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

Gene ID: 56658, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30326469..30343729)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (30190674..30207940)
105.20220307 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: 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. 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. TRIM39R, but not TRIM39B, regulates type I interferon response. Kurata R, et al. Biochem Biophys Res Commun, 2013 Jun 21. PMID 23707810
  4. 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
  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 (42) 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)

Genotypes

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 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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 
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_2023_10

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

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