Human Gene TRAF1 (ENST00000373887.8_7) from GENCODE V47lift37
  Description: TNF receptor associated factor 1, transcript variant 1 (from RefSeq NM_005658.5)
Gencode Transcript: ENST00000373887.8_7
Gencode Gene: ENSG00000056558.11_9
Transcript (Including UTRs)
   Position: hg19 chr9:123,664,671-123,689,074 Size: 24,404 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr9:123,667,298-123,688,353 Size: 21,056 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:123,664,671-123,689,074)mRNA (may differ from genome)Protein (416 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TRAF1_HUMAN
DESCRIPTION: RecName: Full=TNF receptor-associated factor 1; AltName: Full=Epstein-Barr virus-induced protein 6;
FUNCTION: Adapter molecule that regulates the activation of NF- kappa-B and JNK. Plays a role in the regulation of cell survival and apoptosis. The heterotrimer formed by TRAF1 and TRAF2 is part of a E3 ubiquitin-protein ligase complex that promotes ubiquitination of target proteins, such as MAP3K14. The TRAF1/TRAF2 complex recruits the antiapoptotic E3 protein- ubiquitin ligases BIRC2 and BIRC3 to TNFRSF1B/TNFR2.
SUBUNIT: Homotrimer. Heterotrimer with TRAF2. Interacts with TNFRSF1A/TNFR1, TNFRSF1B/TNFR2, TNFRSF4, TNFRSF5/CD40, TNFRSF8/CD30, TNFRSF9/CD137, TNFRSF11A/RANK, TNFRSF13C, TNFRSF18/AITR, TNFRSF17/BCMA, TNFRSF19/TROY, TNFRSF19L/RELT, XEDAR, EDAR, Epstein-Barr virus BNFL1/LMP-1, TANK/ITRAF, TRAIP and RIPK2. Interacts with BIRC2 and BIRC3 N-terminus; a single BIRC2 or BIRC3 molecule interacts with a heterotrimer formed by TRAF1 and TRAF2. Interacts with NFATC2IP, TRAFD1 and with HIVEP3 (By similarity). Interacts with MAP3K14.
INTERACTION: Q14161:GIT2; NbExp=2; IntAct=EBI-359224, EBI-1046878;
DOMAIN: The coiled coil domain mediates homo- and hetero- oligomerization.
DOMAIN: The MATH/TRAF domain binds to receptor cytoplasmic domains.
DOMAIN: Cleavage by CASP8 liberates a C-terminal fragment that promotes apoptosis and inhibits the activation of NF-kappa-B in response to TNF signaling.
PTM: Polyubiquitinated by BIRC2 and/or BIRC3, leading to its subsequent proteasomal degradation.
SIMILARITY: Contains 1 MATH domain.
CAUTION: Lacks a RING domain and has therefore no E3 ubiquitin- protein ligase activity by itself.
SEQUENCE CAUTION: Sequence=BAC03449.1; Type=Frameshift; Positions=111;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: TRAF1
Diseases sorted by gene-association score: hodgkin lymphoma (4), rheumatoid arthritis (2), lymphoma, non-hodgkin (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 54.07 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 314.86 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 -151.80473-0.321 Picture PostScript Text
3' UTR -981.202627-0.374 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
IPR002083 - MATH
IPR012227 - TNF_rcpt--assoc_TRAF
IPR008974 - TRAF-like
IPR013322 - TRAF-type

Pfam Domains:
PF16673 - TNF receptor-associated factor BIRC3 binding domain

SCOP Domains:
49599 - TRAF domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3M0D - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q13077
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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
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005164 tumor necrosis factor receptor binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0031625 ubiquitin protein ligase binding
GO:0031996 thioesterase binding
GO:0042802 identical protein binding

Biological Process:
GO:0006915 apoptotic process
GO:0007165 signal transduction
GO:0010803 regulation of tumor necrosis factor-mediated signaling pathway
GO:0042981 regulation of apoptotic process
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0065003 macromolecular complex assembly
GO:2001236 regulation of extrinsic apoptotic signaling pathway

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AL832989 - Homo sapiens mRNA; cDNA DKFZp666E213 (from clone DKFZp666E213).
AK090468 - Homo sapiens mRNA for FLJ00389 protein.
BC024145 - Homo sapiens TNF receptor-associated factor 1, mRNA (cDNA clone MGC:10353 IMAGE:3832475), complete cds.
U19261 - Homo sapiens Epstein-Barr virus-induced protein mRNA, complete cds.
JD037618 - Sequence 18642 from Patent EP1572962.
JD368782 - Sequence 349806 from Patent EP1572962.
JD346299 - Sequence 327323 from Patent EP1572962.
JD353833 - Sequence 334857 from Patent EP1572962.
JD163123 - Sequence 144147 from Patent EP1572962.
JD084614 - Sequence 65638 from Patent EP1572962.
JD320890 - Sequence 301914 from Patent EP1572962.
JD365430 - Sequence 346454 from Patent EP1572962.
JD320889 - Sequence 301913 from Patent EP1572962.
JD545773 - Sequence 526797 from Patent EP1572962.
JD124487 - Sequence 105511 from Patent EP1572962.
JD374143 - Sequence 355167 from Patent EP1572962.
JD299317 - Sequence 280341 from Patent EP1572962.
JD234569 - Sequence 215593 from Patent EP1572962.
JD541073 - Sequence 522097 from Patent EP1572962.
JD318175 - Sequence 299199 from Patent EP1572962.
JD353289 - Sequence 334313 from Patent EP1572962.
JD396417 - Sequence 377441 from Patent EP1572962.
AK295959 - Homo sapiens cDNA FLJ53047 complete cds, highly similar to TNF receptor-associated factor 1.
JD106687 - Sequence 87711 from Patent EP1572962.
JD493297 - Sequence 474321 from Patent EP1572962.
JD203694 - Sequence 184718 from Patent EP1572962.
JD077638 - Sequence 58662 from Patent EP1572962.
JD172862 - Sequence 153886 from Patent EP1572962.
JD329534 - Sequence 310558 from Patent EP1572962.
JD408894 - Sequence 389918 from Patent EP1572962.
JD552237 - Sequence 533261 from Patent EP1572962.
JD429580 - Sequence 410604 from Patent EP1572962.
BT019408 - Homo sapiens TNF receptor-associated factor 1 mRNA, complete cds.
AK315476 - Homo sapiens cDNA, FLJ96537, Homo sapiens TNF receptor-associated factor 1 (TRAF1), mRNA.
HQ447750 - Synthetic construct Homo sapiens clone IMAGE:100071081; CCSB012438_02 TNF receptor-associated factor 1 (TRAF1) gene, encodes complete protein.
KJ897703 - Synthetic construct Homo sapiens clone ccsbBroadEn_07097 TRAF1 gene, encodes complete protein.
AB590501 - Synthetic construct DNA, clone: pFN21AE1888, Homo sapiens TRAF1 gene for TNF receptor-associated factor 1, without stop codon, in Flexi system.
CU692854 - Synthetic construct Homo sapiens gateway clone IMAGE:100021937 5' read TRAF1 mRNA.
JD383898 - Sequence 364922 from Patent EP1572962.
JD253657 - Sequence 234681 from Patent EP1572962.
JD342082 - Sequence 323106 from Patent EP1572962.
MT163661 - Homo sapiens TNF receptor associated factor 1/ALK receptor tyrosine kinase fusion protein (TRAF1/ALK fusion) mRNA, partial cds.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_HivnefPathway - HIV-I Nef: negative effector of Fas and TNF
h_tnfr2Pathway - TNFR2 Signaling Pathway

Reactome (by CSHL, EBI, and GO)

Protein Q13077 (Reactome details) participates in the following event(s):

R-HSA-5634221 TRAF1 binds TRAF2 within TNFR1 signaling complex
R-HSA-5693108 TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains
R-HSA-5357905 Regulation of TNFR1 signaling
R-HSA-75893 TNF signaling
R-HSA-73887 Death Receptor Signalling
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B4DJ77, EBI6, ENST00000373887.1, ENST00000373887.2, ENST00000373887.3, ENST00000373887.4, ENST00000373887.5, ENST00000373887.6, ENST00000373887.7, NM_005658, Q13077, Q658U1, Q8NF13, TRAF1_HUMAN, uc318ldk.1, uc318ldk.2
UCSC ID: ENST00000373887.8_7
RefSeq Accession: NM_005658.5
Protein: Q13077 (aka TRAF1_HUMAN or TRA1_HUMAN)

-  Gene Model Information
  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.