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

    Gene ID: 373, updated on 9-Dec-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
    mouse all
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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
    • 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 (62) 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)

    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
      UniProtKB/TrEMBL
      A8K9U9

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

      UniProtKB/Swiss-Prot
      P36406, Q9BZY4, Q9BZY5
      UniProtKB/TrEMBL
      A8K9U9

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

      UniProtKB/Swiss-Prot
      P36406, Q9BZY4, Q9BZY5
      UniProtKB/TrEMBL
      A8K9U9

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

      UniProtKB/TrEMBL
      A8K9U9

    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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