Human Gene TRAF3 (uc010txy.2)
  Description: Homo sapiens TNF receptor-associated factor 3 (TRAF3), transcript variant 4, mRNA.
RefSeq Summary (NM_001199427): The protein encoded by this gene is a member of the TNF receptor associated factor (TRAF) protein family. TRAF proteins associate with, and mediate the signal transduction from, members of the TNF receptor (TNFR) superfamily. This protein participates in the signal transduction of CD40, a TNFR family member important for the activation of the immune response. This protein is found to be a critical component of the lymphotoxin-beta receptor (LTbetaR) signaling complex, which induces NF-kappaB activation and cell death initiated by LTbeta ligation. Epstein-Barr virus encoded latent infection membrane protein-1 (LMP1) can interact with this and several other members of the TRAF family, which may be essential for the oncogenic effects of LMP1. The protein also plays a role in the regulation of antiviral response. Mutations in this are associated with Encephalopathy, acute, infection-induced, herpes-specific 5. [provided by RefSeq, Jul 2020].
Transcript (Including UTRs)
   Position: hg19 chr14:103,243,816-103,377,837 Size: 134,022 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr14:103,336,539-103,372,121 Size: 35,583 Coding Exon Count: 7 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:103,243,816-103,377,837)mRNA (may differ from genome)Protein (485 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCLynxMalacardsMGIOMIMPubMed
ReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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.
Click here to open Exonprimer with this transcript

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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TRAF3
CDC HuGE Published Literature: TRAF3
Positive Disease Associations: Brain imaging in schizophrenia (interaction) , Schizophrenia
Related Studies:
  1. Brain imaging in schizophrenia (interaction)
    Potkin ,et al. 2008, A Genome-Wide Association Study of Schizophrenia Using Brain Activation as a Quantitative Phenotype, Schizophrenia bulletin 2009 35- 1 : 96-108. [PubMed 19023125]
    Combining imaging and genetic data from a GWAS identified genes related to forebrain development and stress response, already implicated in schizophrenic dysfunction, as affecting prefrontal efficiency.
  2. Schizophrenia
    Steven G Potkin et al. Schizophrenia bulletin 2009, A genome-wide association study of schizophrenia using brain activation as a quantitative phenotype., Schizophrenia bulletin. [PubMed 19023125]
    Combining imaging and genetic data from a GWAS identified genes related to forebrain development and stress response, already implicated in schizophrenic dysfunction, as affecting prefrontal efficiency. Although the identified genes require confirmation in an independent sample, our approach is a screening method over the whole genome to identify novel SNPs related to risk for schizophrenia.

-  MalaCards Disease Associations
  MalaCards Gene Search: TRAF3
Diseases sorted by gene-association score: herpes simplex encephalitis 3* (905), herpes simplex encephalitis susceptibility 3* (100), herpes simplex encephalitis* (37), encephalitis (20), herpes simplex (20), splenic marginal zone lymphoma (9), fructose intolerance, hereditary (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • C504897 12-(3-adamantan-1-ylureido)dodecanoic acid
  • C016403 2,4-dinitrotoluene
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C027576 4-hydroxy-2-nonenal
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D000082 Acetaminophen
  • D016604 Aflatoxin B1
  • D001554 Benzene
  • D001564 Benzo(a)pyrene
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.71 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 237.59 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 -120.50214-0.563 Picture PostScript Text
3' UTR -2270.225716-0.397 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
  Pfam Domains:
PF02176 - TRAF-type zinc finger

SCOP Domains:
49599 - TRAF domain-like
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on Q13114-2
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  U21092 - Human CD40 receptor associated factor 1 (CRAF1) mRNA, complete cds.
AK303172 - Homo sapiens cDNA FLJ61615 complete cds, highly similar to Homo sapiens TNF receptor-associated factor 3 (TRAF3), transcript variant 2, mRNA.
U15637 - Homo sapiens CD40 binding protein (CD40BP) mRNA, complete cds.
BX247977 - human full-length cDNA clone CS0DF024YF08 of Fetal brain of Homo sapiens (human).
LF209665 - JP 2014500723-A/17168: Polycomb-Associated Non-Coding RNAs.
JD406122 - Sequence 387146 from Patent EP1572962.
JD140241 - Sequence 121265 from Patent EP1572962.
JD406584 - Sequence 387608 from Patent EP1572962.
JD407288 - Sequence 388312 from Patent EP1572962.
JD336095 - Sequence 317119 from Patent EP1572962.
MA445242 - JP 2018138019-A/17168: Polycomb-Associated Non-Coding RNAs.
U19260 - Human LMP1 associated protein mRNA, complete cds.
L38509 - Homo sapiens CD40-associated protein (CAP-1) mRNA, complete cds.
BC075086 - Homo sapiens TNF receptor-associated factor 3, mRNA (cDNA clone MGC:103980 IMAGE:30915387), complete cds.
BC075087 - Homo sapiens TNF receptor-associated factor 3, mRNA (cDNA clone MGC:104143 IMAGE:30915599), complete cds.
AB527628 - Synthetic construct DNA, clone: pF1KB4959, Homo sapiens TRAF3 gene for TNF receptor-associated factor 3, without stop codon, in Flexi system.
KJ897704 - Synthetic construct Homo sapiens clone ccsbBroadEn_07098 TRAF3 gene, encodes complete protein.
AK090587 - Homo sapiens cDNA FLJ33268 fis, clone ASTRO2007515, moderately similar to TNF RECEPTOR ASSOCIATED FACTOR 3.
AX746522 - Sequence 47 from Patent EP1308459.
AF110908 - Homo sapiens TNF-receptor associated factor-3 (TRAF-3) mRNA, partial cds; and 3'UTR.
JD046393 - Sequence 27417 from Patent EP1572962.
JD278896 - Sequence 259920 from Patent EP1572962.
JD152777 - Sequence 133801 from Patent EP1572962.
JD548542 - Sequence 529566 from Patent EP1572962.
JD166020 - Sequence 147044 from Patent EP1572962.
JD236191 - Sequence 217215 from Patent EP1572962.
JD054576 - Sequence 35600 from Patent EP1572962.
DQ573700 - Homo sapiens piRNA piR-41812, complete sequence.
DQ601563 - Homo sapiens piRNA piR-39629, complete sequence.
JD383145 - Sequence 364169 from Patent EP1572962.
JD271184 - Sequence 252208 from Patent EP1572962.
JD253170 - Sequence 234194 from Patent EP1572962.
JD445720 - Sequence 426744 from Patent EP1572962.
JD197333 - Sequence 178357 from Patent EP1572962.
JD547750 - Sequence 528774 from Patent EP1572962.
JD518415 - Sequence 499439 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04620 - Toll-like receptor signaling pathway
hsa04622 - RIG-I-like receptor signaling pathway
hsa05200 - Pathways in cancer
hsa05222 - Small cell lung cancer

BioCarta from NCI Cancer Genome Anatomy Project
h_cd40Pathway - CD40L Signaling Pathway
h_tall1Pathway - TACI and BCMA stimulation of B cell immune responses.
h_tnfr2Pathway - TNFR2 Signaling Pathway

Reactome (by CSHL, EBI, and GO)

Protein Q13114 (Reactome details) participates in the following event(s):

R-HSA-2201338 TRAF3 binds TICAM1:activated TLR4 complex
R-HSA-9013992 TRAF3 binds to TRIF:activated TLR3 complex
R-HSA-918227 Recruitment of TRAF3 to MAVS
R-HSA-936381 OTUD5 deubiquitinates TRAF3
R-HSA-5668543 TRAF3:NIK binds TRAF2:cIAP1/2
R-HSA-5690843 OTUB1, (OTUB2) binds RNF128, TRAF3, TRAF6, RHOA
R-HSA-918225 TBK1/IKK epsilon complex interacts with MAVS bound TRAF3
R-HSA-5362486 TANK binds K63-poly-Ub-TRAF3:TICAM1:activated TLR4
R-HSA-9013985 TANK binds K63-poly-Ub-TRAF3:TICAM1:activated TLR3
R-HSA-5668417 cIAP1,2:TRAF2:TRAF3:NIK complex binds TNFR2 trimer
R-HSA-5676593 TRAF2:TRAF1:cIAP1,2:TRAF3:NIK regulatory complex binds LTBR
R-HSA-5676595 TRAFs bind RANK:RANKL
R-HSA-5676596 TRAF3 binds BAFFR:BAFF
R-HSA-5676597 TRAF2:TRAF1:cIAP1,2:TRAF3:NIK regulatory complex binds CD40
R-HSA-5676598 TRAF2:cIAP1/2 complex binds FN14:TWEAK
R-HSA-918232 Recruitment of IRF3,IRF7
R-HSA-918229 Phosphorylation and release of IRF3/IRF7
R-HSA-936941 Recruitment of TBK1/IKK epsilon to K63-pUb-TANK:K63-pUb-TRAF3:TRIF:activated TLR4 followed by their phosphorylation
R-HSA-9013986 Recruitment of TBK1/IKK epsilon to K63-pUb-TANK:K63-pUb-TRAF3:TRIF:activated TLR3 followed by their phosphorylation
R-HSA-166271 IRF3/IRF7 recruitment to p-TBK1/p-IKK epsilon bound to the activated TLR4
R-HSA-166245 Phosphorylation of IRF-3/IRF7 and their release from the activated TLR complex
R-HSA-9013979 IRF3/IRF7 recruitment to p-TBK1/p-IKK epsilon bound to the activated TLR3
R-HSA-9013978 Phosphorylation of IRF-3/IRF7 and their release from the activated TLR3 complex
R-HSA-936964 Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon
R-HSA-9013973 TICAM1-dependent activation of IRF3/IRF7
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway
R-HSA-918233 TRAF3-dependent IRF activation pathway
R-HSA-936440 Negative regulators of DDX58/IFIH1 signaling
R-HSA-5602571 TRAF3 deficiency - HSE
R-HSA-5689896 Ovarian tumor domain proteases
R-HSA-937061 TRIF(TICAM1)-mediated TLR4 signaling
R-HSA-168164 Toll Like Receptor 3 (TLR3) Cascade
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168928 DDX58/IFIH1-mediated induction of interferon-alpha/beta
R-HSA-5602358 Diseases associated with the TLR signaling cascade
R-HSA-5688426 Deubiquitination
R-HSA-5676594 TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway
R-HSA-166166 MyD88-independent TLR4 cascade
R-HSA-168898 Toll-Like Receptors Cascades
R-HSA-168256 Immune System
R-HSA-168249 Innate Immune System
R-HSA-5260271 Diseases of Immune System
R-HSA-597592 Post-translational protein modification
R-HSA-166016 Toll Like Receptor 4 (TLR4) Cascade
R-HSA-1643685 Disease
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: CAP1, CRAF1, NM_001199427, NP_001186356, Q13114-2
UCSC ID: uc010txy.2
RefSeq Accession: NM_001199427
Protein: Q13114-2, splice isoform of Q13114 CCDS: CCDS55946.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001199427.1
exon count: 8CDS single in 3' UTR: no RNA size: 7405
ORF size: 1458CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2996.00frame shift in genome: no % Coverage: 99.77
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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