TRIM56 tripartite motif containing 56 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TRIM56provided by HGNC
Official Full Name: tripartite motif containing 56provided by HGNC
Primary source: HGNC:HGNC:19028
See related: Ensembl:ENSG00000169871 MIM:616996; AllianceGenome:HGNC:19028
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: RNF109
Summary: Enables RNA binding activity. Predicted to be involved in several processes, including defense response to other organism; positive regulation of macromolecule metabolic process; and protein K63-linked ubiquitination. Predicted to be located in cytoplasm. Predicted to be active in chromatin and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in spleen (RPKM 9.3), ovary (RPKM 7.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q22.1

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (101085481..101097967)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (102408287..102420773)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (100728762..100741248)

Chromosome 7 - NC_000007.14 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TRIM56: a promising prognostic immune biomarker for glioma revealed by pan-cancer and single-cell analysis.
Title: TRIM56: a promising prognostic immune biomarker for glioma revealed by pan-cancer and single-cell analysis.
The Functions of TRIM56 in Antiviral Innate Immunity and Tumorigenesis.
Title: The Functions of TRIM56 in Antiviral Innate Immunity and Tumorigenesis.
Exosomal circZNF451 restrains anti-PD1 treatment in lung adenocarcinoma via polarizing macrophages by complexing with TRIM56 and FXR1.
Title: Exosomal circZNF451 restrains anti-PD1 treatment in lung adenocarcinoma via polarizing macrophages by complexing with TRIM56 and FXR1.
TRIM56 promotes malignant progression of glioblastoma by stabilizing cIAP1 protein.
Title: TRIM56 promotes malignant progression of glioblastoma by stabilizing cIAP1 protein.
TRIM56 impairs HBV infection and replication by inhibiting HBV core promoter activity.
Title: TRIM56 impairs HBV infection and replication by inhibiting HBV core promoter activity.
Impaired Antiviral Responses to Extracellular Double-Stranded RNA and Cytosolic DNA, but Not to Interferon-alpha Stimulation, in TRIM56-Deficient Cells.
Title: Impaired Antiviral Responses to Extracellular Double-Stranded RNA and Cytosolic DNA, but Not to Interferon-α Stimulation, in TRIM56-Deficient Cells.
TRIM56 suppresses the malignant development of hepatocellular carcinoma via targeting RBM24 and inactivating the Wnt signaling.
Title: TRIM56 suppresses the malignant development of hepatocellular carcinoma via targeting RBM24 and inactivating the Wnt signaling.
Suppression of the SAP18/HDAC1 complex by targeting TRIM56 and Nanog is essential for oncogenic viral FLICE-inhibitory protein-induced acetylation of p65/RelA, NF-kappaB activation, and promotion of cell invasion and angiogenesis.
Title: Suppression of the SAP18/HDAC1 complex by targeting TRIM56 and Nanog is essential for oncogenic viral FLICE-inhibitory protein-induced acetylation of p65/RelA, NF-κB activation, and promotion of cell invasion and angiogenesis.
PCBP1 regulates post-transcriptional expression of TRIM56 in ovarian cancer.
Title: Poly r(C) Binding Protein 1 Regulates Posttranscriptional Expression of the Ubiquitin Ligase TRIM56 in Ovarian Cancer.
Altogether, this study reveals TRIM56 is an RNA binding protein that acts as a Zika virus restriction factor and provides new insights into the antiviral mechanism by which this E3 ligase tackles flavivirus infections.
Title: The E3 ligase TRIM56 is a host restriction factor of Zika virus and depends on its RNA-binding activity but not miRNA regulation, for antiviral function.

Submit: New GeneRIF Correction See all GeneRIFs (20)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of tripartite motif containing 56 (TRIM56) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
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	ISS Inferred from Sequence or Structural Similarity more info
enables ubiquitin-protein transferase activity	TAS Traceable Author Statement 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	ISS Inferred from Sequence or Structural Similarity more info
involved_in innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of innate immune response	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of interferon-beta production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of non-canonical NF-kappaB signal transduction	IDA Inferred from Direct Assay more info	PubMed
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 protein K63-linked ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
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 regulation of type I interferon production	TAS Traceable Author Statement more info
involved_in response to type I interferon	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	TAS Traceable Author Statement more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase TRIM56

Names: RING finger protein 109; RING-type E3 ubiquitin transferase TRIM56; tripartite motif-containing protein 56

NP_112223.1

EC 2.3.2.27

XP_011514891.1

EC 2.3.2.27

XP_054215089.1

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_030961.3 → NP_112223.1 E3 ubiquitin-protein ligase TRIM56

See identical proteins and their annotated locations for NP_112223.1

Status: VALIDATED

Source sequence(s)

AC105446, BC005847, BC048194

Consensus CDS

CCDS43625.1

UniProtKB/Swiss-Prot

Q6PJS5, Q86VT6, Q8N2H8, Q8NAC0, Q9BRZ2, Q9H031

Related

ENSP00000305161.6, ENST00000306085.11

Conserved Domains (6) summary

cd00021
Location:169 → 205

BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.

cd05819
Location:598 → 626

NHL; NHL repeat [structural motif]

sd00039
Location:593 → 627

7WD40; WD40 repeat [structural motif]

cl18310
Location:521 → 748

NHL; NHL repeat unit of beta-propeller proteins

cd16584
Location:19 → 60

RING-HC_TRIM56_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar proteins

cl28410
Location:8 → 214

RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

101085481..101097967

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011516589.4 → XP_011514891.1 E3 ubiquitin-protein ligase TRIM56 isoform X1

See identical proteins and their annotated locations for XP_011514891.1

UniProtKB/Swiss-Prot

Q6PJS5, Q86VT6, Q8N2H8, Q8NAC0, Q9BRZ2, Q9H031

Conserved Domains (6) summary

cd00021
Location:169 → 205

BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.

cd05819
Location:598 → 626

NHL; NHL repeat [structural motif]

sd00039
Location:593 → 627

7WD40; WD40 repeat [structural motif]

cl18310
Location:521 → 748

NHL; NHL repeat unit of beta-propeller proteins

cd16584
Location:19 → 60

RING-HC_TRIM56_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar proteins

cl28410
Location:8 → 214

RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]