Aliases for TRIM56 Gene

Aliases for TRIM56 Gene

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

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. Diseases associated with TRIM56 include Aicardi-Goutieres Syndrome. Among its related pathways are Cytosolic sensors of pathogen-associated DNA and Innate Immune System. Gene Ontology (GO) annotations related to this gene include ubiquitin-protein transferase activity. An important paralog of this gene is TRIM14.

UniProtKB/Swiss-Prot Summary 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 STING1 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 , Rfam classification and piRNA Summary for TRIM56 Gene

Genomics for TRIM56 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TRIM56 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRIM56 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRIM56

Genomic Locations for TRIM56 Gene

Latest Assembly
chr7:101,085,424-101,097,967
(GRCh38/hg38)
Size:
12,544 bases
Orientation:
Plus strand

Previous Assembly
chr7:100,728,762-100,741,248
(GRCh37/hg19 by Entrez Gene)
Size:
12,487 bases
Orientation:
Plus strand

chr7:100,728,720-100,735,017
(GRCh37/hg19 by Ensembl)
Size:
6,298 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 STING1 (By similarity). Interacts with TICAM1 (PubMed:22948160).
    SequenceCaution:
    • Sequence=AAH11882.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=BAC11500.1; Type=Erroneous initiation; Note=Truncated N-terminus.; 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

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

Protein Domains for TRIM56 Gene

InterPro:
Blocks:
  • Zn-finger, RING
  • RNA-binding region RNP-1 (RNA recognition motif)
  • B-box zinc finger signature

Suggested Antigen Peptide Sequences for TRIM56 Gene

GenScript: Design optimal peptide antigens:
  • Tripartite motif-containing protein 56 (TRI56_HUMAN)

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 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 STING1 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 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;.
UniProtKB/Swiss-Prot Induction:
Up-regulated by IFN-alpha.

Enzyme Numbers (IUBMB) for TRIM56 Gene

Phenotypes From GWAS Catalog for TRIM56 Gene

Gene Ontology (GO) - Molecular Function for TRIM56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0004842 ubiquitin-protein transferase activity TAS --
GO:0005515 protein binding IPI 22948160
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity 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:
  • Trim56 Trim56<tm1a(EUCOMM)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRIM56

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
nucleus 5
cytosol 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRIM56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IBA 21873635
GO:0005654 nucleoplasm IBA 21873635
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:0002376 immune system process IEA --
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 IBA 21873635
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

mRNA/cDNA for TRIM56 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRIM56

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

No ASD Table

Relevant External Links for TRIM56 Gene

GeneLoc Exon Structure for
TRIM56

Expression for TRIM56 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for TRIM56 Gene



Protein tissue co-expression partners for TRIM56 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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(4.4)
  • Spleen(4.4)
  • Liver(4.3)
  • Thyroid gland(4.1)
genes like me logo Genes that share expression patterns with TRIM56: view

Primer products for research

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 29 30
  • 98.89 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TRIM56 29
  • 87.15 (n)
-- 30
  • 19 (a)
ManyToMany
Cow
(Bos Taurus)
Mammalia TRIM56 29 30
  • 85.3 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Trim56 29 16 30
  • 79.22 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 19 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia TRIM56 30
  • 47 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta abba 30
  • 6 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea nhl-1 30
  • 11 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 13 (a)
OneToMany
Species where no ortholog for TRIM56 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)
  • 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for TRIM56: view image
Alliance of Genome Resources:
Additional Orthologs for TRIM56

Paralogs for TRIM56 Gene

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

  • TRI56_HUMAN
  • C9JI91_HUMAN
genes like me logo Genes that share paralogs with TRIM56: view

Variants for TRIM56 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRIM56 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
rs36004695 Benign: not provided 101,087,711(+) C/T
NM_030961.3(TRIM56):c.399C>T (p.Asp133=)
SYNONYMOUS
rs80324038 Benign: not provided 101,088,495(+) C/T
NM_030961.3(TRIM56):c.1183C>T (p.Arg395Trp)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TRIM56 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for TRIM56 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRIM56
Leiden Open Variation Database (LOVD)
TRIM56

SNP Genotyping and Copy Number Assays for research

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

Disorders for TRIM56 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TRIM56 Gene - From: COP

Disorder Aliases PubMed IDs
aicardi-goutieres syndrome
  • cree encephalitis
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TRIM56

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

No data available for 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 (Journal of virology 2014) 3 4
  2. TRIM56 is an essential component of the TLR3 antiviral signaling pathway. (PMID: 22948160) Shen Y … Li K (The Journal of biological chemistry 2012) 3 4
  3. TRIM56 is a virus- and interferon-inducible E3 ubiquitin ligase that restricts pestivirus infection. (PMID: 21289118) Wang J … Li K (Journal of virology 2011) 3 4
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for TRIM56 Gene

Sources for TRIM56 Gene