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Aliases for TRIM6 Gene

Aliases for TRIM6 Gene

  • Tripartite Motif Containing 6 2 3 5
  • RING-Type E3 Ubiquitin Transferase TRIM6 3 4
  • RING Finger Protein 89 3 4
  • RNF89 3 4
  • Tripartite Motif-Containing Protein 6 3
  • Tripartite Motif-Containing 6 2
  • EC 2.3.2.27 4
  • EC 6.3.2 61

External Ids for TRIM6 Gene

Previous GeneCards Identifiers for TRIM6 Gene

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

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 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

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRIM6 Gene

Genomics for TRIM6 Gene

Regulatory Elements for TRIM6 Gene

Enhancers for TRIM6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G005595 1 ENCODE 15.5 +1.0 985 3.2 PKNOX1 FOXA2 ATF1 ARNT E2F7 SIN3A TCF12 GLIS2 GATA2 FOS TRIM6 OR52H1 TRIM6-TRIM34 PIR57907
GH11G005599 1.4 Ensembl ENCODE dbSUPER 10.9 +4.5 4468 1.4 HDAC1 FOXA2 ATF1 CBX3 CREB3L1 SIN3A ZBTB40 RAD21 RARA TCF12 TRIM6 TRIM6-TRIM34 PIR57907
GH11G005618 1.3 Ensembl ENCODE dbSUPER 11.5 +24.2 24249 3.8 TFAP4 FOXA2 TAL1 SIN3A RARA ZNF7 TCF12 FOXM1 CTBP1 GATA3 TRIM5 UBQLNL ENSG00000239920 HBG2 TRIM6 TRIM22 TRIM34
GH11G005808 1 Ensembl ENCODE 10.3 +212.9 212901 1.2 CTCF RBBP5 EBF1 RAD21 ZBTB48 ZNF143 ZNF207 SMC3 ZNF654 RNF2 OR52N3P TRIM5 TRIM22 TRIM6 OR52N1 OR52N2 OR52E6
GH11G005683 1 ENCODE 9.9 +88.9 88937 2.7 CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 YY1 ZNF766 CBX5 ZNF143 TRIM22 TRIM5 HBG2 TRIM6 OR52D1 OR52N3P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TRIM6 on UCSC Golden Path with GeneCards custom track

Promoters for TRIM6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000036230 499 1201 PKNOX1 ARNT E2F7 SIN3A TCF12 GATA2 KDM4B ZNF263 NCOA1 MBD2

Genomic Location for TRIM6 Gene

Chromosome:
11
Start:
5,596,101 bp from pter
End:
5,612,958 bp from pter
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).
    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

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 CatalyticActivity:
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.
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).

Enzyme Numbers (IUBMB) for TRIM6 Gene

Gene Ontology (GO) - Molecular Function for TRIM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005515 protein binding IPI 25127057
GO:0008134 transcription factor binding IEA --
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
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

miRNA for TRIM6 Gene

miRTarBase miRNAs that target TRIM6

Inhibitory RNA Products

Flow Cytometry Products

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

Gene Ontology (GO) - Cellular Components for TRIM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA,IDA 17156811
GO:0005829 cytosol IEA --
genes like me logo Genes that share ontologies with TRIM6: view

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 --
GO:0002230 positive regulation of defense response to virus by host IMP 24882218
GO:0002741 positive regulation of cytokine secretion involved in immune response IMP 24882218
GO:0010628 positive regulation of gene expression IEA --
GO:0010629 negative regulation of gene expression IMP 24882218
genes like me logo Genes that share ontologies with TRIM6: view

No data available for SIGNOR curated interactions for TRIM6 Gene

Transcripts for TRIM6 Gene

Unigene Clusters for TRIM6 Gene

Tripartite motif containing 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

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
ECgene alternative splicing isoforms for
TRIM6

Expression for TRIM6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, and MOPED for TRIM6 Gene



NURSA nuclear receptor signaling pathways regulating expression of TRIM6 Gene:

TRIM6

SOURCE GeneReport for Unigene cluster for TRIM6 Gene:

Hs.729048

Evidence on tissue expression from TISSUES for TRIM6 Gene

  • Kidney(4.3)
  • Nervous system(4)
genes like me logo Genes that share expression patterns with TRIM6: view

Primer Products

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 34 35
  • 99.25 (n)
dog
(Canis familiaris)
Mammalia TRIM6 34
  • 86.17 (n)
cow
(Bos Taurus)
Mammalia TRIM6 34
  • 84.94 (n)
-- 35
  • 43 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Trim6 34
  • 81.83 (n)
mouse
(Mus musculus)
Mammalia Trim6 34 16 35
  • 81.63 (n)
chicken
(Gallus gallus)
Aves -- 35
  • 33 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 33 (a)
OneToMany
Species where no ortholog for TRIM6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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)

Paralogs for TRIM6 Gene

Variants for TRIM6 Gene

Sequence variations from dbSNP and Humsavar for TRIM6 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1000045375 -- 5,613,101(+) ATGGA(C/T)TCAGG intron-variant, downstream-variant-500B
rs1000137673 -- 5,598,084(+) TCTGC(C/T)AATTT intron-variant
rs1000190275 -- 5,598,418(+) TATCT(A/G)CAGCG intron-variant
rs1000373977 -- 5,603,422(+) CCAAG(C/T)CTGCA intron-variant, reference, missense
rs1000474907 -- 5,609,142(+) TCTAT(C/G/T)ACATA intron-variant

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)

Relevant External Links for TRIM6 Gene

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

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

Disorders for TRIM6 Gene

Relevant External Links for TRIM6

Genetic Association Database (GAD)
TRIM6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 22 64
  2. The tripartite motif family identifies cell compartments. (PMID: 11331580) Reymond A. … Ballabio A. (EMBO J. 2001) 2 3 4 64
  3. Unanchored K48-linked polyubiquitin synthesized by the E3-ubiquitin ligase TRIM6 stimulates the interferon-IKKI/ kinase-mediated antiviral response. (PMID: 24882218) Rajsbaum R. … GarcA-a-Sastre A. (Immunity 2014) 3 4 64
  4. Determinants of the higher order association of the restriction factor TRIM5alpha and other tripartite motif (TRIM) proteins. (PMID: 21680743) Li X. … Sodroski J. (J. Biol. Chem. 2011) 3 4 64
  5. Discordant evolution of the adjacent antiretroviral genes TRIM22 and TRIM5 in mammals. (PMID: 18159944) Sawyer S.L. … Malik H.S. (PLoS Pathog. 2007) 3 22 64

Products for TRIM6 Gene

Sources for TRIM6 Gene

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