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Aliases for TRIM56 Gene

Aliases for TRIM56 Gene

  • Tripartite Motif Containing 56 2 3 5
  • RING-Type E3 Ubiquitin Transferase TRIM56 3 4
  • Tripartite Motif-Containing Protein 56 3 4
  • RING Finger Protein 109 3 4
  • RNF109 3 4
  • E3 Ubiquitin-Protein Ligase TRIM56 3
  • Tripartite Motif-Containing 56 2
  • EC 2.3.2.27 4

External Ids for TRIM56 Gene

Previous GeneCards Identifiers for TRIM56 Gene

  • GC07P099213
  • GC07P100275
  • GC07P100288
  • GC07P100322
  • GC07P100515
  • GC07P100728
  • GC07P095322

Summaries for TRIM56 Gene

GeneCards Summary for TRIM56 Gene

TRIM56 (Tripartite Motif Containing 56) is a Protein Coding gene. Among its related pathways are Innate Immune System and Cytosolic sensors of pathogen-associated DNA. GO annotations related to this gene include poly(A) RNA binding and ubiquitin-protein transferase activity. An important paralog of this gene is TRIM45.

UniProtKB/Swiss-Prot for TRIM56 Gene

  • E3 ubiquitin-protein ligase that plays a key role in innate antiviral immunity (PubMed:21289118). In response to pathogen- and host-derived double-stranded DNA (dsDNA), targets TMEM173/STING to Lys-63-linked ubiquitination, thereby promoting its homodimerization, a step required for the production of type I interferon IFN-beta (By similarity). Independently of its E3 ubiquitin ligase activity, positive regulator of TLR3 signaling. Potentiates extracellular double stranded RNA (dsRNA)-induced expression of IFNB1 and interferon-stimulated genes ISG15, IFIT1/ISG56, CXCL10, OASL and CCL5/RANTES. Promotes establishment of an antiviral state by TLR3 ligand and TLR3-mediated chemokine induction following infection by hepatitis C virus (PubMed:22948160).

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRIM56 Gene

Genomics for TRIM56 Gene

Regulatory Elements for TRIM56 Gene

Enhancers for TRIM56 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
GH07G101098 2.1 FANTOM5 Ensembl ENCODE dbSUPER 7.4 +16.6 16598 6.4 MLX CREB3L1 DMAP1 YY1 SLC30A9 MEF2D SSRP1 GLIS1 RCOR2 NBN SERPINE1 VGF NAT16 MUC12 MBLAC1 MUC3A MUC17 TRIM56 PCOLCE-AS1 LOC102724094
GH07G101943 1.4 Ensembl ENCODE dbSUPER 4.9 +858.9 858858 1.9 PKNOX1 CBX3 ZSCAN4 ZNF76 FEZF1 ZNF335 GLIS2 SCRT2 NFYC USF2 TRIM56 ENSG00000272219 GC07P101859
GH07G101116 2.1 FANTOM5 Ensembl ENCODE dbSUPER 2.6 +38.3 38320 15.1 MLX ZFP64 DMAP1 YY1 ZNF143 ZNF416 TBX21 MEF2D SSRP1 ZNF610 ENSG00000242798 GIGYF1 STAG3L5P PCOLCE-AS1 MBLAC1 ACTL6B PPP1R35 SERPINE1 NYAP1 MEPCE
GH07G101106 0.7 FANTOM5 dbSUPER 2.9 +21.2 21157 0.1 CEBPB FOXA1 VGF NAT16 MUC12 MUC3A MUC17 PCOLCE-AS1 TRIM56 GC07P101095 SERPINE1
GH07G101084 1.4 ENCODE dbSUPER 0.7 +0.5 509 2.9 HDGF PKNOX1 MLX ARNT SIN3A ARID4B DMAP1 ZNF2 YY1 SLC30A9 AP1S1 EPHB4 TRIM56 GC07P101095
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TRIM56 on UCSC Golden Path with GeneCards custom track

Promoters for TRIM56 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000215888 376 1201 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9

Genomic Location for TRIM56 Gene

Chromosome:
7
Start:
101,085,424 bp from pter
End:
101,097,967 bp from pter
Size:
12,544 bases
Orientation:
Plus strand

Genomic View for TRIM56 Gene

Genes around TRIM56 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRIM56 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRIM56 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRIM56 Gene

Proteins for TRIM56 Gene

  • Protein details for TRIM56 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BRZ2-TRI56_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase TRIM56
    Protein Accession:
    Q9BRZ2
    Secondary Accessions:
    • Q6PJS5
    • Q86VT6
    • Q8N2H8
    • Q8NAC0
    • Q9H031

    Protein attributes for TRIM56 Gene

    Size:
    755 amino acids
    Molecular mass:
    81488 Da
    Quaternary structure:
    • Homooligomer. Interacts with TMEM173/STING (By similarity). Interacts with TICAM1 (PubMed:22948160).
    SequenceCaution:
    • Sequence=AAH11882.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAC11500.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TRIM56 Gene

    Alternative splice isoforms for TRIM56 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRIM56 Gene

Post-translational modifications for TRIM56 Gene

Other Protein References for TRIM56 Gene

No data available for DME Specific Peptides for TRIM56 Gene

Domains & Families for TRIM56 Gene

Gene Families for TRIM56 Gene

Suggested Antigen Peptide Sequences for TRIM56 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9BRZ2

UniProtKB/Swiss-Prot:

TRI56_HUMAN :
  • Belongs to the TRIM/RBCC family.
Family:
  • Belongs to the TRIM/RBCC family.
genes like me logo Genes that share domains with TRIM56: view

Function for TRIM56 Gene

Molecular function for TRIM56 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 that plays a key role in innate antiviral immunity (PubMed:21289118). In response to pathogen- and host-derived double-stranded DNA (dsDNA), targets TMEM173/STING to Lys-63-linked ubiquitination, thereby promoting its homodimerization, a step required for the production of type I interferon IFN-beta (By similarity). Independently of its E3 ubiquitin ligase activity, positive regulator of TLR3 signaling. Potentiates extracellular double stranded RNA (dsRNA)-induced expression of IFNB1 and interferon-stimulated genes ISG15, IFIT1/ISG56, CXCL10, OASL and CCL5/RANTES. Promotes establishment of an antiviral state by TLR3 ligand and TLR3-mediated chemokine induction following infection by hepatitis C virus (PubMed:22948160).
UniProtKB/Swiss-Prot Induction:
Up-regulated by IFN-alpha.

Enzyme Numbers (IUBMB) for TRIM56 Gene

Gene Ontology (GO) - Molecular Function for TRIM56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0004842 ubiquitin-protein transferase activity TAS --
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with TRIM56: view
genes like me logo Genes that share phenotypes with TRIM56: view

Animal Models for TRIM56 Gene

MGI Knock Outs for TRIM56:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TRIM56 Gene

Localization for TRIM56 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRIM56 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 TRIM56 gene
Compartment Confidence
cytosol 5
nucleus 4

Gene Ontology (GO) - Cellular Components for TRIM56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005737 cytoplasm ISS --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with TRIM56: view

Pathways & Interactions for TRIM56 Gene

genes like me logo Genes that share pathways with TRIM56: view

Gene Ontology (GO) - Biological Process for TRIM56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032479 regulation of type I interferon production TAS --
GO:0032608 interferon-beta production ISS --
GO:0034340 response to type I interferon ISS --
GO:0045087 innate immune response IEA --
GO:0051607 defense response to virus ISS --
genes like me logo Genes that share ontologies with TRIM56: view

No data available for SIGNOR curated interactions for TRIM56 Gene

Drugs & Compounds for TRIM56 Gene

No Compound Related Data Available

Transcripts for TRIM56 Gene

Unigene Clusters for TRIM56 Gene

Tripartite motif containing 56:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TRIM56 Gene

No ASD Table

Relevant External Links for TRIM56 Gene

GeneLoc Exon Structure for
TRIM56
ECgene alternative splicing isoforms for
TRIM56

Expression for TRIM56 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TRIM56 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TRIM56 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (12.0), Cervix (10.9), and Lung (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TRIM56 Gene



Protein tissue co-expression partners for TRIM56 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TRIM56 Gene:

TRIM56

SOURCE GeneReport for Unigene cluster for TRIM56 Gene:

Hs.521092

mRNA Expression by UniProt/SwissProt for TRIM56 Gene:

Q9BRZ2-TRI56_HUMAN
Tissue specificity: Widely expressed (at protein level).

Evidence on tissue expression from TISSUES for TRIM56 Gene

  • Lymph node(4.2)
  • Spleen(4.2)
  • Liver(4.1)
  • Thyroid gland(4.1)
genes like me logo Genes that share expression patterns with TRIM56: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRIM56 Gene

Orthologs for TRIM56 Gene

This gene was present in the common ancestor of animals.

Orthologs for TRIM56 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TRIM56 34 35
  • 98.89 (n)
dog
(Canis familiaris)
Mammalia TRIM56 34
  • 87.15 (n)
-- 35
  • 19 (a)
ManyToMany
cow
(Bos Taurus)
Mammalia TRIM56 34 35
  • 85.3 (n)
mouse
(Mus musculus)
Mammalia Trim56 34 16 35
  • 79.22 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 19 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia TRIM56 35
  • 47 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta abba 35
  • 6 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea nhl-1 35
  • 11 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 13 (a)
OneToMany
Species where no ortholog for TRIM56 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)
  • chicken (Gallus gallus)
  • 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • zebrafish (Danio rerio)

Evolution for TRIM56 Gene

ENSEMBL:
Gene Tree for TRIM56 (if available)
TreeFam:
Gene Tree for TRIM56 (if available)

Paralogs for TRIM56 Gene

Paralogs for TRIM56 Gene

(2) SIMAP similar genes for TRIM56 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with TRIM56: view

Variants for TRIM56 Gene

Sequence variations from dbSNP and Humsavar for TRIM56 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs1000151433 -- 101,085,532(+) TCAGG(A/C)CCCCT utr-variant-5-prime
rs1000904371 -- 101,097,497(+) ATCAG(A/G)ACAGG utr-variant-3-prime
rs1000937424 -- 101,093,120(+) GTTAA(A/G)CAGAT utr-variant-3-prime
rs1000990039 -- 101,093,259(+) ATCTG(C/T)TGACC utr-variant-3-prime
rs1001272992 -- 101,097,798(+) ACATT(G/T)CCATG utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for TRIM56 Gene

Variant ID Type Subtype PubMed ID
esv2734888 CNV deletion 23290073
esv2759547 CNV gain+loss 17122850
nsv1030604 CNV gain 25217958
nsv1033081 CNV gain 25217958
nsv428181 CNV gain+loss 18775914
nsv831074 CNV loss 17160897
nsv831075 CNV loss 17160897

Variation tolerance for TRIM56 Gene

Residual Variation Intolerance Score: 7.25% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.14; 51.46% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TRIM56 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRIM56

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRIM56 Gene

Disorders for TRIM56 Gene

Relevant External Links for TRIM56

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TRIM56

No disorders were found for TRIM56 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TRIM56 Gene

Publications for TRIM56 Gene

  1. Overlapping and distinct molecular determinants dictating the antiviral activities of TRIM56 against flaviviruses and coronavirus. (PMID: 25253338) Liu B. … Li K. (J. Virol. 2014) 3 4 64
  2. TRIM56 is an essential component of the TLR3 antiviral signaling pathway. (PMID: 22948160) Shen Y. … Li K. (J. Biol. Chem. 2012) 3 4 64
  3. TRIM56 is a virus- and interferon-inducible E3 ubiquitin ligase that restricts pestivirus infection. (PMID: 21289118) Wang J. … Li K. (J. Virol. 2011) 3 4 64
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for TRIM56 Gene

Sources for TRIM56 Gene

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