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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

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 Class I MHC mediated antigen processing and presentation and Innate Immune System. 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

Regulatory Elements for TRIM39 Gene

Enhancers for TRIM39 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H030611 1.7 Ensembl ENCODE dbSUPER 68.2 +289.1 289074 8 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D SSRP1 MDC1 DDX39B TRIM39 PPP1R10 ABCF1 NRM DHX16 ZNRD1 GTF2H4 TRIM26
GH06H030907 1.2 ENCODE 95.8 +582.0 581979 2 DMAP1 YBX1 YY1 ZNF416 ZNF143 ZNF548 SP3 NFYC ZC3H11A MEF2D MDC1 GTF2H4 TRIM39 LY6G5B LSM2 DDX39B HCG18 PPP1R10 ENSG00000233892 DHX16
GH06H030715 1.5 ENCODE dbSUPER 70 +393.0 393048 7 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 NFYC MDC1 LY6G5B TRIM39 DDX39B DHX16 ABCF1 PPP1R10 ZNRD1 NRM HCG18
GH06H030162 1.1 ENCODE 62.1 -162.7 -162714 2 ZFP64 ARID4B DMAP1 YY1 SLC30A9 ZNF302 SP3 SP5 ZC3H11A MXD4 MDC1 HCG18 GTF2H4 ZNRD1ASP TRIM39 PPP1R10 HLA-U ETF1P1 ERVK9-12 ENSG00000233892
GH06H030554 1.4 ENCODE dbSUPER 43 +230.1 230146 3 DMAP1 YY1 SLC30A9 ZNF143 SP3 SSRP1 GLIS1 NBN NR2C1 KDM1A DDX39B TRIM39 DHX16 PPP1R10 NRM ZNRD1 MDC1 TCF19 ETF1P1 ENSG00000233892
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TRIM39 on UCSC Golden Path with GeneCards custom track

Promoters for TRIM39 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000195385 21 2201 HDGF PKNOX1 ARNT ARID4B SIN3A YBX1 FEZF1 DMAP1 ZNF2 SLC30A9

Genomic Location for TRIM39 Gene

Chromosome:
6
Start:
30,326,479 bp from pter
End:
30,343,729 bp from pter
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:
    • 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

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

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 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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TRIM39
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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)

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 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: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

No Compound Related Data Available

Transcripts for TRIM39 Gene

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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TRIM39
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, 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

Primer Products

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

Pseudogenes.org Pseudogenes for TRIM39 Gene

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

Variants for TRIM39 Gene

Sequence variations from dbSNP and Humsavar for TRIM39 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000247515 -- 30,327,440(+) CTCTC(A/G)GGAGA intron-variant, upstream-variant-2KB, utr-variant-5-prime
rs1000849666 -- 30,343,376(+) TTGCT(G/T)GTTTG intron-variant, upstream-variant-2KB, utr-variant-3-prime
rs1001018233 -- 30,326,345(+) CGGGG(A/T)GAACT intron-variant, nc-transcript-variant, upstream-variant-2KB
rs1001032100 -- 30,335,575(+) CCCTC(A/G)GCCTC intron-variant
rs1001134805 -- 30,333,465(+) CCATT(C/G)TCCTG 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)

Relevant External Links 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's disease
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for TRIM39

Genetic Association Database (GAD)
TRIM39
Human Genome Epidemiology (HuGE) Navigator
TRIM39
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TRIM39
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 60
  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 60
  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 45 60
  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 60
  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 60

Products for TRIM39 Gene

Sources for TRIM39 Gene

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