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 cluste... See more...

Aliases for TRIM6 Gene

Aliases for TRIM6 Gene

  • Tripartite Motif Containing 6 2 3 5
  • RNF89 2 3 4
  • RING-Type E3 Ubiquitin Transferase TRIM6 3 4
  • Tripartite Motif-Containing Protein 6 3 4
  • RING Finger Protein 89 3 4
  • Tripartite Motif-Containing 6 2
  • EC 2.3.2.27 4
  • EC 6.3.2 51
  • TRIM6 5

External Ids for TRIM6 Gene

Previous GeneCards Identifiers for TRIM6 Gene

  • GC11P006365
  • GC11P005919
  • GC11P005576
  • GC11P005581
  • GC11P005573
  • GC11P005276
  • GC11P005617

Summaries for TRIM6 Gene

Entrez Gene Summary for TRIM6 Gene

  • 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]

GeneCards Summary for TRIM6 Gene

TRIM6 (Tripartite Motif Containing 6) is a Protein Coding gene. Among its related pathways are Interferon gamma signaling and Innate Immune System. An important paralog of this gene is TRIM6-TRIM34.

UniProtKB/Swiss-Prot Summary for TRIM6 Gene

  • E3 ubiquitin-protein ligase which ubiquitinates MYC and inhibits its transcription activation activity, maintaining the pluripotency of embryonic stem cells (By similarity). Involved in the synthesis of unanchored K48-linked polyubiquitin chains which interact with and activate the serine/threonine kinase IKBKE, leading to phosphorylation of STAT1 and stimulation of an antiviral response (PubMed:24882218).

Gene Wiki entry for TRIM6 Gene

Additional gene information for TRIM6 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRIM6 Gene

Genomics for TRIM6 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TRIM6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J005595 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 615.5 +1.0 1047 3.3 LEF1 IKZF1 JUND DDX20 PKNOX1 NR2C1 BRD9 ZNF24 DPF2 HDAC1 TRIM6 TRIM6-TRIM34 OR52H1 piR-34862 TRIM34 lnc-OR52H1-1 ENSG00000239920 TRIM5
GH11J005603 Promoter/Enhancer 1.1 EPDnew Ensembl ENCODE dbSUPER 607.8 +8.6 8602 3 RAD21 CTCF SMC3 ZNF335 BHLHE40 TRIM6 TRIM5 TRIM6-TRIM34 piR-34862 TRIM34 lnc-OR52H1-1 ENSG00000239920
GH11J005683 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 10 +88.7 88677 3.2 SP1 CREB1 GATAD2A CTCF PRDM10 REST LEF1 IKZF1 POLR2A JUND TRIM5 piR-31470-069 piR-39099-048 piR-58297-068 TRIM22 HBG2 TRIM6 OR52D1 OR52N3P ENSG00000239920
GH11J005618 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 11.5 +24.2 24240 3.8 IKZF1 ZNF7 FOXA1 REST CEBPA EP300 SCRT2 SP1 CEBPB CTBP1 TRIM34 TRIM5 UBQLNL ENSG00000239920 HBG2 TRIM6 TRIM22 lnc-OR52H1-1 TRIM6-TRIM34
GH11J005688 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 10 +94.6 94633 4.5 POLR2A BACH1 STAT3 RELA MTA1 REST IKZF2 RCOR1 DPF2 SOX6 TRIM22 TRIM5 OR52N1 TRIM6 OR52D1 HBG2 lnc-OR52N5-1 OR52N4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRIM6 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRIM6

Top Transcription factor binding sites by QIAGEN in the TRIM6 gene promoter:
  • AP-1
  • C/EBPalpha
  • LCR-F1
  • Meis-1
  • MyoD
  • Sp1

Genomic Locations for TRIM6 Gene

Genomic Locations for TRIM6 Gene
chr11:5,596,109-5,612,958
(GRCh38/hg38)
Size:
16,850 bases
Orientation:
Plus strand
chr11:5,617,331-5,634,188
(GRCh37/hg19)
Size:
16,858 bases
Orientation:
Plus strand

Genomic View for TRIM6 Gene

Genes around TRIM6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRIM6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRIM6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRIM6 Gene

Proteins for TRIM6 Gene

  • Protein details for TRIM6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9C030-TRIM6_HUMAN
    Recommended name:
    Tripartite motif-containing protein 6
    Protein Accession:
    Q9C030
    Secondary Accessions:
    • A8K2A7
    • B4DDQ5
    • Q86WZ8
    • Q9HCR1

    Protein attributes for TRIM6 Gene

    Size:
    488 amino acids
    Molecular mass:
    56400 Da
    Quaternary structure:
    • Homotrimer (PubMed:17156811). Forms heteromultimers (via B30.2/SPRY domain) with TRIM5 (PubMed:21680743). Interacts with MYC (By similarity). Interacts (via SPRY domain) with IKBKE (PubMed:24882218). Interacts with HIV-1 capsid complexes (PubMed:17156811).
    • (Microbial infection) Interacts with ebolavirus protein VP35; this interaction plays an important role in promoting efficient viral replication.
    SequenceCaution:
    • Sequence=BAB17050.1; Type=Miscellaneous discrepancy; Note=Chimeric cDNA. The in vivo relevance of this transcript of the TRIM34 (AC Q9BYJ4) and TRIM6 genes that codes for a chimeric protein of 842 residues is uncertain.; Evidence={ECO:0000305};

    Alternative splice isoforms for TRIM6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRIM6 Gene

Selected DME Specific Peptides for TRIM6 Gene

Q9C030:
  • CPICLEL
  • ICWLCERSQEHRGH
  • EEVAQEY
  • RVGVFLDYEA
  • AWILGVC
  • GYWVIGL

Post-translational modifications for TRIM6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for TRIM6 Gene

Gene Families for TRIM6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for TRIM6 Gene

InterPro:
Blocks:
  • Zn-finger, RING
  • Butyrophylin C-terminal DUF signature
  • SPRY-associated domain
  • B-box zinc finger signature
ProtoNet:

Suggested Antigen Peptide Sequences for TRIM6 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ79188, highly similar to Tripartite motif-containing protein 6 (B4DDQ5_HUMAN)
  • TRIM6 protein (Q6P0L0_HUMAN)
  • RING finger protein 89 (TRIM6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9C030

UniProtKB/Swiss-Prot:

TRIM6_HUMAN :
  • The B-box zinc finger and the linker region between the coiled coil and B30.2/SPRY domains contribute to higher order self-association.
  • Belongs to the TRIM/RBCC family.
Domain:
  • The B-box zinc finger and the linker region between the coiled coil and B30.2/SPRY domains contribute to higher order self-association.
Family:
  • Belongs to the TRIM/RBCC family.
genes like me logo Genes that share domains with TRIM6: view

Function for TRIM6 Gene

Molecular function for TRIM6 Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase which ubiquitinates MYC and inhibits its transcription activation activity, maintaining the pluripotency of embryonic stem cells (By similarity). Involved in the synthesis of unanchored K48-linked polyubiquitin chains which interact with and activate the serine/threonine kinase IKBKE, leading to phosphorylation of STAT1 and stimulation of an antiviral response (PubMed:24882218).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.; EC=2.3.2.27; Evidence={ECO:0000250|UniProtKB:Q8BGE7};.

Enzyme Numbers (IUBMB) for TRIM6 Gene

Phenotypes From GWAS Catalog for TRIM6 Gene

Gene Ontology (GO) - Molecular Function for TRIM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA,IPI 25127057
GO:0008134 transcription factor binding IEA --
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
GO:0019901 protein kinase binding IPI 24882218
genes like me logo Genes that share ontologies with TRIM6: view
genes like me logo Genes that share phenotypes with TRIM6: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRIM6

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TRIM6 Gene

Localization for TRIM6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRIM6 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TRIM6 gene
Compartment Confidence
nucleus 4
cytosol 3
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for TRIM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IBA 21873635
GO:0005737 cytoplasm IEA,IDA 17156811
GO:0005829 cytosol IEA --
genes like me logo Genes that share ontologies with TRIM6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TRIM6 Gene

Pathways & Interactions for TRIM6 Gene

genes like me logo Genes that share pathways with TRIM6: view

Pathways by source for TRIM6 Gene

UniProtKB/Swiss-Prot Q9C030-TRIM6_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for TRIM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000209 protein polyubiquitination IEA,IBA 21873635
GO:0002230 positive regulation of defense response to virus by host IMP 24882218
GO:0002720 positive regulation of cytokine production involved in immune response IMP 24882218
GO:0002741 positive regulation of cytokine secretion involved in immune response IMP --
GO:0010468 regulation of gene expression IBA 21873635
genes like me logo Genes that share ontologies with TRIM6: view

No data available for SIGNOR curated interactions for TRIM6 Gene

Drugs & Compounds for TRIM6 Gene

No Compound Related Data Available

Transcripts for TRIM6 Gene

mRNA/cDNA for TRIM6 Gene

4 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRIM6

Alternative Splicing Database (ASD) splice patterns (SP) for TRIM6 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16
SP1: -
SP2: - - -
SP3: - -
SP4: -
SP5:
SP6: -
SP7:
SP8:
SP9:

Relevant External Links for TRIM6 Gene

GeneLoc Exon Structure for
TRIM6

Expression for TRIM6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRIM6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TRIM6 Gene

This gene is overexpressed in Kidney - Cortex (x9.4).

Protein differential expression in normal tissues from HIPED for TRIM6 Gene

This gene is overexpressed in Bone marrow stromal cell (20.3), Breast (18.4), Uterus (13.1), and Urine (8.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TRIM6 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRIM6

SOURCE GeneReport for Unigene cluster for TRIM6 Gene:

Hs.729048

Evidence on tissue expression from TISSUES for TRIM6 Gene

  • Kidney(4.4)
  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with TRIM6: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRIM6 Gene

Orthologs for TRIM6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TRIM6 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TRIM6 30 31
  • 99.25 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TRIM6 30
  • 86.17 (n)
Cow
(Bos Taurus)
Mammalia TRIM6 30
  • 84.94 (n)
-- 31
  • 43 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Trim6 30
  • 81.83 (n)
Mouse
(Mus musculus)
Mammalia Trim6 30 17 31
  • 81.63 (n)
OneToOne
Chicken
(Gallus gallus)
Aves -- 31
  • 33 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 33 (a)
OneToMany
Species where no ortholog for TRIM6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for TRIM6 Gene

ENSEMBL:
Gene Tree for TRIM6 (if available)
TreeFam:
Gene Tree for TRIM6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRIM6: view image

Paralogs for TRIM6 Gene

(29) SIMAP similar genes for TRIM6 Gene using alignment to 4 proteins:

  • TRIM6_HUMAN
  • C9JNQ0_HUMAN
  • E9PFM0_HUMAN
  • Q6P0L0_HUMAN
genes like me logo Genes that share paralogs with TRIM6: view

Variants for TRIM6 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRIM6 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
727334 Likely Benign: not provided 5,604,536(+) G/T MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT
752556 Likely Benign: not provided 5,604,572(+) G/A SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT
rs57856328 - p.Glu154Lys

Additional dbSNP identifiers (rs#s) for TRIM6 Gene

Structural Variations from Database of Genomic Variants (DGV) for TRIM6 Gene

Variant ID Type Subtype PubMed ID
esv2658921 CNV deletion 23128226
esv2760210 CNV gain 21179565
esv3547256 CNV deletion 23714750
esv3625236 CNV loss 21293372
esv3625237 CNV loss 21293372
esv3625238 CNV loss 21293372
esv3625239 CNV loss 21293372
nsv1041568 CNV loss 25217958
nsv1046068 CNV gain 25217958
nsv1048455 CNV gain 25217958
nsv1048608 CNV gain 25217958
nsv1053414 CNV gain 25217958
nsv1054035 CNV gain 25217958
nsv471746 CNV loss 16327809
nsv553241 CNV gain 21841781
nsv553260 CNV loss 21841781

Variation tolerance for TRIM6 Gene

Residual Variation Intolerance Score: 50.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.25; 70.12% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRIM6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRIM6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRIM6 Gene

Disorders for TRIM6 Gene

Additional Disease Information for TRIM6

No disorders were found for TRIM6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TRIM6 Gene

Publications for TRIM6 Gene

  1. Unique features of TRIM5alpha among closely related human TRIM family members. (PMID: 17156811) Li X … Sodroski J (Virology 2007) 3 4 23
  2. The tripartite motif family identifies cell compartments. (PMID: 11331580) Reymond A … Ballabio A (The EMBO journal 2001) 2 3 4
  3. The Host E3-Ubiquitin Ligase TRIM6 Ubiquitinates the Ebola Virus VP35 Protein and Promotes Virus Replication. (PMID: 28679761) Bharaj P … Rajsbaum R (Journal of virology 2017) 3 4
  4. Unanchored K48-linked polyubiquitin synthesized by the E3-ubiquitin ligase TRIM6 stimulates the interferon-IKKε kinase-mediated antiviral response. (PMID: 24882218) Rajsbaum R … García-Sastre A (Immunity 2014) 3 4
  5. Determinants of the higher order association of the restriction factor TRIM5alpha and other tripartite motif (TRIM) proteins. (PMID: 21680743) Li X … Sodroski J (The Journal of biological chemistry 2011) 3 4

Products for TRIM6 Gene

Sources for TRIM6 Gene