Human Gene TRIM9 (ENST00000298355.7) from GENCODE V44
  Description: 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. (from UniProt Q9C026)
RefSeq Summary (NM_015163): 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].
Gencode Transcript: ENST00000298355.7
Gencode Gene: ENSG00000100505.14
Transcript (Including UTRs)
   Position: hg38 chr14:50,975,262-51,096,061 Size: 120,800 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg38 chr14:50,977,291-51,094,939 Size: 117,649 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:50,975,262-51,096,061)mRNA (may differ from genome)Protein (710 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
HPRDLynxMalacardsMGIneXtProtPubMed
ReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: TRIM9_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase TRIM9; EC=6.3.2.-; AltName: Full=RING finger protein 91; AltName: Full=Tripartite motif-containing protein 9;
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.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with SNAP25 (By similarity).
SUBCELLULAR LOCATION: Cytoplasm. Cell projection, dendrite. Cytoplasmic vesicle, secretory vesicle, synaptic vesicle (By similarity). Cell junction, synapse (By similarity). Cytoplasm, cytoskeleton (By similarity). 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.
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.
DOMAIN: The coiled coil domain mediates the interaction with the N-terminal t-SNARE domain of SNAP25 (By similarity).
PTM: Auto-ubiquitinated. Poly-ubiquitinated in cultured cells, whereas it is monoubiquitinated in vitro.
SIMILARITY: Belongs to the TRIM/RBCC family.
SIMILARITY: Contains 2 B box-type zinc fingers.
SIMILARITY: Contains 1 B30.2/SPRY domain.
SIMILARITY: Contains 1 COS domain.
SIMILARITY: Contains 1 fibronectin type-III domain.
SIMILARITY: Contains 1 RING-type zinc finger.
SEQUENCE CAUTION: Sequence=AAG53490.1; Type=Frameshift; Positions=660; Sequence=AAG53492.1; Type=Frameshift; Positions=655; Sequence=BAA13398.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAA13398.2; Type=Frameshift; Positions=660;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 64.00 RPKM in Brain - Cerebellum
Total median expression: 315.82 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -497.501122-0.443 Picture PostScript Text
3' UTR -555.402029-0.274 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001870 - B30.2/SPRY
IPR003649 - Bbox_C
IPR008985 - ConA-like_lec_gl_sf
IPR017903 - COS_domain
IPR003961 - Fibronectin_type3
IPR013783 - Ig-like_fold
IPR003877 - SPRY_rcpt
IPR000315 - Znf_B-box
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00041 - Fibronectin type III domain
PF00622 - SPRY domain
PF00643 - B-box zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2DB8 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9C026
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsemblWormBase 
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 
AlignmentAlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000149 SNARE binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0019904 protein domain specific binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding

Biological Process:
GO:0016079 synaptic vesicle exocytosis
GO:0016567 protein ubiquitination
GO:0035544 negative regulation of SNARE complex assembly
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045955 negative regulation of calcium ion-dependent exocytosis

Cellular Component:
GO:0005622 intracellular
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0008021 synaptic vesicle
GO:0030054 cell junction
GO:0030425 dendrite
GO:0031410 cytoplasmic vesicle
GO:0042995 cell projection
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  BC063872 - Homo sapiens tripartite motif-containing 9, mRNA (cDNA clone MGC:75399 IMAGE:6471552), complete cds.
AF220036 - Homo sapiens tripartite motif protein TRIM9 isoform alpha (TRIM9) mRNA, complete cds; alternatively spliced.
AF220037 - Homo sapiens tripartite motif protein TRIM9 isoform beta (TRIM9) mRNA, complete cds; alternatively spliced.
AF220038 - Homo sapiens tripartite motif protein TRIM9 isoform gamma (TRIM9) mRNA, complete cds; alternatively spliced.
D87458 - Homo sapiens mRNA for KIAA0282 gene, partial cds.
AK055388 - Homo sapiens cDNA FLJ30826 fis, clone FEBRA2001715, weakly similar to ZINC-BINDING PROTEIN A33.
AB383836 - Synthetic construct DNA, clone: pF1KSDA0282, Homo sapiens TRIM9 gene for tripartite motif-containing protein 9, complete cds, without stop codon, in Flexi system.
JD525078 - Sequence 506102 from Patent EP1572962.
JD146591 - Sequence 127615 from Patent EP1572962.
JD506995 - Sequence 488019 from Patent EP1572962.
JD251260 - Sequence 232284 from Patent EP1572962.
JD233956 - Sequence 214980 from Patent EP1572962.
JD495385 - Sequence 476409 from Patent EP1572962.
JD267956 - Sequence 248980 from Patent EP1572962.
JD351059 - Sequence 332083 from Patent EP1572962.
JD110920 - Sequence 91944 from Patent EP1572962.
JD089220 - Sequence 70244 from Patent EP1572962.
JD330070 - Sequence 311094 from Patent EP1572962.
JD168385 - Sequence 149409 from Patent EP1572962.
JD429669 - Sequence 410693 from Patent EP1572962.
JD562926 - Sequence 543950 from Patent EP1572962.
JD225908 - Sequence 206932 from Patent EP1572962.
JD485408 - Sequence 466432 from Patent EP1572962.
JD360389 - Sequence 341413 from Patent EP1572962.
JD491525 - Sequence 472549 from Patent EP1572962.
JD049090 - Sequence 30114 from Patent EP1572962.
JD132729 - Sequence 113753 from Patent EP1572962.
JD511279 - Sequence 492303 from Patent EP1572962.
JD021998 - Sequence 3022 from Patent EP1572962.
JD404151 - Sequence 385175 from Patent EP1572962.
JD215539 - Sequence 196563 from Patent EP1572962.
JD029044 - Sequence 10068 from Patent EP1572962.
JD452847 - Sequence 433871 from Patent EP1572962.
JD399873 - Sequence 380897 from Patent EP1572962.
JD193985 - Sequence 175009 from Patent EP1572962.
JD496687 - Sequence 477711 from Patent EP1572962.
AK054781 - Homo sapiens cDNA FLJ30219 fis, clone BRACE2001726.
BC013414 - Homo sapiens tripartite motif-containing 9, mRNA (cDNA clone MGC:4626 IMAGE:3510374), complete cds.
KJ895261 - Synthetic construct Homo sapiens clone ccsbBroadEn_04655 TRIM9 gene, encodes complete protein.
CU680598 - Synthetic construct Homo sapiens gateway clone IMAGE:100019842 5' read TRIM9 mRNA.
JD409465 - Sequence 390489 from Patent EP1572962.
JD156185 - Sequence 137209 from Patent EP1572962.
JD199985 - Sequence 181009 from Patent EP1572962.
JD129828 - Sequence 110852 from Patent EP1572962.
JD256447 - Sequence 237471 from Patent EP1572962.
JD069265 - Sequence 50289 from Patent EP1572962.
JD053952 - Sequence 34976 from Patent EP1572962.
JD053951 - Sequence 34975 from Patent EP1572962.
JD337277 - Sequence 318301 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9C026 (Reactome details) participates in the following event(s):

R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: D3DSB7, D3DSB8, ENST00000298355.1, ENST00000298355.2, ENST00000298355.3, ENST00000298355.4, ENST00000298355.5, ENST00000298355.6, KIAA0282, NR_170652, Q92557, Q96D24, Q96NI4, Q9C025, Q9C026, Q9C027, RNF91, TRIM9_HUMAN, uc001wyx.1, uc001wyx.2, uc001wyx.3, uc001wyx.4, uc001wyx.5
UCSC ID: ENST00000298355.7
RefSeq Accession: NM_015163
Protein: Q9C026 (aka TRIM9_HUMAN or TRM9_HUMAN)
CCDS: CCDS9703.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.