neighboring gene uncharacterized LOC105372809 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:42931079-42932278 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:42934014-42934514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:42934515-42935015 Neighboring gene TMPRSS2 androgen receptor-responsive -60 kb enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18483 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:42952959-42954158 Neighboring gene prostate cancer expressed EZH2 associated transcript

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. TMPRSS2 and COVID-19: Serendipity or Opportunity for Intervention? Stopsack KH, et al. Cancer Discov, 2020 Jun. PMID 32276929, Free PMC Article
  2. MRGBP promotes AR-mediated transactivation of KLK3 and TMPRSS2 via acetylation of histone H2A.Z in prostate cancer cells. Ito S, et al. Biochim Biophys Acta Gene Regul Mech, 2018 Aug 1. PMID 30076933
  3. Genome-wide CpG island methylation analysis implicates novel genes in the pathogenesis of renal cell carcinoma. Ricketts CJ, et al. Epigenetics, 2012 Mar. PMID 22430804, Free PMC Article
  4. Androgen receptor-driven chromatin looping in prostate cancer. Wu D, et al. Trends Endocrinol Metab, 2011 Dec. PMID 21889355, Free PMC Article
  5. Prostate cancer stem cells: do they have a basal or luminal phenotype? Maitland NJ, et al. Horm Cancer, 2011 Feb. PMID 21761340, Free PMC Article

See all (47) citations in PubMed

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)

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_068150.1 

    Range
    101..2474
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    41529122..41531495
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    39918657..39921032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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