Human Gene TRIM39 (ENST00000376659.9) Description and Page Index
  Description: Homo sapiens tripartite motif containing 39 (TRIM39), transcript variant 2, mRNA. (from RefSeq NM_172016)
RefSeq Summary (NM_172016): 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].
Gencode Transcript: ENST00000376659.9
Gencode Gene: ENSG00000204599.14
Transcript (Including UTRs)
   Position: hg38 chr6:30,327,259-30,343,729 Size: 16,471 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr6:30,329,318-30,342,259 Size: 12,942 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:30,327,259-30,343,729)mRNA (may differ from genome)Protein (488 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
LynxMGIneXtProtOMIMPubMedReactome
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: TRI39_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase TRIM39; EC=6.3.2.-; AltName: Full=RING finger protein 23; AltName: Full=Testis-abundant finger protein; AltName: Full=Tripartite motif-containing protein 39;
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.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with MOAP1.
INTERACTION: Self; NbExp=4; IntAct=EBI-739510, EBI-739510; P16333:NCK1; NbExp=2; IntAct=EBI-739510, EBI-389883; Q9Y577:TRIM17; NbExp=3; IntAct=EBI-739510, EBI-743894;
SUBCELLULAR LOCATION: Cytoplasm, cytosol. Mitochondrion. Note=Found predominantly in the cytosol. Partial shift from the cytosol to the mitochondria when co-localized with MOAP1.
TISSUE SPECIFICITY: Ubiquitous; highly expressed in brain, heart, kidney, liver, skeletal muscle, spleen and testis.
PTM: Autoubiquitinated.
SIMILARITY: Belongs to the TRIM/RBCC family.
SIMILARITY: Contains 1 B box-type zinc finger.
SIMILARITY: Contains 1 B30.2/SPRY domain.
SIMILARITY: Contains 1 RING-type zinc finger.

-  MalaCards Disease Associations
  MalaCards Gene Search: TRIM39
Diseases sorted by gene-association score: multiple personality disorder (2), behcet syndrome (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.07 RPKM in Testis
Total median expression: 85.21 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 -182.60598-0.305 Picture PostScript Text
3' UTR -498.901470-0.339 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
IPR003879 - Butyrophylin
IPR008985 - ConA-like_lec_gl_sf
IPR006574 - PRY
IPR018355 - SPla/RYanodine_receptor_subgr
IPR003877 - SPRY_rcpt
IPR000315 - Znf_B-box
IPR018957 - Znf_C3HC4_RING-type
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00622 - SPRY domain
PF00643 - B-box zinc finger
PF00097 - Zinc finger, C3HC4 type (RING finger)

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

2DID
- NMR MuPIT

2DIF
- NMR MuPIT

2ECJ
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9HCM9
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0006915 apoptotic process
GO:0016567 protein ubiquitination
GO:2000059 negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process
GO:2001235 positive regulation of apoptotic signaling pathway

Cellular Component:
GO:0005622 intracellular
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BC053512 - Homo sapiens tripartite motif-containing 39, mRNA (cDNA clone IMAGE:6536841), **** WARNING: chimeric clone ****.
AK292512 - Homo sapiens cDNA FLJ76683 complete cds, highly similar to Homo sapiens tripartite motif-containing 39 (TRIM39), transcript variant 1, mRNA.
BC034985 - Homo sapiens tripartite motif-containing 39, mRNA (cDNA clone MGC:32984 IMAGE:5268723), complete cds.
JD055733 - Sequence 36757 from Patent EP1572962.
JD297896 - Sequence 278920 from Patent EP1572962.
JD132599 - Sequence 113623 from Patent EP1572962.
JD447521 - Sequence 428545 from Patent EP1572962.
JD280865 - Sequence 261889 from Patent EP1572962.
JD120252 - Sequence 101276 from Patent EP1572962.
AX776007 - Sequence 277 from Patent WO03048202.
BC007661 - Homo sapiens tripartite motif-containing 39, mRNA (cDNA clone MGC:2475 IMAGE:3051389), complete cds.
JD228253 - Sequence 209277 from Patent EP1572962.
AB046381 - Homo sapiens mRNA for testis-abundant finger protein, complete cds.
JD083552 - Sequence 64576 from Patent EP1572962.
JD496451 - Sequence 477475 from Patent EP1572962.
JD046466 - Sequence 27490 from Patent EP1572962.
CU690008 - Synthetic construct Homo sapiens gateway clone IMAGE:100019633 5' read TRIM39 mRNA.
CU675745 - Synthetic construct Homo sapiens gateway clone IMAGE:100017357 5' read TRIM39 mRNA.
AB587493 - Synthetic construct DNA, clone: pF1KB8733, Homo sapiens TRIM39 gene for tripartite motif-containing 39, without stop codon, in Flexi system.
BT007370 - Homo sapiens tripartite motif-containing 39 mRNA, complete cds.
KJ894340 - Synthetic construct Homo sapiens clone ccsbBroadEn_03734 TRIM39 gene, encodes complete protein.
KJ899254 - Synthetic construct Homo sapiens clone ccsbBroadEn_08648 TRIM39 gene, encodes complete protein.
AB209284 - Homo sapiens mRNA for tripartite motif-containing 39 isoform 2 variant protein.
EU012025 - Homo sapiens TRIM39-like protein (TRIM39R) mRNA, partial cds.
JD092741 - Sequence 73765 from Patent EP1572962.
JD207456 - Sequence 188480 from Patent EP1572962.
JD282936 - Sequence 263960 from Patent EP1572962.
JD265437 - Sequence 246461 from Patent EP1572962.
JD141500 - Sequence 122524 from Patent EP1572962.
JD403472 - Sequence 384496 from Patent EP1572962.
JD241557 - Sequence 222581 from Patent EP1572962.
JD372071 - Sequence 353095 from Patent EP1572962.
JD174997 - Sequence 156021 from Patent EP1572962.
JD150136 - Sequence 131160 from Patent EP1572962.
JD466875 - Sequence 447899 from Patent EP1572962.
JD096931 - Sequence 77955 from Patent EP1572962.
JD361747 - Sequence 342771 from Patent EP1572962.
JD219482 - Sequence 200506 from Patent EP1572962.
JD305064 - Sequence 286088 from Patent EP1572962.
JD494272 - Sequence 475296 from Patent EP1572962.
JD091862 - Sequence 72886 from Patent EP1572962.
DQ589123 - Homo sapiens piRNA piR-56235, complete sequence.
JD507416 - Sequence 488440 from Patent EP1572962.
JD530171 - Sequence 511195 from Patent EP1572962.
DQ595495 - Homo sapiens piRNA piR-61607, complete sequence.
JD384546 - Sequence 365570 from Patent EP1572962.
JD082819 - Sequence 63843 from Patent EP1572962.
JD559822 - Sequence 540846 from Patent EP1572962.
JD167784 - Sequence 148808 from Patent EP1572962.
JD415101 - Sequence 396125 from Patent EP1572962.
JD342830 - Sequence 323854 from Patent EP1572962.
JD561760 - Sequence 542784 from Patent EP1572962.
JD048249 - Sequence 29273 from Patent EP1572962.
JD208487 - Sequence 189511 from Patent EP1572962.
JD382348 - Sequence 363372 from Patent EP1572962.
JD430802 - Sequence 411826 from Patent EP1572962.

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

Protein Q9HCM9 (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: NM_172016, Q5STG3, Q5STG4, Q76BL3, Q8IYT9, Q96IB6, Q9HCM9, RNF23, TFP, TRI39_HUMAN, uc003nqb.1, uc003nqb.2, uc003nqb.3, uc003nqb.4
UCSC ID: uc003nqb.4
RefSeq Accession: NM_172016
Protein: Q9HCM9 (aka TRI39_HUMAN or RN23_HUMAN)
CCDS: CCDS34378.1

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