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

Summary

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 symbiont; positive regulation of interferon-beta production; and protein ubiquitination. Located in cytoplasm. Orthologous to human TRIM56 (tripartite motif containing 56). [provided by Alliance of Genome Resources, Nov 2024]
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

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_000071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Key roles for phosphorylation and the Coiled-coil domain in TRIM56-mediated positive regulation of TLR3-TRIF-dependent innate immunity.
Title: Key roles for phosphorylation and the Coiled-coil domain in TRIM56-mediated positive regulation of TLR3-TRIF-dependent innate immunity.
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)

Endonuclease-mediated (2)
Targeted (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
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
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	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
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info

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

EC 2.3.2.27

XP_006504504.1

EC 2.3.2.27

XP_011239185.1

EC 2.3.2.27

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)

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

NC_000071.7 Reference GRCm39 C57BL/6J

Range

137140140..137145313 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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