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Trim56 tripartite motif-containing 56 [ Mus musculus (house mouse) ]

Gene ID: 384309, updated on 10-Mar-2024

Summary

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Official Symbol
Trim56provided by MGI
Official Full Name
tripartite motif-containing 56provided by MGI
Primary source
MGI:MGI:2685298
See related
Ensembl:ENSMUSG00000043279 AllianceGenome:MGI:2685298
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Gm452; RNF109; A130009K11Rik
Summary
Enables ubiquitin protein ligase activity. Involved in several processes, including defense response to other organism; positive regulation of interferon-beta production; and protein K63-linked ubiquitination. Located in cytoplasm. Orthologous to human TRIM56 (tripartite motif containing 56). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in thymus adult (RPKM 6.7), spleen adult (RPKM 5.3) and 21 other tissues See more
Orthologs
human all
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Genomic context

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Location:
5 G2; 5 76.19 cM
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (137140140..137145313, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (137111286..137116462, complement)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E4796 Neighboring gene adaptor protein complex AP-1, sigma 1 Neighboring gene serine (or cysteine) peptidase inhibitor, clade E, member 1 Neighboring gene STARR-seq mESC enhancer starr_14636 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:137579031-137579214 Neighboring gene mucin 17, cell surface associated Neighboring gene predicted gene, 40348 Neighboring gene predicted gene, 31160

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. TRIM56-mediated monoubiquitination of cGAS for cytosolic DNA sensing. Seo GJ, et al. Nat Commun, 2018 Feb 9. PMID 29426904, Free PMC Article
  2. UBXN3B positively regulates STING-mediated antiviral immune responses. Yang L, et al. Nat Commun, 2018 Jun 13. PMID 29899553, Free PMC Article
  3. The ubiquitin ligase TRIM56 regulates innate immune responses to intracellular double-stranded DNA. Tsuchida T, et al. Immunity, 2010 Nov 24. PMID 21074459
  4. TRIM E3 ligases interfere with early and late stages of the retroviral life cycle. Uchil PD, et al. PLoS Pathog, 2008 Feb 8. PMID 18248090, Free PMC Article
  5. The TRIM9/TRIM67 neuronal interactome reveals novel activators of morphogenesis. Menon S, et al. Mol Biol Cell, 2021 Feb 15. PMID 33378226, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TRIM56 protects against nonalcoholic fatty liver disease by promoting the degradation of fatty acid synthase.
    Title: TRIM56 protects against nonalcoholic fatty liver disease by promoting the degradation of fatty acid synthase.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (1) 
  • Endonuclease-mediated (2) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • MGC37358

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
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 ISO
Inferred from Sequence Orthology
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in defense response to virus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in defense response to virus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in defense response to virus ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within immune system process IEA
Inferred from Electronic Annotation
more info
  
involved_in innate immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in innate immune response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of viral entry into host cell IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of innate immune response ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of interferon-beta production IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of non-canonical NF-kappaB signal transduction ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of type I interferon-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
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 ISO
Inferred from Sequence Orthology
more info
  
involved_in protein K63-linked ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein monoubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein monoubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein monoubiquitination ISO
Inferred from Sequence Orthology
more info
  
involved_in response to type I interferon IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in suppression of viral release by host IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
E3 ubiquitin-protein ligase TRIM56
Names
RING-type E3 ubiquitin transferase TRIM56
tripartite motif-containing protein 56
NP_958761.1
XP_006504504.1
XP_011239185.1

NCBI Reference Sequences (RefSeq)

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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_201373.4 → NP_958761.1  E3 ubiquitin-protein ligase TRIM56

    See identical proteins and their annotated locations for NP_958761.1

    Status: VALIDATED

    Source sequence(s)
    AC147986
    Consensus CDS
    CCDS19762.1
    UniProtKB/Swiss-Prot
    Q80VI1, Q8CAY0
    UniProtKB/TrEMBL
    A0A0R4J0Q6
    Related
    ENSMUSP00000058109.6, ENSMUST00000054384.6
    Conserved Domains (7) summary
    cd05819
    Location:531 → 569
    NHL; NHL repeat [structural motif]
    TIGR02168
    Location:205 → 336
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    sd00039
    Location:540 → 568
    7WD40; WD40 repeat [structural motif]
    cl18310
    Location:500 → 727
    NHL; NHL repeat unit of beta-propeller proteins
    cd19810
    Location:99 → 149
    Bbox1_TRIM56_C-V; B-box-type 1 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar proteins
    cl00034
    Location:165 → 209
    Bbox_SF; B-box-type zinc finger superfamily
    cl17238
    Location:19 → 60
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    137140140..137145313 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011240883.3 → XP_011239185.1  E3 ubiquitin-protein ligase TRIM56 isoform X1

    See identical proteins and their annotated locations for XP_011239185.1

    UniProtKB/Swiss-Prot
    Q80VI1, Q8CAY0
    UniProtKB/TrEMBL
    A0A0R4J0Q6
    Conserved Domains (7) summary
    cd05819
    Location:531 → 569
    NHL; NHL repeat [structural motif]
    TIGR02168
    Location:205 → 336
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    sd00039
    Location:540 → 568
    7WD40; WD40 repeat [structural motif]
    cl18310
    Location:500 → 727
    NHL; NHL repeat unit of beta-propeller proteins
    cd19810
    Location:99 → 149
    Bbox1_TRIM56_C-V; B-box-type 1 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar proteins
    cl00034
    Location:165 → 209
    Bbox_SF; B-box-type zinc finger superfamily
    cl17238
    Location:19 → 60
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

  2. XM_006504441.5 → XP_006504504.1  E3 ubiquitin-protein ligase TRIM56 isoform X1

    See identical proteins and their annotated locations for XP_006504504.1

    UniProtKB/Swiss-Prot
    Q80VI1, Q8CAY0
    UniProtKB/TrEMBL
    A0A0R4J0Q6
    Conserved Domains (7) summary
    cd05819
    Location:531 → 569
    NHL; NHL repeat [structural motif]
    TIGR02168
    Location:205 → 336
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    sd00039
    Location:540 → 568
    7WD40; WD40 repeat [structural motif]
    cl18310
    Location:500 → 727
    NHL; NHL repeat unit of beta-propeller proteins
    cd19810
    Location:99 → 149
    Bbox1_TRIM56_C-V; B-box-type 1 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar proteins
    cl00034
    Location:165 → 209
    Bbox_SF; B-box-type zinc finger superfamily
    cl17238
    Location:19 → 60
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q80VI1.1 GenPept UniProtKB/Swiss-Prot:Q80VI1

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