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 ... See more...

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

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
  • GC06P032270
  • GC06P032443
  • GC06P032572
  • GC06P033230
  • GC06P030456
  • GC06P030523
  • GC06P030729
  • GC06P030887
  • GC06P031044
  • GC06P031195
  • GC06P031398
  • GC06P032040

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 Summary for TRIM39 Gene

  • [Isoform 1]: E3 ubiquitin-protein ligase (PubMed:22529100). May facilitate apoptosis by inhibiting APC/C-Cdh1-mediated poly-ubiquitination and subsequent proteasome-mediated degradation of the pro-apoptotic protein MOAP1 (PubMed:19100260, PubMed:22529100). Regulates the G1/S transition of the cell cycle and DNA damage-induced G2 arrest by stabilizing CDKN1A/p21 (PubMed:23213251). Positively regulates CDKN1A/p21 stability by competing with DTL for CDKN1A/p21 binding, therefore disrupting DCX(DTL) E3 ubiquitin ligase complex-mediated CDKN1A/p21 ubiquitination and degradation (PubMed:23213251).
  • [Isoform 2]: Regulates the G1/S transition of the cell cycle and DNA damage-induced G2 arrest by stabilizing CDKN1A/p21 (PubMed:23213251). Positively regulates CDKN1A/p21 stability by competing with DTL for CDKN1A/p21 binding, therefore disrupting DCX(DTL) E3 ubiquitin ligase complex-mediated CDKN1A/p21 ubiquitination and degradation (PubMed:23213251). Negatively regulates the canonical NF-kappa-B signaling pathway via stabilization of CACTIN in an ubiquitination-independent manner (PubMed:26363554).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRIM39 Gene

Genomics for TRIM39 Gene

GeneHancer (GH) Regulatory Elements Pubs

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
GH06J030321 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 615.7 -1.6 -1551 6.6 RNF2 ARHGAP35 HNRNPL CREB1 GATAD2A PRDM10 ZNF629 RFX1 LEF1 IKZF1 HCG18 TRIM39 HCG17 GTF2H4 MDC1 HLA-U HLA-L PPP1R10 ZNRD1ASP RPL23AP1
GH06J030340 Promoter 0.9 EPDnew 600.4 +14.1 14134 0.1 LEF1 JUND MTA1 HDAC1 SOX6 GATAD2B EP300 SCRT2 GTF2E2 ZNF766 TRIM39 RPP21 piR-56235 TRIM39-RPP21 RF00017-5399
GH06J030611 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 120.2 +289.1 289124 8.6 BRCA1 ARHGAP35 CEBPG SP1 HNRNPL CREB1 GATAD2A CTCF ATF7 PRDM10 MRPS18B PPP1R10 MDC1 DDX39B TRIM39 DHX16 GTF2H4 TRIM26 PAIP1P1 ABCF1
GH06J030328 Promoter 0.4 EPDnew 600.7 +2.6 2555 0.1 ZNF512 HCG18 TRIM39 TRIM39-RPP21 piR-56235 RPP21 RF00017-5399
GH06J030907 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 98.6 +582.0 581988 2.2 ZNF221 ARHGAP35 SP1 HNRNPL CREB1 GATAD2A PRDM10 REST ZNF629 SIX5 GTF2H4 ENSG00000288473 lnc-GTF2H4-1 MDC1 DDX39B LY6G5B PPP1R10 TRIM39 LSM2 PAIP1P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRIM39 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRIM39

Top Transcription factor binding sites by QIAGEN in the TRIM39 gene promoter:
  • AML1a
  • MRF-2
  • Nkx2-2
  • Nkx2-5
  • NRF-2

Genomic Locations for TRIM39 Gene

Genomic Locations for TRIM39 Gene
chr6:30,326,469-30,343,729
(GRCh38/hg38)
Size:
17,261 bases
Orientation:
Plus strand
chr6:30,294,256-30,311,506
(GRCh37/hg19)
Size:
17,251 bases
Orientation:
Plus strand

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 StructureGene Density

Proteins for TRIM39 Gene

  • 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:
    • Isoform 1 interacts with MOAP1 (PubMed:19100260). Isoform 1 and isoform 2 interact with CDKN1A (PubMed:23213251). Isoform 2 interacts (via domain B box-type) with CACTIN (PubMed:26363554).

    Three dimensional structures from OCA and Proteopedia for TRIM39 Gene

    Alternative splice isoforms for TRIM39 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRIM39 Gene

Post-translational modifications for TRIM39 Gene

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:
  • Zn-finger, RING
  • Butyrophylin C-terminal DUF signature
  • SPRY-associated domain
  • B-box zinc finger signature
ProtoNet:

Suggested Antigen Peptide Sequences for TRIM39 Gene

GenScript: Design optimal peptide antigens:
  • Tripartite motif-containing 39 (A2AAZ7_HUMAN)
  • cDNA FLJ76683, highly similar to Homo sapiens tripartite motif-containing 39 (TRIM39), transcript variant 1, mRNA (Q5STG3_HUMAN)
  • Testis-abundant finger protein (TRI39_HUMAN)

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

Molecular function for TRIM39 Gene

UniProtKB/Swiss-Prot Function:
[Isoform 1]: E3 ubiquitin-protein ligase (PubMed:22529100). May facilitate apoptosis by inhibiting APC/C-Cdh1-mediated poly-ubiquitination and subsequent proteasome-mediated degradation of the pro-apoptotic protein MOAP1 (PubMed:19100260, PubMed:22529100). Regulates the G1/S transition of the cell cycle and DNA damage-induced G2 arrest by stabilizing CDKN1A/p21 (PubMed:23213251). Positively regulates CDKN1A/p21 stability by competing with DTL for CDKN1A/p21 binding, therefore disrupting DCX(DTL) E3 ubiquitin ligase complex-mediated CDKN1A/p21 ubiquitination and degradation (PubMed:23213251).
UniProtKB/Swiss-Prot Function:
[Isoform 2]: Regulates the G1/S transition of the cell cycle and DNA damage-induced G2 arrest by stabilizing CDKN1A/p21 (PubMed:23213251). Positively regulates CDKN1A/p21 stability by competing with DTL for CDKN1A/p21 binding, therefore disrupting DCX(DTL) E3 ubiquitin ligase complex-mediated CDKN1A/p21 ubiquitination and degradation (PubMed:23213251). Negatively regulates the canonical NF-kappa-B signaling pathway via stabilization of CACTIN in an ubiquitination-independent manner (PubMed:26363554).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=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.; EC=2.3.2.27;.

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 Models for TRIM39 Gene

MGI Knock Outs for TRIM39:
  • Trim39 Trim39<tm1b(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRIM39

Clone Products

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

Localization for TRIM39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRIM39 Gene

[Isoform 1]: Cytoplasm, cytosol. Mitochondrion. Nucleus. Note=Found predominantly in the cytosol. Partial shift from the cytosol to the mitochondria when colocalized with MOAP1. Colocalizes with CDKN1A in the nucleus. {ECO:0000269 PubMed:19100260, ECO:0000269 PubMed:23213251}.
[Isoform 2]: Nucleus. Note=Colocalizes with CDKN1A in the nucleus. {ECO:0000269 PubMed:23213251}.

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
nucleus 5
mitochondrion 4
cytosol 4
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TRIM39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 23213251
GO:0005737 cytoplasm IEA,IBA 21873635
GO:0005739 mitochondrion IDA 19100260
GO:0005829 cytosol IEA,IDA 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:0007049 cell cycle IEA --
GO:0007095 mitotic G2 DNA damage checkpoint IMP 23213251
GO:0010468 regulation of gene expression IBA 21873635
GO:0016567 protein ubiquitination IEA --
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

No Compound Related Data Available

Transcripts for TRIM39 Gene

mRNA/cDNA for TRIM39 Gene

5 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRIM39

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

Expression for TRIM39 Gene

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



Protein tissue co-expression partners for TRIM39 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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

  • Blood(4.3)
  • Intestine(4.2)
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 30 31
  • 99.86 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TRIM39 30 31
  • 94.33 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TRIM39 30
  • 94.06 (n)
Mouse
(Mus musculus)
Mammalia Trim39 30 17 31
  • 90.44 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 90 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Trim39 30
  • 89.48 (n)
Chicken
(Gallus gallus)
Aves TRIM39 30
  • 52.94 (n)
TRIM27.1 31
  • 36 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 69 (a)
OneToMany
Zebrafish
(Danio rerio)
Actinopterygii LOC101883816 30
  • 49.49 (n)
Species where no ortholog for TRIM39 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for TRIM39: view image

Paralogs for TRIM39 Gene

Pseudogenes.org Pseudogenes for TRIM39 Gene

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

Variants for TRIM39 Gene

Additional dbSNP identifiers (rs#s) for TRIM39 Gene

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 and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP 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
Open Targets Platform
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 23
  2. TRIM39 negatively regulates the NFκB-mediated signaling pathway through stabilization of Cactin. (PMID: 26363554) Suzuki M … Hatakeyama S (Cellular and molecular life sciences : CMLS 2016) 3 4
  3. 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
  4. TRIM39 regulates cell cycle progression and DNA damage responses via stabilizing p21. (PMID: 23213251) Zhang L … You H (Proceedings of the National Academy of Sciences of the United States of America 2012) 3 4
  5. 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

Products for TRIM39 Gene

  • Signalway Proteins for TRIM39

Sources for TRIM39 Gene