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TRIM39 Gene(Protein Coding)

Tripartite Motif Containing 39

GCID:
GC06P031195
GIFtS:
46
Genes Participants
UDN Logo

Aliases for TRIM39 Gene

Aliases for TRIM39 Gene

  • Tripartite Motif Containing 39 2 3 5
  • RING-Type E3 Ubiquitin Transferase TRIM39 3 4
  • Tripartite Motif-Containing Protein 39 3 4
  • Testis-Abundant Finger Protein 3 4
  • Ring Finger Protein 23 2 3
  • RNF23 3 4
  • TFP 3 4
  • E3 Ubiquitin-Protein Ligase TRIM39 3
  • Tripartite Motif-Containing 39 2
  • RING Finger Protein 23 4
  • EC 2.3.2.27 4
  • TRIM39B 3

External Ids for TRIM39 Gene

Previous HGNC Symbols for TRIM39 Gene

  • RNF23

Previous GeneCards Identifiers for TRIM39 Gene

  • GC06P030352
  • GC06P030065
  • GC06P030401
  • GC06P030403
  • GC06P030294
  • GC06P030092
  • GC06P030331
  • GC06P030441
  • GC06P030456
  • GC06P030523
  • GC06P030729
  • GC06P030887
  • GC06P031044

Summaries for TRIM39 Gene

Entrez Gene Summary for TRIM39 Gene

  • 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]

GeneCards Summary for TRIM39 Gene

TRIM39 (Tripartite Motif Containing 39) is a Protein Coding gene. Diseases associated with TRIM39 include Multiple Personality Disorder and Behcet Syndrome. Among its related pathways are Innate Immune System and Class I MHC mediated antigen processing and presentation. Gene Ontology (GO) annotations related to this gene include identical protein binding and ligase activity. An important paralog of this gene is TRIM39-RPP21.

UniProtKB/Swiss-Prot for TRIM39 Gene

  • E3 ubiquitin-protein ligase. May facilitate apoptosis by inhibiting APC/C-Cdh1-mediated poly-ubiquitination and subsequent proteasome-mediated degradation of the pro-apoptotic protein MOAP1.

Additional gene information for TRIM39 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRIM39 Gene

Genomics for TRIM39 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for TRIM39 Gene

Promoters and enhancers for TRIM39 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH06I030324 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 -0.1 -51 3.5 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A YBX1 FEZF1 DMAP1 ZNF2 HCG18 TRIM39 HCG17 RPL23AP1 MICD GABBR1 HLA-E GTF2H4 VARS2 ZNRD1ASP
GH06I030715 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 95.8 +393.0 393047 7.7 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 MDC1 TUBB DDX39B TRIM39 DHX16 LY6G5B PPP1R10 ZNRD1 PAIP1P1 NRM
GH06I030611 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 78.9 +289.1 289073 8.7 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 PPP1R10 MRPS18B DDX39B MDC1 TRIM39 ABCF1 NRM DHX16 ZNRD1 TRIM26
GH06I030907 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 85.5 +582.0 581978 2.2 CLOCK DMAP1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 GTF2H4 VARS2 GC06P031581 MDC1 DDX39B LY6G5B TRIM39 LSM2 PPP1R10 HCG18
GH06I030162 Promoter/Enhancer 1.5 EPDnew ENCODE 72.6 -162.7 -162713 2.8 ZFP64 ARID4B DMAP1 YY1 SLC30A9 ZNF213 ZNF302 SP3 SP5 ZC3H11A TRIM15 TRIM10 MDC1 GTF2H4 HCG18 ZNRD1ASP PPP1R10 TRIM39 ETF1P1 PAIP1P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TRIM39 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TRIM39 gene promoter:

Genomic Locations for TRIM39 Gene

Genomic Locations for TRIM39 Gene
chr6:30,326,479-30,343,729
(GRCh38/hg38)
Size:
17,251 bases
Orientation:
Plus strand
chr6:30,294,256-30,311,506
(GRCh37/hg19)

Genomic View for TRIM39 Gene

Genes around TRIM39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRIM39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRIM39 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TRIM39 Gene

Proteins for TRIM39 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for TRIM39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HCM9-TRI39_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase TRIM39
    Protein Accession:
    Q9HCM9
    Secondary Accessions:
    • Q5STG3
    • Q5STG4
    • Q76BL3
    • Q8IYT9
    • Q96IB6

    Protein attributes for TRIM39 Gene

    Size:
    518 amino acids
    Molecular mass:
    59690 Da
    Quaternary structure:
    • Interacts with MOAP1.

    Three dimensional structures from OCA and Proteopedia for TRIM39 Gene

    Alternative splice isoforms for TRIM39 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRIM39 Gene

Protein Expression for TRIM39 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TRIM39 Gene

Other Protein References for TRIM39 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TRIM39 Gene

Domains & Families for TRIM39 Gene

Gene Families for TRIM39 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for TRIM39 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TRIM39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9HCM9

UniProtKB/Swiss-Prot:

TRI39_HUMAN :
  • Belongs to the TRIM/RBCC family.
Family:
  • Belongs to the TRIM/RBCC family.
genes like me logo Genes that share domains with TRIM39: view

Function for TRIM39 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for TRIM39 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.
UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase. May facilitate apoptosis by inhibiting APC/C-Cdh1-mediated poly-ubiquitination and subsequent proteasome-mediated degradation of the pro-apoptotic protein MOAP1.

Enzyme Numbers (IUBMB) for TRIM39 Gene

Phenotypes From GWAS Catalog for TRIM39 Gene

Gene Ontology (GO) - Molecular Function for TRIM39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
GO:0042802 identical protein binding IPI 16189514
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with TRIM39: view
genes like me logo Genes that share phenotypes with TRIM39: view

Animal Model Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TRIM39 Gene

Localization for TRIM39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRIM39 Gene

Cytoplasm, cytosol. Mitochondrion. Note=Found predominantly in the cytosol. Partial shift from the cytosol to the mitochondria when colocalized with MOAP1.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TRIM39 gene
Compartment Confidence
mitochondrion 4
cytosol 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRIM39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IDA 19100260
GO:0005829 cytosol IDA,IEA 19100260
genes like me logo Genes that share ontologies with TRIM39: view

Pathways & Interactions for TRIM39 Gene

genes like me logo Genes that share pathways with TRIM39: view

UniProtKB/Swiss-Prot Q9HCM9-TRI39_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for TRIM39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006915 apoptotic process IEA --
GO:0016567 protein ubiquitination IEA --
GO:2000059 negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process IDA 19100260
GO:2001235 positive regulation of apoptotic signaling pathway IDA 19100260
genes like me logo Genes that share ontologies with TRIM39: view

No data available for SIGNOR curated interactions for TRIM39 Gene

Drugs & Compounds for TRIM39 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for TRIM39 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for TRIM39 Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(7) Selected AceView cDNA sequences:
(11) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TRIM39 Gene

Tripartite motif containing 39:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TRIM39 Gene

No ASD Table

Relevant External Links for TRIM39 Gene

GeneLoc Exon Structure for
TRIM39
ECgene alternative splicing isoforms for
TRIM39

Expression for TRIM39 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TRIM39 Gene

mRNA expression in normal human tissues for TRIM39 Gene
mRNA expression by GTEx for TRIM39 GenemRNA expression by BioGPS for TRIM39 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TRIM39 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for TRIM39 Gene



Protein tissue co-expression partners for TRIM39 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TRIM39 Gene:

TRIM39

SOURCE GeneReport for Unigene cluster for TRIM39 Gene:

Hs.413493

mRNA Expression by UniProt/SwissProt for TRIM39 Gene:

Q9HCM9-TRI39_HUMAN
Tissue specificity: Ubiquitous; highly expressed in brain, heart, kidney, liver, skeletal muscle, spleen and testis.

Evidence on tissue expression from TISSUES for TRIM39 Gene

  • Intestine(4.1)
  • Blood(4)
genes like me logo Genes that share expression patterns with TRIM39: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRIM39 Gene

Orthologs for TRIM39 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TRIM39 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia TRIM39 33 34
  • 99.86 (n)
dog
(Canis familiaris)
 Mammalia TRIM39 33 34
  • 94.33 (n)
cow
(Bos Taurus)
 Mammalia TRIM39 33
  • 94.06 (n)
mouse
(Mus musculus)
 Mammalia Trim39 33 16 34
  • 90.44 (n)
oppossum
(Monodelphis domestica)
 Mammalia -- 34
  • 90 (a)
 OneToMany
rat
(Rattus norvegicus)
 Mammalia Trim39 33
  • 89.48 (n)
chicken
(Gallus gallus)
 Aves TRIM39 33
  • 52.94 (n)
TRIM27.1 34
  • 36 (a)
 ManyToMany
lizard
(Anolis carolinensis)
 Reptilia -- 34
  • 69 (a)
 OneToMany
zebrafish
(Danio rerio)
 Actinopterygii LOC101883816 33
  • 49.49 (n)
Species where no ortholog for TRIM39 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TRIM39 Gene

ENSEMBL:
Gene Tree for TRIM39 (if available)
TreeFam:
Gene Tree for TRIM39 (if available)

Paralogs for TRIM39 Gene

Paralogs for TRIM39 Gene

(88) SIMAP similar genes for TRIM39 Gene using alignment to 8 proteins:

Pseudogenes.org Pseudogenes for TRIM39 Gene

genes like me logo Genes that share paralogs with TRIM39: view

Variants for TRIM39 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for TRIM39 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000247515 -- 30,327,440(+) A/G 5_prime_UTR_variant, intron_variant
rs1000849666 -- 30,343,376(+) T/G 3_prime_UTR_variant
rs1001018233 -- 30,326,345(+) A/T upstream_transcript_variant
rs1001032100 -- 30,335,575(+) G/A intron_variant
rs1001134805 -- 30,333,465(+) C/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TRIM39 Gene

Variant ID Type Subtype PubMed ID
esv3411275 CNV duplication 20981092
nsv1074389 CNV deletion 25765185
nsv1122126 CNV deletion 24896259
nsv1144137 CNV deletion 24896259
nsv5241 CNV insertion 18451855
nsv601264 CNV loss 21841781

Variation tolerance for TRIM39 Gene

Residual Variation Intolerance Score: 16.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.25; 40.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRIM39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRIM39

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRIM39 Gene

Disorders for TRIM39 Gene

MalaCards: The human disease database

(2) MalaCards diseases for TRIM39 Gene - From: DISEASES

Disorder Aliases PubMed IDs
multiple personality disorder
  • dissociative identity disorder
behcet syndrome
  • behcet disease; bd
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TRIM39

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TRIM39: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TRIM39 Gene

Publications for TRIM39 Gene

  1. Molecular cloning of testis-abundant finger Protein/Ring finger protein 23 (RNF23), a novel RING-B box-coiled coil-B30.2 protein on the class I region of the human MHC. (PMID: 11006080) Orimo A … Muramatsu M (Biochemical and biophysical research communications 2000) 2 3 4 22 58
  2. The Trim39 ubiquitin ligase inhibits APC/CCdh1-mediated degradation of the Bax activator MOAP-1. (PMID: 22529100) Huang NJ … Kornbluth S (The Journal of cell biology 2012) 3 4 58
  3. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos LF … Criswell LA (PLoS genetics 2009) 3 44 58
  4. TRIM39 is a MOAP-1-binding protein that stabilizes MOAP-1 through inhibition of its poly-ubiquitination process. (PMID: 19100260) Lee SS … Yu VC (Experimental cell research 2009) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for TRIM39 Gene

Sources for TRIM39 Gene

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