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TRIM6 tripartite motif containing 6 [ Homo sapiens (human) ]

Gene ID: 117854, updated on 7-Apr-2024

Summary

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Official Symbol
TRIM6provided by HGNC
Official Full Name
tripartite motif containing 6provided by HGNC
Primary source
HGNC:HGNC:16277
See related
Ensembl:ENSG00000121236 MIM:607564; AllianceGenome:HGNC:16277
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
RNF89
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, B-box type 1 and B-box type 2 domain, and a coiled-coil region. The protein localizes to the nucleus, but its specific function has not been identified. This gene is mapped to chromosome 11p15, where it resides within a TRIM gene cluster. Alternative splicing results in multiple transcript variants. A read-through transcript from this gene into the downstream TRIM34 gene has also been observed, which results in a fusion product from these neighboring family members. [provided by RefSeq, Oct 2010]
Expression
Broad expression in kidney (RPKM 10.6), testis (RPKM 6.4) and 15 other tissues See more
Orthologs
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Genomic context

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See TRIM6 in Genome Data Viewer
Location:
11p15.4
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (5596111..5612952)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (5655518..5672393)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (5617341..5634182)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 53 Neighboring gene Sharpr-MPRA regulatory region 4920 Neighboring gene olfactory receptor family 52 subfamily B member 6 Neighboring gene Sharpr-MPRA regulatory region 11830 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:5617638-5618555 Neighboring gene TRIM6-TRIM34 readthrough Neighboring gene tripartite motif containing 5 Neighboring gene Sharpr-MPRA regulatory region 4679 Neighboring gene NANOG hESC enhancer GRCh37_chr11:5642663-5643271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4329 Neighboring gene tripartite motif containing 34 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4330 Neighboring gene uncharacterized LOC107984302

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. Tripartite motif-containing protein 6 facilitates growth and migration of breast cancer through degradation of STUB1. Wei C, et al. Eur J Histochem, 2021 Mar 10. PMID 33728863, Free PMC Article
  2. VAMP8 Contributes to the TRIM6-Mediated Type I Interferon Antiviral Response during West Nile Virus Infection. van Tol S, et al. J Virol, 2020 Jan 6. PMID 31694946, Free PMC Article
  3. The Host E3-Ubiquitin Ligase TRIM6 Ubiquitinates the Ebola Virus VP35 Protein and Promotes Virus Replication. Bharaj P, et al. J Virol, 2017 Sep 15. PMID 28679761, Free PMC Article
  4. Molecular cloning of ring finger protein 21 (RNF21)/interferon-responsive finger protein (ifp1), which possesses two RING-B box-coiled coil domains in tandem. Orimo A, et al. Genomics, 2000 Oct 1. PMID 11013086
  5. TRIM6 Reduces Ferroptosis and Chemosensitivity by Targeting SLC1A5 in Lung Cancer. Zhang Y, et al. Oxid Med Cell Longev, 2023. PMID 36654781, Free PMC Article

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TRIM6 facilitates SARS-CoV-2 proliferation by catalyzing the K29-typed ubiquitination of NP to enhance the ability to bind viral genomes.
    Title: TRIM6 facilitates SARS-CoV-2 proliferation by catalyzing the K29-typed ubiquitination of NP to enhance the ability to bind viral genomes.
  2. TRIM6 Promotes ROS-Mediated Inflammasome Activation and Pyroptosis in Renal Tubular Epithelial Cells via Ubiquitination and Degradation of GPX3 Protein.
    Title: TRIM6 Promotes ROS-Mediated Inflammasome Activation and Pyroptosis in Renal Tubular Epithelial Cells via Ubiquitination and Degradation of GPX3 Protein.
  3. TRIM6: An Upregulated Biomarker with Prognostic Significance and Immune Correlations in Gliomas.
    Title: TRIM6: An Upregulated Biomarker with Prognostic Significance and Immune Correlations in Gliomas.
  4. TRIM6 silencing for inhibiting growth and angiogenesis of gliomas by regulating VEGFA.
    Title: TRIM6 silencing for inhibiting growth and angiogenesis of gliomas by regulating VEGFA.
  5. TRIM6 Reduces Ferroptosis and Chemosensitivity by Targeting SLC1A5 in Lung Cancer.
    Title: TRIM6 Reduces Ferroptosis and Chemosensitivity by Targeting SLC1A5 in Lung Cancer.
  6. Tripartite motif-containing protein 6 facilitates growth and migration of breast cancer through degradation of STUB1.
    Title: Tripartite motif-containing protein 6 facilitates growth and migration of breast cancer through degradation of STUB1.
  7. TRIM6 promotes colorectal cancer cells proliferation and response to thiostrepton by TIS21/FoxM1.
    Title: TRIM6 promotes colorectal cancer cells proliferation and response to thiostrepton by TIS21/FoxM1.
  8. these results provide evidence that TRIM6 contributes to the antiviral response against WNV and identify VAMP8 as a novel regulator of the IFN-I system.
    Title: VAMP8 Contributes to the TRIM6-Mediated Type I Interferon Antiviral Response during West Nile Virus Infection.
  9. Intriguingly, the authors also found that TRIM6 enhances ebola virus polymerase activity in a minigenome assay and TRIM6 knockout cells have reduced replication of infectious ebola virus, suggesting that VP35 hijacks TRIM6 to promote ebola virus replication through ubiquitination.
    Title: The Host E3-Ubiquitin Ligase TRIM6 Ubiquitinates the Ebola Virus VP35 Protein and Promotes Virus Replication.
  10. Live NiV infection, but not a recombinant NiV lacking the M protein, reduced the levels of endogenous TRIM6 protein expression. To our knowledge, matrix proteins of paramyxoviruses have never been reported to be involved in innate immune antagonism. We report here a novel mechanism of viral innate immune evasion by targeting TRIM6, IKKepsilon and unanchored polyubiquitin chains.
    Title: The Matrix Protein of Nipah Virus Targets the E3-Ubiquitin Ligase TRIM6 to Inhibit the IKKε Kinase-Mediated Type-I IFN Antiviral Response.
Submit: New GeneRIF Correction See all GeneRIFs (12)

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
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
capsid gag Human TRIM6 binds in vitro assembled HIV-1 CA-NC complexes PubMed
gag The RING, B-box 2, and coiled-coil domains of TRIM6 can functionally replace the corresponding domains of rhesus monkey TRIM5alpha with respect to inhibition of HIV-1 infection through the binding of the chimeras to HIV-1 capsid complexes PubMed
nucleocapsid gag Human TRIM6 binds in vitro assembled HIV-1 CA-NC complexes PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Readthrough TRIM6-TRIM34

Readthrough gene: TRIM6-TRIM34, Included gene: TRIM34

Homology

Clone Names

  • MGC176399

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein kinase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein kinase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein tyrosine kinase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-macromolecule adaptor activity 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 ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin protein ligase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in antiviral innate immune response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to interferon-beta IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cellular response to virus IEA
Inferred from Electronic Annotation
more info
  
involved_in free ubiquitin chain polymerization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in free ubiquitin chain polymerization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in innate immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of stem cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of viral genome replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of NF-kappaB transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of autophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of canonical NF-kappaB signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cytokine production involved in immune response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of defense response to virus by host IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of peptidyl-serine phosphorylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of peptidyl-threonine phosphorylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription regulatory region DNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of type I interferon-mediated signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of type I interferon-mediated signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein K48-linked ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein polyubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
NOT involved_in regulation of non-canonical NF-kappaB signal transduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of protein localization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of viral entry into host cell IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to lipopolysaccharide IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
tripartite motif-containing protein 6
Names
RING finger protein 89
RING-type E3 ubiquitin transferase TRIM6
NP_001003818.1
NP_001185573.1
NP_001185574.1
NP_477514.1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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_001003818.3 → NP_001003818.1  tripartite motif-containing protein 6 isoform 1

    See identical proteins and their annotated locations for NP_001003818.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF220030, AK290172, AK316178, BC047564
    Consensus CDS
    CCDS31389.1
    UniProtKB/TrEMBL
    E9PFM0
    Related
    ENSP00000369440.3, ENST00000380097.8
    Conserved Domains (4) summary
    smart00336
    Location:121 → 161
    BBOX; B-Box-type zinc finger
    cd15823
    Location:327 → 514
    SPRY_PRY_TRIM6; PRY/SPRY domain in tripartite motif-binding protein 6 (TRIM6), also known as RING finger protein 89 (RNF89)
    cl17238
    Location:43 → 87
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    cl23765
    Location:170 → 287
    iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

  2. NM_001198644.2 → NP_001185573.1  tripartite motif-containing protein 6 isoform 3

    See identical proteins and their annotated locations for NP_001185573.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the 5' coding region, and uses a downstream AUG start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Both variants 3 and 4 encode the same isoform.
    Source sequence(s)
    AF220030, AK290172, AK293295, AK298301, AK316178, BC047564, DA401634
    Consensus CDS
    CCDS55738.1
    UniProtKB/Swiss-Prot
    Q9C030
    Related
    ENSP00000421079.1, ENST00000506134.5
    Conserved Domains (1) summary
    cd15823
    Location:124 → 311
    SPRY_PRY_TRIM6; PRY/SPRY domain in tripartite motif-binding protein 6 (TRIM6), also known as RING finger protein 89 (RNF89)

  3. NM_001198645.2 → NP_001185574.1  tripartite motif-containing protein 6 isoform 3

    See identical proteins and their annotated locations for NP_001185574.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two alternate exons in the 5' coding region, and uses a downstream AUG start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Both variants 3 and 4 encode the same isoform.
    Source sequence(s)
    AF220030, AK290172, AK293295, BC047564, DA401634
    Consensus CDS
    CCDS55738.1
    UniProtKB/Swiss-Prot
    Q9C030
    Related
    ENSP00000421802.1, ENST00000515022.5
    Conserved Domains (1) summary
    cd15823
    Location:124 → 311
    SPRY_PRY_TRIM6; PRY/SPRY domain in tripartite motif-binding protein 6 (TRIM6), also known as RING finger protein 89 (RNF89)

  4. NM_058166.5 → NP_477514.1  tripartite motif-containing protein 6 isoform 2

    See identical proteins and their annotated locations for NP_477514.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream AUG start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AF220030, AK027664, AK290172, DC354457
    Consensus CDS
    CCDS31390.1
    UniProtKB/Swiss-Prot
    A8K2A7, B4DDQ5, Q86WZ8, Q9C030
    UniProtKB/TrEMBL
    E9PFM0
    Related
    ENSP00000278302.5, ENST00000278302.9
    Conserved Domains (4) summary
    smart00336
    Location:93 → 133
    BBOX; B-Box-type zinc finger
    cd15823
    Location:299 → 486
    SPRY_PRY_TRIM6; PRY/SPRY domain in tripartite motif-binding protein 6 (TRIM6), also known as RING finger protein 89 (RNF89)
    cl17238
    Location:15 → 59
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    cl23765
    Location:142 → 259
    iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    5596111..5612952
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    5655518..5672393
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9C030.1 GenPept UniProtKB/Swiss-Prot:Q9C030

Gene LinkOut

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