Human Gene TRAFD1 (uc001ttp.3)
  Description: Homo sapiens TRAF-type zinc finger domain containing 1 (TRAFD1), transcript variant 2, mRNA.
RefSeq Summary (NM_006700): The innate immune system confers host defense against viral and microbial infection, and TRAFD1 is a negative feedback regulator that controls excessive immune responses (Sanada et al., 2008 [PubMed 18849341]).[supplied by OMIM, Dec 2009].
Transcript (Including UTRs)
   Position: hg19 chr12:112,563,349-112,591,408 Size: 28,060 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr12:112,568,327-112,590,595 Size: 22,269 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:112,563,349-112,591,408)mRNA (may differ from genome)Protein (582 aa)
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TRAD1_HUMAN
DESCRIPTION: RecName: Full=TRAF-type zinc finger domain-containing protein 1; AltName: Full=Protein FLN29;
FUNCTION: Negative feedback regulator that controls excessive innate immune responses. Regulates both Toll-like receptor 4 (TLR4) and DDX58/RIG1-like helicases (RLH) pathways. May inhibit the LTR pathway by direct interaction with TRAF6 and attenuation of NF-kappa-B activation. May negatively regulate the RLH pathway downstream from MAVS and upstream of NF-kappa-B and IRF3 (By similarity).
SUBUNIT: Interacts with MAVS, TICAM1, TRAF1, TRAF2, TRAF3 (By similarity). Interacts with TRAF6.
SIMILARITY: Contains 1 TRAF-type zinc finger.

-  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): TRAFD1
CDC HuGE Published Literature: TRAFD1
Positive Disease Associations: hemoglobin , type 1 diabetes
Related Studies:
  1. hemoglobin
    Ganesh ,et al. 2009, Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium, Nature genetics 2009 41- 11 : 1191-8. [PubMed 19862010]
  2. type 1 diabetes
    WTCCC ,et al. 2007, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls, Nature 2007 447- 7145 : 661-78. [PubMed 17554300]

-  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: 36.36 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 602.19 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 -25.2086-0.293 Picture PostScript Text
3' UTR -308.26813-0.379 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
IPR015880 - Znf_C2H2-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2D9K - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O14545
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0034097 response to cytokine
GO:0045824 negative regulation of innate immune response


-  Descriptions from all associated GenBank mRNAs
  LF384013 - JP 2014500723-A/191516: Polycomb-Associated Non-Coding RNAs.
AK291331 - Homo sapiens cDNA FLJ76844 complete cds, highly similar to Homo sapiens TRAF-type zinc finger domain containing 1 (TRAFD1), mRNA.
AK122620 - Homo sapiens cDNA FLJ16040 fis, clone BRACE2006319, highly similar to Homo sapiens mRNA for Fln29.
AB007447 - Homo sapiens mRNA for Fln29, complete cds.
BC003553 - Homo sapiens TRAF-type zinc finger domain containing 1, mRNA (cDNA clone MGC:1295 IMAGE:3547039), complete cds.
MA619590 - JP 2018138019-A/191516: Polycomb-Associated Non-Coding RNAs.
AK309916 - Homo sapiens cDNA, FLJ99957.
AK312601 - Homo sapiens cDNA, FLJ92978.
AK295474 - Homo sapiens cDNA FLJ55063 complete cds, highly similar to Homo sapiens TRAF-type zinc finger domain containing 1 (TRAFD1), mRNA.
JD043692 - Sequence 24716 from Patent EP1572962.
CU678494 - Synthetic construct Homo sapiens gateway clone IMAGE:100020394 5' read TRAFD1 mRNA.
AB528329 - Synthetic construct DNA, clone: pF1KE1044, Homo sapiens TRAFD1 gene for TRAF-type zinc finger domain containing 1, without stop codon, in Flexi system.
DQ895741 - Synthetic construct Homo sapiens clone IMAGE:100010201; FLH187205.01L; RZPDo839E1162D TRAF-type zinc finger domain containing 1 (TRAFD1) gene, encodes complete protein.
DQ892530 - Synthetic construct clone IMAGE:100005160; FLH187209.01X; RZPDo839E1172D TRAF-type zinc finger domain containing 1 (TRAFD1) gene, encodes complete protein.
KJ893160 - Synthetic construct Homo sapiens clone ccsbBroadEn_02554 TRAFD1 gene, encodes complete protein.
LF359565 - JP 2014500723-A/167068: Polycomb-Associated Non-Coding RNAs.
LF359564 - JP 2014500723-A/167067: Polycomb-Associated Non-Coding RNAs.
LF359563 - JP 2014500723-A/167066: Polycomb-Associated Non-Coding RNAs.
LF359562 - JP 2014500723-A/167065: Polycomb-Associated Non-Coding RNAs.
LF359561 - JP 2014500723-A/167064: Polycomb-Associated Non-Coding RNAs.
JD136634 - Sequence 117658 from Patent EP1572962.
JD427546 - Sequence 408570 from Patent EP1572962.
JD445385 - Sequence 426409 from Patent EP1572962.
JD343138 - Sequence 324162 from Patent EP1572962.
JD200614 - Sequence 181638 from Patent EP1572962.
MA595142 - JP 2018138019-A/167068: Polycomb-Associated Non-Coding RNAs.
MA595141 - JP 2018138019-A/167067: Polycomb-Associated Non-Coding RNAs.
MA595140 - JP 2018138019-A/167066: Polycomb-Associated Non-Coding RNAs.
MA595139 - JP 2018138019-A/167065: Polycomb-Associated Non-Coding RNAs.
MA595138 - JP 2018138019-A/167064: Polycomb-Associated Non-Coding RNAs.
JD152398 - Sequence 133422 from Patent EP1572962.
JD114869 - Sequence 95893 from Patent EP1572962.
JD510884 - Sequence 491908 from Patent EP1572962.
JD179938 - Sequence 160962 from Patent EP1572962.
JD385448 - Sequence 366472 from Patent EP1572962.
JD292119 - Sequence 273143 from Patent EP1572962.
JD164278 - Sequence 145302 from Patent EP1572962.
JD560492 - Sequence 541516 from Patent EP1572962.
JD238878 - Sequence 219902 from Patent EP1572962.
JD157251 - Sequence 138275 from Patent EP1572962.
JD433797 - Sequence 414821 from Patent EP1572962.
JD328622 - Sequence 309646 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K5L6, FLN29, NM_006700, NP_006691, O14545, TRAD1_HUMAN
UCSC ID: uc001ttp.3
RefSeq Accession: NM_006700
Protein: O14545 (aka TRAD1_HUMAN)
CCDS: CCDS9160.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006700.2
exon count: 12CDS single in 3' UTR: no RNA size: 2665
ORF size: 1749CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3698.00frame shift in genome: no % Coverage: 99.36
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.