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TRIM23 tripartite motif containing 23 [ Homo sapiens (human) ]

Gene ID: 373, updated on 2-Nov-2024

Summary

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Official Symbol
TRIM23provided by HGNC
Official Full Name
tripartite motif containing 23provided by HGNC
Primary source
HGNC:HGNC:660
See related
Ensembl:ENSG00000113595 MIM:601747; AllianceGenome:HGNC:660
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ARD1; ARFD1; RNF46
Summary
The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This protein is also a member of the ADP ribosylation factor family of guanine nucleotide-binding family of proteins. Its carboxy terminus contains an ADP-ribosylation factor domain and a guanine nucleotide binding site, while the amino terminus contains a GTPase activating protein domain which acts on the guanine nucleotide binding site. The protein localizes to lysosomes and the Golgi apparatus. It plays a role in the formation of intracellular transport vesicles, their movement from one compartment to another, and phopholipase D activation. Three alternatively spliced transcript variants for this gene have been described. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in brain (RPKM 18.0), prostate (RPKM 7.0) and 24 other tissues See more
Orthologs
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Genomic context

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See TRIM23 in Genome Data Viewer
Location:
5q12.3
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (65589690..65624333, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (66411457..66448919, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (64885517..64920160, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene centromere protein K Neighboring gene MPRA-validated peak5269 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:64855281-64855780 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64858250-64858911 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64858912-64859572 Neighboring gene peptidylprolyl isomerase domain and WD repeat containing 1 Neighboring gene RNA, U6 small nuclear 540, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22608 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:64934876-64935323 Neighboring gene trafficking protein particle complex subunit 13 Neighboring gene shieldin complex subunit 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22609 Neighboring gene small glutamine rich tetratricopeptide repeat co-chaperone beta Neighboring gene ReSE screen-validated silencer GRCh37_chr5:65015266-65015462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16056 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16058 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:65018623-65019444 Neighboring gene neurolysin

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. TRIM27 Promotes Hepatitis C Virus Replication by Suppressing Type I Interferon Response. Zheng F, et al. Inflammation, 2019 Aug. PMID 30847745
  2. Characterization of a GDP dissociation inhibitory region of ADP-ribosylation factor domain protein ARD1. Vitale N, et al. J Biol Chem, 1997 Oct 3. PMID 9312116
  3. Molecular characterization of the GTPase-activating domain of ADP-ribosylation factor domain protein 1 (ARD1). Vitale N, et al. J Biol Chem, 1998 Jan 30. PMID 9446556
  4. Elevated TRIM23 expression predicts poor prognosis in Chinese gastric cancer. Yao Y, et al. Pathol Res Pract, 2018 Dec. PMID 30477642
  5. Identification of lysosomal and Golgi localization signals in GAP and ARF domains of ARF domain protein 1. Vitale N, et al. Mol Cell Biol, 2000 Oct. PMID 10982851, Free PMC Article

See all (61) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Herpesvirus-mediated stabilization of ICP0 expression neutralizes restriction by TRIM23.
    Title: Herpesvirus-mediated stabilization of ICP0 expression neutralizes restriction by TRIM23.
  2. TRIM23 overexpression is a poor prognostic factor and contributes to carcinogenesis in colorectal cancer.
    Title: TRIM23 overexpression is a poor prognostic factor and contributes to carcinogenesis in colorectal cancer.
  3. Opposing roles of E3 ligases TRIM23 and TRIM21 in regulation of ion channel ANO1 protein levels.
    Title: Opposing roles of E3 ligases TRIM23 and TRIM21 in regulation of ion channel ANO1 protein levels.
  4. Data report that the Us11 protein targets TRIM23, which is a key regulator of autophagy-mediated antiviral defense mediated by TBK1. In virus-infected cells, the Us11 protein drastically reduces the formation of autophagosomes mediated by TRIM23 or TBK1. This autophagy-inhibitory effect is attributable to the binding of the Us11 protein to the ARF domain in TRIM23.
    Title: Disassembly of the TRIM23-TBK1 Complex by the Us11 Protein of Herpes Simplex Virus 1 Impairs Autophagy.
  5. Study found that TRIM23 was upregulated in lung adenocarcinoma (LUAD), and elevated TRIM23 expression was correlated with high expression of NF-kappaB, poor cellular differentiation, and adverse overall survival and disease-free survival. Furthermore, TRIM23 acted as an oncogene in LUAD and promoted cisplatin-resistance by regulating glucose metabolism.
    Title: Elevated TRIM23 expression predicts cisplatin resistance in lung adenocarcinoma.
  6. study identifies TRIM27 as a novel positive regulator of HCV replication
    Title: TRIM27 Promotes Hepatitis C Virus Replication by Suppressing Type I Interferon Response.
  7. TRIM23 may be associated with progression of gastric cancer
    Title: Elevated TRIM23 expression predicts poor prognosis in Chinese gastric cancer.
  8. work identifies the TRIM23-TBK1-p62 axis as a key component of selective autophagy and further reveals a role for K27-linked ubiquitination in GTPase-dependent TBK1 activation
    Title: TRIM23 mediates virus-induced autophagy via activation of TBK1.
  9. Our results indicate that TRIM23 enzymatic activity requires RING dimerization, consistent with the general model of TRIM activation
    Title: Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase.
  10. TRIM23 regulates adipocyte differentiation via stabilization of the adipogenic activator PPARgamma2.
    Title: The E3 ubiquitin ligase TRIM23 regulates adipocyte differentiation via stabilization of the adipogenic activator PPARγ.
Submit: New GeneRIF Correction See all GeneRIFs (13)

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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GDP binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables GTP binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GTP binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables enzyme activator activity TAS
Traceable Author Statement
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of autophagy IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
involved_in vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in Golgi membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lysosomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
E3 ubiquitin-protein ligase TRIM23
Names
ADP-ribosylation factor domain protein 1, 64kDa
ADP-ribosylation factor domain-containing protein 1
ARF domain protein 1
GTP-binding protein ARD-1
RING finger protein 46
RING-type E3 ubiquitin transferase TRIM23
tripartite motif protein TRIM23
tripartite motif-containing protein 23
NP_001647.1
NP_150230.1
NP_150231.1
XP_016864933.1
XP_047273111.1
XP_054208503.1
XP_054208504.1
XP_054208505.1
XP_054208506.1
XP_054208507.1

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_001656.4 → NP_001647.1  E3 ubiquitin-protein ligase TRIM23 isoform alpha

    See identical proteins and their annotated locations for NP_001647.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (alpha) encodes the longest isoform. It has a unique C-terminus compared to isoforms beta and gamma of this protein.
    Source sequence(s)
    BC022510, BI859501, L04510
    Consensus CDS
    CCDS3987.1
    UniProtKB/Swiss-Prot
    P36406, Q9BZY4, Q9BZY5
    UniProtKB/TrEMBL
    A8K9U9
    Related
    ENSP00000231524.9, ENST00000231524.14
    Conserved Domains (5) summary
    smart00502
    Location:226 → 370
    BBC; B-Box C-terminal domain
    cd04158
    Location:406 → 574
    ARD1; (ADP-ribosylation factor domain protein 1 (ARD1)
    cd16645
    Location:28 → 77
    mRING-HC-C3HC3D_TRIM23_C-IX; Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein 23 (TRIM23) and similar proteins
    cd19773
    Location:123 → 172
    Bbox2_TRIM23_C-IX_rpt1; first B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins
    cd19774
    Location:174 → 223
    Bbox2_TRIM23_C-IX_rpt2; second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins

  2. NM_033227.3 → NP_150230.1  E3 ubiquitin-protein ligase TRIM23 isoform beta

    See identical proteins and their annotated locations for NP_150230.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (beta) is alternatively spliced near the 3' end of the coding region. This introduces a frameshift and the encoded isoform beta has a unique C-terminus compared to isoforms alpha and gamma.
    Source sequence(s)
    AF230398, BC022510, BI859501
    Consensus CDS
    CCDS43322.1
    UniProtKB/TrEMBL
    A8K9U9
    Related
    ENSP00000370406.3, ENST00000381018.7
    Conserved Domains (5) summary
    smart00502
    Location:226 → 370
    BBC; B-Box C-terminal domain
    cd16645
    Location:28 → 77
    mRING-HC-C3HC3D_TRIM23_C-IX; Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein 23 (TRIM23) and similar proteins
    cd19773
    Location:123 → 172
    Bbox2_TRIM23_C-IX_rpt1; first B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins
    cd19774
    Location:174 → 223
    Bbox2_TRIM23_C-IX_rpt2; second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins
    cl38936
    Location:406 → 550
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  3. NM_033228.3 → NP_150231.1  E3 ubiquitin-protein ligase TRIM23 isoform gamma

    See identical proteins and their annotated locations for NP_150231.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (gamma) is alternatively spliced near the 3' end of the coding region. This introduces a frameshift and the encoded isoform gamma has a unique C-terminus compared to isoforms alpha and beta.
    Source sequence(s)
    AF230399, BC022510, BI859501
    Consensus CDS
    CCDS3986.1
    UniProtKB/TrEMBL
    A8K9U9
    Related
    ENSP00000274327.7, ENST00000274327.11
    Conserved Domains (5) summary
    smart00502
    Location:226 → 370
    BBC; B-Box C-terminal domain
    smart00336
    Location:173 → 219
    BBOX; B-Box-type zinc finger
    cd00021
    Location:125 → 168
    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.
    cd16645
    Location:28 → 77
    mRING-HC-C3HC3D_TRIM23_C-IX; Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein 23 (TRIM23) and similar proteins
    cl21455
    Location:406 → 540
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    65589690..65624333 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017009444.3 → XP_016864933.1  E3 ubiquitin-protein ligase TRIM23 isoform X2

    UniProtKB/TrEMBL
    A8K9U9
    Conserved Domains (5) summary
    smart00502
    Location:226 → 370
    BBC; B-Box C-terminal domain
    cd16645
    Location:28 → 77
    mRING-HC-C3HC3D_TRIM23_C-IX; Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein 23 (TRIM23) and similar proteins
    cd19773
    Location:123 → 172
    Bbox2_TRIM23_C-IX_rpt1; first B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins
    cd19774
    Location:174 → 223
    Bbox2_TRIM23_C-IX_rpt2; second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins
    cl38936
    Location:406 → 550
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  2. XM_047417155.1 → XP_047273111.1  E3 ubiquitin-protein ligase TRIM23 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    66411457..66448919 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352528.1 → XP_054208503.1  E3 ubiquitin-protein ligase TRIM23 isoform X3

    UniProtKB/Swiss-Prot
    P36406, Q9BZY4, Q9BZY5

  2. XM_054352530.1 → XP_054208505.1  E3 ubiquitin-protein ligase TRIM23 isoform X3

    UniProtKB/Swiss-Prot
    P36406, Q9BZY4, Q9BZY5

  3. XM_054352529.1 → XP_054208504.1  E3 ubiquitin-protein ligase TRIM23 isoform X3

    UniProtKB/Swiss-Prot
    P36406, Q9BZY4, Q9BZY5

  4. XM_054352532.1 → XP_054208507.1  E3 ubiquitin-protein ligase TRIM23 isoform X2

  5. XM_054352531.1 → XP_054208506.1  E3 ubiquitin-protein ligase TRIM23 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P36406.1 GenPept UniProtKB/Swiss-Prot:P36406

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