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    TRIM39 tripartite motif containing 39 [ Homo sapiens (human) ]

    Gene ID: 56658, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TRIM39provided by HGNC
    Official Full Name
    tripartite motif containing 39provided by HGNC
    Primary source
    HGNC:HGNC:10065
    See related
    Ensembl:ENSG00000204599 MIM:605700; AllianceGenome:HGNC:10065
    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
    TFP; RNF23; TRIM39B
    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. The function of this protein has not been identified. This gene lies within the major histocompatibility complex class I region on chromosome 6. Alternate splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 12.0), thyroid (RPKM 6.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TRIM39 in Genome Data Viewer
    Location:
    6p22.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30326469..30343729)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (30190674..30207940)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30294246..30311506)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene tripartite motif containing 26B, pseudogene Neighboring gene HLA complex group 17 Neighboring gene MPRA-validated peak5750 silencer Neighboring gene major histocompatibility complex, class I, L (pseudogene) Neighboring gene HLA complex group 18 Neighboring gene MPRA-validated peak5752 silencer Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:30292740-30293383 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:30296621-30297820 Neighboring gene TRIM39-RPP21 readthrough Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:30308084-30309283 Neighboring gene ribonuclease P/MRP subunit p21 Neighboring gene major histocompatibility complex, class I, N (pseudogene)

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. TRIM39 is a poor prognostic factor for patients with estrogen receptor-positive breast cancer and promotes cell cycle progression. Ogura T, et al. Pathol Int, 2022 Feb. PMID 35174936
    2. Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA and novel non-HLA TRIM31 and TRIM39 loci. Ning L, et al. Commun Biol, 2020 Dec 11. PMID 33311639, Free PMC Article
    3. TRIM39 and RNF39 are associated with Behçet's disease independently of HLA-B∗51 and -A∗26. Kurata R, et al. Biochem Biophys Res Commun, 2010 Oct 29. PMID 20875797
    4. TRIM39R, but not TRIM39B, regulates type I interferon response. Kurata R, et al. Biochem Biophys Res Commun, 2013 Jun 21. PMID 23707810
    5. Ubiquitylation of p53 by the APC/C inhibitor Trim39. Zhang L, et al. Proc Natl Acad Sci U S A, 2012 Dec 18. PMID 23213260, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRIM39 is a poor prognostic factor for patients with estrogen receptor-positive breast cancer and promotes cell cycle progression.
      Title: TRIM39 is a poor prognostic factor for patients with estrogen receptor-positive breast cancer and promotes cell cycle progression.
    2. TRIM39 deficiency inhibits tumor progression and autophagic flux in colorectal cancer via suppressing the activity of Rab7.
      Title: TRIM39 deficiency inhibits tumor progression and autophagic flux in colorectal cancer via suppressing the activity of Rab7.
    3. Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA and novel non-HLA TRIM31 and TRIM39 loci.
      Title: Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA and novel non-HLA TRIM31 and TRIM39 loci.
    4. TRIM39 negatively regulates the NFkappaB signaling pathway possibly via stabilization of cactin.
      Title: TRIM39 negatively regulates the NFκB-mediated signaling pathway through stabilization of Cactin.
    5. TRIM39R, but not TRIM39B, regulates type I interferon response
      Title: TRIM39R, but not TRIM39B, regulates type I interferon response.
    6. analysis of ubiquitylation of p53 by the APC/C inhibitor Trim39
      Title: Ubiquitylation of p53 by the APC/C inhibitor Trim39.
    7. TRIM39 has a role in regulating cell cycle progression and the balance between cytostasis and apoptosis after DNA damage via stabilizing p21
      Title: TRIM39 regulates cell cycle progression and DNA damage responses via stabilizing p21.
    8. these findings suggest that RNF39 and TRIM39 are involved in the etiology of Behcet's disease.
      Title: TRIM39 and RNF39 are associated with Behçet's disease independently of HLA-B∗51 and -A∗26.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions.
    10. Data suggest that TRIM39 can promote apoptosis signalling through stabilization of MOAP-1.
      Title: TRIM39 is a MOAP-1-binding protein that stabilizes MOAP-1 through inhibition of its poly-ubiquitination process.
    Submit: New GeneRIF Correction

    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

    Clone Names

    • MGC32984

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in innate immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitotic G2 DNA damage checkpoint signaling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of canonical NF-kappaB signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of apoptotic signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of apoptotic signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein stabilization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein stabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell cycle G1/S phase transition IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase TRIM39
    Names
    RING-type E3 ubiquitin transferase TRIM39
    ring finger protein 23
    testis-abundant finger protein
    tripartite motif-containing protein 39
    NP_001356450.1
    NP_001356451.1
    NP_001356452.1
    NP_067076.2
    NP_742013.1

    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_001369521.2 → NP_001356450.1  E3 ubiquitin-protein ligase TRIM39 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL662795
      Consensus CDS
      CCDS34378.1
      Related
      ENSP00000379800.3, ENST00000396551.9
      Conserved Domains (4) summary
      TIGR02169
      Location:149 → 270
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
      cd13745
      Location:305 → 483
      SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
      cd16601
      Location:26 → 69
      RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins
      cd19780
      Location:103 → 146
      Bbox2_TRIM39-like; B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM39, TRIM58 and similar proteins

    2. NM_001369522.1 → NP_001356451.1  E3 ubiquitin-protein ligase TRIM39 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL662795
      Consensus CDS
      CCDS34378.1
      Conserved Domains (4) summary
      TIGR02169
      Location:149 → 270
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
      cd13745
      Location:305 → 483
      SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
      cd16601
      Location:26 → 69
      RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins
      cd19780
      Location:103 → 146
      Bbox2_TRIM39-like; B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM39, TRIM58 and similar proteins

    3. NM_001369523.1 → NP_001356452.1  E3 ubiquitin-protein ligase TRIM39 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL662795
      Consensus CDS
      CCDS34378.1
      Related
      ENSP00000379797.1, ENST00000396548.5
      Conserved Domains (4) summary
      TIGR02169
      Location:149 → 270
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
      cd13745
      Location:305 → 483
      SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
      cd16601
      Location:26 → 69
      RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins
      cd19780
      Location:103 → 146
      Bbox2_TRIM39-like; B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM39, TRIM58 and similar proteins

    4. NM_021253.4 → NP_067076.2  E3 ubiquitin-protein ligase TRIM39 isoform 1

      See identical proteins and their annotated locations for NP_067076.2

      Status: REVIEWED

      Source sequence(s)
      AL662795
      Consensus CDS
      CCDS34377.1
      UniProtKB/Swiss-Prot
      Q5STG3, Q5STG4, Q76BL3, Q8IYT9, Q96IB6, Q9HCM9
      UniProtKB/TrEMBL
      A0A024RCP5
      Related
      ENSP00000365844.4, ENST00000376656.8
      Conserved Domains (4) summary
      cd13745
      Location:335 → 513
      SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
      cd16601
      Location:26 → 69
      RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins
      cl28410
      Location:20 → 179
      RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
      cl28522
      Location:175 → 352
      AtpF; FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]

    5. NM_172016.2 → NP_742013.1  E3 ubiquitin-protein ligase TRIM39 isoform 2

      See identical proteins and their annotated locations for NP_742013.1

      Status: REVIEWED

      Source sequence(s)
      AL662795, BC034985, DB071507
      Consensus CDS
      CCDS34378.1
      Related
      ENSP00000365847.5, ENST00000376659.9
      Conserved Domains (4) summary
      TIGR02169
      Location:149 → 270
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
      cd13745
      Location:305 → 483
      SPRY_PRY_TRIM39; PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like
      cd16601
      Location:26 → 69
      RING-HC_TRIM39_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins
      cd19780
      Location:103 → 146
      Bbox2_TRIM39-like; B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM39, TRIM58 and similar proteins

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      30326469..30343729
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      1655959..1673225
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      1806146..1823410
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      1582309..1599575
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      1636694..1653960
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      1581544..1598811
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      1624923..1642186
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      30190674..30207940
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HCM9.2 GenPept UniProtKB/Swiss-Prot:Q9HCM9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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