Human Gene TRAF5 (uc010psx.2) Description and Page Index
  Description: Homo sapiens TNF receptor-associated factor 5 (TRAF5), transcript variant 3, mRNA.
RefSeq Summary (NM_001033910): The scaffold protein encoded by this gene is a member of the tumor necrosis factor receptor-associated factor (TRAF) protein family and contains a meprin and TRAF homology (MATH) domain, a RING-type zinc finger, and two TRAF-type zinc fingers. TRAF proteins are associated with, and mediate signal transduction from members of the TNF receptor superfamily. This protein is one of the components of a multiple protein complex which binds to tumor necrosis factor (TNF) receptor cytoplasmic domains and mediates TNF-induced activation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016].
Transcript (Including UTRs)
   Position: hg19 chr1:211,500,148-211,548,286 Size: 48,139 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr1:211,526,582-211,546,044 Size: 19,463 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:211,500,148-211,548,286)mRNA (may differ from genome)Protein (568 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: B4E0A2_HUMAN
DESCRIPTION: SubName: Full=cDNA FLJ55439, highly similar to TNF receptor-associated factor 5;
SIMILARITY: Contains 1 MATH domain.
SIMILARITY: Contains 1 RING-type zinc finger.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TRAF5
CDC HuGE Published Literature: TRAF5
Positive Disease Associations: Hemoglobin A, Glycosylated , rheumatoid arthritis
Related Studies:
  1. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
  2. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
  3. rheumatoid arthritis
    Potter, C. et al. 2007, Investigation of association between the TRAF family genes and RA susceptibility, Ann Rheum Dis 2007. [PubMed 17277003]
    These findings provide evidence for the association of a SNP upstream of a strong candidate RA susceptibility gene, TRAF5, in a large cohort of patients and controls.
           more ... click here to view the complete list

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.21 RPKM in Fallopian Tube
Total median expression: 252.75 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -35.9085-0.422 Picture PostScript Text
3' UTR -603.132242-0.269 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
IPR018957 - Znf_C3HC4_RING-type
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS
IPR001293 - Znf_TRAF

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF02176 - TRAF-type zinc finger

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

ModBase Predicted Comparative 3D Structure on B4E0A2
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
  BC032830 - Homo sapiens TNF receptor-associated factor 5, mRNA (cDNA clone IMAGE:4821810), with apparent retained intron.
JD417107 - Sequence 398131 from Patent EP1572962.
AK295766 - Homo sapiens cDNA FLJ60573 complete cds, highly similar to TNF receptor-associated factor 5.
JD455238 - Sequence 436262 from Patent EP1572962.
AK303286 - Homo sapiens cDNA FLJ55439 complete cds, highly similar to TNF receptor-associated factor 5.
AB000509 - Homo sapiens mRNA for TRAF5, complete cds.
BC029600 - Homo sapiens TNF receptor-associated factor 5, mRNA (cDNA clone MGC:39780 IMAGE:5295897), complete cds.
CU688710 - Synthetic construct Homo sapiens gateway clone IMAGE:100019860 5' read TRAF5 mRNA.
AB590631 - Synthetic construct DNA, clone: pFN21AE1979, Homo sapiens TRAF5 gene for TNF receptor-associated factor 5, without stop codon, in Flexi system.
GQ129370 - Synthetic construct Homo sapiens clone HAIB:100068695; DKFZo004E0936 TNF receptor-associated factor 5 protein (TRAF5) gene, partial cds.
GQ129371 - Synthetic construct Homo sapiens clone HAIB:100068598; DKFZo008E0935 TNF receptor-associated factor 5 protein (TRAF5) gene, complete cds.
KJ904578 - Synthetic construct Homo sapiens clone ccsbBroadEn_13972 TRAF5-like gene, encodes complete protein.
CR536557 - Homo sapiens full open reading frame cDNA clone RZPDo834A0922D for gene TRAF5, TNF receptor-associated factor 5; complete cds, incl. stopcodon.
U69108 - Homo sapiens TNF receptor associated factor 5 mRNA, partial cds.
AK130801 - Homo sapiens cDNA FLJ27291 fis, clone TMS02182.
AK126502 - Homo sapiens cDNA FLJ44538 fis, clone UTERU3005159, highly similar to TNF receptor-associated factor 5.
JD409977 - Sequence 391001 from Patent EP1572962.
JD235172 - Sequence 216196 from Patent EP1572962.
JD042037 - Sequence 23061 from Patent EP1572962.
JD544466 - Sequence 525490 from Patent EP1572962.
JD091568 - Sequence 72592 from Patent EP1572962.
JD423846 - Sequence 404870 from Patent EP1572962.
JD352446 - Sequence 333470 from Patent EP1572962.
JD524671 - Sequence 505695 from Patent EP1572962.
JD414454 - Sequence 395478 from Patent EP1572962.
JD514405 - Sequence 495429 from Patent EP1572962.
JD371240 - Sequence 352264 from Patent EP1572962.
JD268693 - Sequence 249717 from Patent EP1572962.
JD253784 - Sequence 234808 from Patent EP1572962.
JD345655 - Sequence 326679 from Patent EP1572962.
JD364131 - Sequence 345155 from Patent EP1572962.
JD120677 - Sequence 101701 from Patent EP1572962.
JD456240 - Sequence 437264 from Patent EP1572962.
JD311705 - Sequence 292729 from Patent EP1572962.
JD272328 - Sequence 253352 from Patent EP1572962.
JD505222 - Sequence 486246 from Patent EP1572962.
JD264297 - Sequence 245321 from Patent EP1572962.
JD234954 - Sequence 215978 from Patent EP1572962.
JD391063 - Sequence 372087 from Patent EP1572962.
JD278007 - Sequence 259031 from Patent EP1572962.
JD553920 - Sequence 534944 from Patent EP1572962.
JD096820 - Sequence 77844 from Patent EP1572962.
JD334069 - Sequence 315093 from Patent EP1572962.
JD348072 - Sequence 329096 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa05200 - Pathways in cancer
hsa05222 - Small cell lung cancer

-  Other Names for This Gene
  Alternate Gene Symbols: AK303286, B4E0A2, B4E0A2_HUMAN, NM_001033910, NP_665702
UCSC ID: uc010psx.2
RefSeq Accession: NM_001033910
Protein: B4E0A2 CCDS: CCDS1497.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK303286.1
exon count: 11CDS single in 3' UTR: no RNA size: 2170
ORF size: 1707CDS single in intron: no Alignment % ID: 99.95
txCdsPredict score: 3614.00frame shift in genome: no % Coverage: 100.00
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.