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Aliases for TRIM9 Gene

Aliases for TRIM9 Gene

  • Tripartite Motif Containing 9 2 3 5
  • RING-Type E3 Ubiquitin Transferase TRIM9 3 4
  • Tripartite Motif-Containing Protein 9 3 4
  • RING Finger Protein 91 3 4
  • RNF91 3 4
  • E3 Ubiquitin-Protein Ligase TRIM9 3
  • Homolog Of Rat RING Finger Spring 3
  • Tripartite Motif-Containing 9 2
  • EC 2.3.2.27 4
  • KIAA0282 4
  • SPRING 3

External Ids for TRIM9 Gene

Previous GeneCards Identifiers for TRIM9 Gene

  • GC14M048763
  • GC14M045237
  • GC14M049432
  • GC14M050511
  • GC14M051441
  • GC14M031567

Summaries for TRIM9 Gene

Entrez Gene Summary for TRIM9 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 protein localizes to cytoplasmic bodies. Its function has not been identified. Alternate splicing of this gene generates two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for TRIM9 Gene

TRIM9 (Tripartite Motif Containing 9) is a Protein Coding gene. Among its related pathways are Class I MHC mediated antigen processing and presentation and Innate Immune System. GO annotations related to this gene include protein homodimerization activity and ubiquitin-protein transferase activity. An important paralog of this gene is TRIM67.

UniProtKB/Swiss-Prot for TRIM9 Gene

  • E3 ubiquitin-protein ligase which ubiquitinates itself in cooperation with an E2 enzyme UBE2D2/UBC4 and serves as a targeting signal for proteasomal degradation. May play a role in regulation of neuronal functions and may also participate in the formation or breakdown of abnormal inclusions in neurodegenerative disorders. May act as a regulator of synaptic vesicle exocytosis by controlling the availability of SNAP25 for the SNARE complex formation.

Gene Wiki entry for TRIM9 Gene

Additional gene information for TRIM9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRIM9 Gene

Genomics for TRIM9 Gene

Regulatory Elements for TRIM9 Gene

Enhancers for TRIM9 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
GH14H051644 0.9 FANTOM5 dbSUPER 12.5 -548.1 -548132 0 HIC1 ZNF148 PKNOX1 ZSCAN4 SALL2 ZNF398 TRIM9 GPR137C RNU6-301P FRMD6 ENSG00000277050 FRMD6-AS1
GH14H051004 1.4 Ensembl ENCODE dbSUPER 7.3 +90.0 89996 3 PKNOX1 FOXA2 FEZF1 FOS TSHZ1 NFIL3 ATF4 ZNF585B ZSCAN16 MYNN TRIM9 PYGL GC14P050964 ENSG00000259055
GH14H051138 0.8 Ensembl ENCODE 9.3 -43.0 -43044 1 ZFHX2 RFX1 HLF ZNF350 FOS TRIM28 TMX1 TRIM9
GH14H051095 1.2 ENCODE dbSUPER 5.8 +0.6 563 1 HDGF PKNOX1 ARID4B SIN3A ZNF121 GLIS2 ZNF143 FOS SP3 NFYC ENSG00000259055 TRIM9
GH14H051018 0.7 ENCODE dbSUPER 6.9 +76.2 76172 3 POLR2A RCOR1 PYGL TRIM9 GC14P050964 ENSG00000259055
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TRIM9 on UCSC Golden Path with GeneCards custom track

Promoters for TRIM9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000068215 761 1001 HDGF PKNOX1 ARID4B SIN3A ZNF121 GLIS2 ZNF143 FOS SP3 NFYC

Genomic Location for TRIM9 Gene

Chromosome:
14
Start:
50,975,261 bp from pter
End:
51,096,061 bp from pter
Size:
120,801 bases
Orientation:
Minus strand

Genomic View for TRIM9 Gene

Genes around TRIM9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRIM9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRIM9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRIM9 Gene

Proteins for TRIM9 Gene

  • Protein details for TRIM9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9C026-TRIM9_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase TRIM9
    Protein Accession:
    Q9C026
    Secondary Accessions:
    • D3DSB7
    • D3DSB8
    • Q92557
    • Q96D24
    • Q96NI4
    • Q9C025
    • Q9C027

    Protein attributes for TRIM9 Gene

    Size:
    710 amino acids
    Molecular mass:
    79177 Da
    Quaternary structure:
    • Interacts with SNAP25.
    SequenceCaution:
    • Sequence=AAG53490.1; Type=Frameshift; Positions=660; Evidence={ECO:0000305}; Sequence=AAG53492.1; Type=Frameshift; Positions=655; Evidence={ECO:0000305}; Sequence=BAA13398.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAA13398.2; Type=Frameshift; Positions=660; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TRIM9 Gene

    Alternative splice isoforms for TRIM9 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRIM9 Gene

Post-translational modifications for TRIM9 Gene

  • Auto-ubiquitinated. Poly-ubiquitinated in cultured cells, whereas it is monoubiquitinated in vitro.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for TRIM9

No data available for DME Specific Peptides for TRIM9 Gene

Domains & Families for TRIM9 Gene

Suggested Antigen Peptide Sequences for TRIM9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9C026

UniProtKB/Swiss-Prot:

TRIM9_HUMAN :
  • The coiled coil domain mediates the interaction with the N-terminal t-SNARE domain of SNAP25.
  • Belongs to the TRIM/RBCC family.
Domain:
  • The coiled coil domain mediates the interaction with the N-terminal t-SNARE domain of SNAP25.
Family:
  • Belongs to the TRIM/RBCC family.
genes like me logo Genes that share domains with TRIM9: view

Function for TRIM9 Gene

Molecular function for TRIM9 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 which ubiquitinates itself in cooperation with an E2 enzyme UBE2D2/UBC4 and serves as a targeting signal for proteasomal degradation. May play a role in regulation of neuronal functions and may also participate in the formation or breakdown of abnormal inclusions in neurodegenerative disorders. May act as a regulator of synaptic vesicle exocytosis by controlling the availability of SNAP25 for the SNARE complex formation.

Enzyme Numbers (IUBMB) for TRIM9 Gene

Phenotypes From GWAS Catalog for TRIM9 Gene

Gene Ontology (GO) - Molecular Function for TRIM9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000149 SNARE binding IEA --
GO:0004842 ubiquitin-protein transferase activity IDA 20085810
GO:0005515 protein binding IPI 16189514
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with TRIM9: view
genes like me logo Genes that share phenotypes with TRIM9: view

Animal Models for TRIM9 Gene

MGI Knock Outs for TRIM9:

Animal Model Products

CRISPR Products

miRNA for TRIM9 Gene

miRTarBase miRNAs that target TRIM9

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for TRIM9
  • Applied Biological Materials Clones for TRIM9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TRIM9 Gene

Localization for TRIM9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRIM9 Gene

Cytoplasm. Cell projection, dendrite. Cytoplasmic vesicle, secretory vesicle, synaptic vesicle. Cell junction, synapse. Cytoplasm, cytoskeleton. Note=Enriched at synaptic terminals where it exists in a soluble form and a synaptic vesicle-associated form. Associated with the cytoskeleton (By similarity). Found in proximal dendrites of pyramidal neurons in the cerebral cortex and hippocampus, and Purkinje cells in the cerebellum (Ref.7). {ECO:0000250 UniProtKB:Q91ZY8, ECO:0000269 PubMed:20085810}.

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 TRIM9 gene
Compartment Confidence
cytosol 4
cytoskeleton 3
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TRIM9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005737 cytoplasm IEA,IDA 11331580
GO:0005829 cytosol IDA --
GO:0005856 cytoskeleton IEA --
GO:0008021 synaptic vesicle IEA --
genes like me logo Genes that share ontologies with TRIM9: view

Pathways & Interactions for TRIM9 Gene

genes like me logo Genes that share pathways with TRIM9: view

UniProtKB/Swiss-Prot Q9C026-TRIM9_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for TRIM9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016079 synaptic vesicle exocytosis IEA --
GO:0016567 protein ubiquitination IEA --
GO:0035544 negative regulation of SNARE complex assembly IEA --
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process IDA 20085810
GO:0045955 negative regulation of calcium ion-dependent exocytosis IEA --
genes like me logo Genes that share ontologies with TRIM9: view

No data available for SIGNOR curated interactions for TRIM9 Gene

Drugs & Compounds for TRIM9 Gene

No Compound Related Data Available

Transcripts for TRIM9 Gene

Unigene Clusters for TRIM9 Gene

Tripartite motif containing 9:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for TRIM9
  • Applied Biological Materials Clones for TRIM9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for TRIM9 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c ^ 12a · 12b ^ 13a · 13b · 13c ^ 14
SP1: - - - - - - -
SP2: - - - - - - - - - -
SP3:
SP4: -
SP5:
SP6:

Relevant External Links for TRIM9 Gene

GeneLoc Exon Structure for
TRIM9
ECgene alternative splicing isoforms for
TRIM9

Expression for TRIM9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TRIM9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TRIM9 Gene

This gene is overexpressed in Brain - Cerebellum (x8.6), Brain - Cerebellar Hemisphere (x7.7), Brain - Cortex (x4.6), and Brain - Frontal Cortex (BA9) (x4.2).

Protein differential expression in normal tissues from HIPED for TRIM9 Gene

This gene is overexpressed in Platelet (51.0) and Fetal Brain (11.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TRIM9 Gene



Protein tissue co-expression partners for TRIM9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TRIM9 Gene:

TRIM9

SOURCE GeneReport for Unigene cluster for TRIM9 Gene:

Hs.654750

mRNA Expression by UniProt/SwissProt for TRIM9 Gene:

Q9C026-TRIM9_HUMAN
Tissue specificity: Brain. Highly expressed in the cerebral cortex (at protein level). Severely decreased in the affected brain areas in Parkinson disease and dementia with Lewy bodies.

Evidence on tissue expression from TISSUES for TRIM9 Gene

  • Nervous system(5)
genes like me logo Genes that share expression patterns with TRIM9: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for TRIM9 Gene

Orthologs for TRIM9 Gene

This gene was present in the common ancestor of animals.

Orthologs for TRIM9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TRIM9 33 34
  • 99.39 (n)
dog
(Canis familiaris)
Mammalia TRIM9 33 34
  • 93.62 (n)
cow
(Bos Taurus)
Mammalia TRIM9 33 34
  • 92.44 (n)
mouse
(Mus musculus)
Mammalia Trim9 33 16 34
  • 90.73 (n)
rat
(Rattus norvegicus)
Mammalia Trim9 33
  • 90.66 (n)
oppossum
(Monodelphis domestica)
Mammalia TRIM9 34
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TRIM9 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves TRIM9 34
  • 79 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TRIM9 34
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia trim9 33
  • 79.74 (n)
zebrafish
(Danio rerio)
Actinopterygii trim9 33 34
  • 75.39 (n)
fruit fly
(Drosophila melanogaster)
Insecta Trim9 33 34
  • 55.52 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008750 33
  • 54.6 (n)
worm
(Caenorhabditis elegans)
Secernentea trim-9 33 34
  • 50.76 (n)
C39F7.2 35
  • 37 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 44 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.14178 33
Species where no ortholog for TRIM9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for TRIM9 Gene

ENSEMBL:
Gene Tree for TRIM9 (if available)
TreeFam:
Gene Tree for TRIM9 (if available)

Paralogs for TRIM9 Gene

(1) SIMAP similar genes for TRIM9 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with TRIM9: view

Variants for TRIM9 Gene

Sequence variations from dbSNP and Humsavar for TRIM9 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs1000011370 -- 51,057,855(+) AAGTG(A/G)AAAAG intron-variant
rs1000033057 -- 51,066,487(+) GCTGT(C/G)GCTTC intron-variant
rs1000048087 -- 51,027,407(+) CCAAA(G/T)TGCTG intron-variant
rs1000205997 -- 51,008,800(+) TGATG(A/G)TCTCT intron-variant
rs1000232559 -- 51,104,775(+) CTGGC(A/T)TCTGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TRIM9 Gene

Variant ID Type Subtype PubMed ID
nsv476560 CNV novel sequence insertion 20440878
nsv84409 CNV deletion 16902084

Variation tolerance for TRIM9 Gene

Residual Variation Intolerance Score: 4.37% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.70; 46.30% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TRIM9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRIM9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRIM9 Gene

Disorders for TRIM9 Gene

Relevant External Links for TRIM9

Genetic Association Database (GAD)
TRIM9
Human Genome Epidemiology (HuGE) Navigator
TRIM9
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TRIM9

No disorders were found for TRIM9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TRIM9 Gene

Publications for TRIM9 Gene

  1. The tripartite motif family identifies cell compartments. (PMID: 11331580) Reymond A … Ballabio A (The EMBO journal 2001) 2 3 4 60
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  3. TRIM9, a novel brain-specific E3 ubiquitin ligase, is repressed in the brain of Parkinson's disease and dementia with Lewy bodies. (PMID: 20085810) Tanji K … Wakabayashi K (Neurobiology of disease 2010) 3 4 60
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 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 TRIM9 Gene

  • Addgene plasmids for TRIM9

Sources for TRIM9 Gene

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