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    TRIM4 tripartite motif containing 4 [ Homo sapiens (human) ]

    Gene ID: 89122, updated on 5-May-2024

    Summary

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    Official Symbol
    TRIM4provided by HGNC
    Official Full Name
    tripartite motif containing 4provided by HGNC
    Primary source
    HGNC:HGNC:16275
    See related
    Ensembl:ENSG00000146833 AllianceGenome:HGNC:16275
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RNF87
    Summary
    The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to cytoplasmic bodies. Its function has not been identified. Alternatively spliced transcript variants that encode different isoforms have been described.[provided by RefSeq, Jul 2010]
    Expression
    Ubiquitous expression in ovary (RPKM 16.5), thyroid (RPKM 12.9) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See TRIM4 in Genome Data Viewer
    Location:
    7q22.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (99890403..99919530, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101129904..101159031, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (99488026..99517153, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene cytochrome P450 family 3 subfamily A member 52, pseudogene Neighboring gene olfactory receptor family 2 subfamily AE member 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:99484893-99485660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26329 Neighboring gene uncharacterized LOC101927610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26330 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99526456-99527041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99527042-99527626 Neighboring gene gap junction protein gamma 3 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99541581-99542436 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99543294-99544149 Neighboring gene small nucleolar RNA SNORA40

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. TRIM4 is associated with neural tube defects based on genome-wide DNA methylation analysis. Zhang H, et al. Clin Epigenetics, 2019 Feb 1. PMID 30709423, Free PMC Article
    2. TRIM4; a novel mitochondrial interacting RING E3 ligase, sensitizes the cells to hydrogen peroxide (H2O2) induced cell death. Tomar D, et al. Free Radic Biol Med, 2015 Dec. PMID 26524401
    3. TRIM4 modulates type I interferon induction and cellular antiviral response by targeting RIG-I for K63-linked ubiquitination. Yan J, et al. J Mol Cell Biol, 2014 Apr. PMID 24755855
    4. TRIM4 interacts with TRPM8 and regulates its channel function through K423-mediated ubiquitination. Huang Y, et al. J Cell Physiol, 2021 Apr. PMID 33037615
    5. Histone demethylase LSD1 promotes RIG-I poly-ubiquitination and anti-viral gene expression. Hu QX, et al. PLoS Pathog, 2021 Sep. PMID 34529741, Free PMC Article

    See all (45) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRIM4 Expression Related to Malignant Progression and Cisplatin Resistance in Osteosarcoma.
      Title: TRIM4 Expression Related to Malignant Progression and Cisplatin Resistance in Osteosarcoma.
    2. SARS-CoV-2 Nsp8 suppresses MDA5 antiviral immune responses by impairing TRIM4-mediated K63-linked polyubiquitination.
      Title: SARS-CoV-2 Nsp8 suppresses MDA5 antiviral immune responses by impairing TRIM4-mediated K63-linked polyubiquitination.
    3. The E3 Ligase TRIM4 Facilitates SET Ubiquitin-Mediated Degradation to Enhance ER-alpha Action in Breast Cancer.
      Title: The E3 Ligase TRIM4 Facilitates SET Ubiquitin-Mediated Degradation to Enhance ER-α Action in Breast Cancer.
    4. TRIM4 interacts with TRPM8 and regulates its channel function through K423-mediated ubiquitination.
      Title: TRIM4 interacts with TRPM8 and regulates its channel function through K423-mediated ubiquitination.
    5. Findings suggest that spinal cord tissues in cases with neural tube defects (NTDs) had a different genome-wide methylation pattern compared to controls. Abnormal methylation patterns in TRIM4 in immunity pathways might be involved in NTD pathogenesis. Genetic variants in TRIM4 genes only slightly contribute to the etiology of human NTDs.
      Title: TRIM4 is associated with neural tube defects based on genome-wide DNA methylation analysis.
    6. TRIM4 is an important regulator of the virus-induced interferon induction pathways by mediating RIG-I for K63-linked ubiquitination.
      Title: TRIM4 modulates type I interferon induction and cellular antiviral response by targeting RIG-I for K63-linked ubiquitination.
    7. ZNF198-FGFR1 is associated with phosphorylation of several proteins including SSBP2, ABL, FLJ14235, CALM and TRIM4 proteins.
      Title: Phosphorylation of the SSBP2 and ABL proteins by the ZNF198-FGFR1 fusion kinase seen in atypical myeloproliferative disorders as revealed by phosphopeptide-specific MS.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Eight common genetic variants associated with serum DHEAS levels suggest a key role in ageing mechanisms.
    EBI GWAS Catalog
    Human metabolic individuality in biomedical and pharmaceutical research.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin-protein transferase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in innate immune response TAS
    Traceable Author Statement
    more info
    		  
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase TRIM4
    Names
    RING finger protein 87
    RING-type E3 ubiquitin transferase TRIM4
    tripartite motif protein 4
    NP_148977.2
    NP_149082.1

    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.

    mRNA and Protein(s)

    1. NM_033017.4 → NP_148977.2  E3 ubiquitin-protein ligase TRIM4 isoform alpha

      See identical proteins and their annotated locations for NP_148977.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (alpha) represents the longer transcript and encodes the longer isoform (alpha).
      Source sequence(s)
      AC011904
      Consensus CDS
      CCDS5679.1
      UniProtKB/Swiss-Prot
      A4D298, Q75MK1, Q96F06, Q9C036, Q9C037
      UniProtKB/TrEMBL
      B3KS62
      Related
      ENSP00000348216.2, ENST00000355947.6
      Conserved Domains (3) summary
      cd00021
      Location:86 → 123
      BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
      pfam15227
      Location:12 → 52
      zf-C3HC4_4; zinc finger of C3HC4-type, RING
      cd15809
      Location:305 → 494
      SPRY_PRY_TRIM4; PRY/SPRY domain in tripartite motif-binding protein 4 (TRIM4), also known as RING finger protein 87 (RNF87)

    2. NM_033091.3 → NP_149082.1  E3 ubiquitin-protein ligase TRIM4 isoform beta

      See identical proteins and their annotated locations for NP_149082.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (beta) lacks an in-frame exon in the 5' coding region compared to variant alpha. The resulting protein (isoform beta) is shorter but has the same N- and C-termini compared to isoform alpha.
      Source sequence(s)
      AC011904
      Consensus CDS
      CCDS5678.1
      UniProtKB/TrEMBL
      B3KS62
      Related
      ENSP00000275736.4, ENST00000349062.7
      Conserved Domains (3) summary
      cd00021
      Location:86 → 123
      BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
      pfam15227
      Location:12 → 52
      zf-C3HC4_4; zinc finger of C3HC4-type, RING
      cd15809
      Location:279 → 468
      SPRY_PRY_TRIM4; PRY/SPRY domain in tripartite motif-binding protein 4 (TRIM4), also known as RING finger protein 87 (RNF87)

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      99890403..99919530 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      101129904..101159031 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9C037.2 GenPept UniProtKB/Swiss-Prot:Q9C037

    Gene LinkOut

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