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] See more...

Aliases for TRAFD1 Gene

Aliases for TRAFD1 Gene

  • TRAF-Type Zinc Finger Domain Containing 1 2 3 5
  • FLN29 2 3 4
  • TRAF-Type Zinc Finger Domain-Containing Protein 1 3 4
  • FLN29 Gene Product 3
  • Protein FLN29 4
  • TRAFD1 5

External Ids for TRAFD1 Gene

Previous GeneCards Identifiers for TRAFD1 Gene

  • GC12P111027
  • GC12P112563
  • GC12P109576

Summaries for TRAFD1 Gene

Entrez Gene Summary for TRAFD1 Gene

  • 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]

GeneCards Summary for TRAFD1 Gene

TRAFD1 (TRAF-Type Zinc Finger Domain Containing 1) is a Protein Coding gene. Diseases associated with TRAFD1 include Choroid Plexus Meningioma and Diabetes Mellitus, Insulin-Dependent, 19. Among its related pathways are Toll-like Receptor Signaling Pathway. An important paralog of this gene is XAF1.

UniProtKB/Swiss-Prot Summary for TRAFD1 Gene

  • 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).

Gene Wiki entry for TRAFD1 Gene

Additional gene information for TRAFD1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRAFD1 Gene

Genomics for TRAFD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TRAFD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J112124 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +2.8 2763 8.2 SP1 CREB1 ZNF629 IKZF1 ZNF692 POLR2A BACH1 FOS JUND FOXA1 TRAFD1 TMEM116 MAPKAPK5 ADAM1A NAA25 ERP29 MN309607 HECTD4
GH12J111840 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 12.9 -283.3 -283337 4 ZNF221 BRCA1 SP1 CREB1 GATAD2A ZBTB33 ATF7 PRDM10 REST ZNF629 MAPKAPK5 MAPKAPK5-AS1 ATXN2 HECTD4 RPS2P41 ALDH2 TRAFD1 TMEM116 RPL6 ADAM1A
GH12J111684 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 12.9 -439.8 -439825 3.4 SP1 CREB1 PRDM10 ZNF629 IKZF1 NFKBIZ KDM1A CTCF ZNF692 POLR2A ACAD10 BRAP HSALNG0094051 ALDH2 TRAFD1 RPL6 ADAM1A HSPA8P14 RPS2P41 PCNPP1
GH12J112005 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 13.6 -119.7 -119720 1.2 PRDM10 ZNF512 LEF1 IKZF1 JUND PRDM1 MTA2 PKNOX1 MTA1 NR2C1 TMEM116 TRAFD1 LOC724085 lnc-NAA25-5 MAPKAPK5
GH12J112011 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.1 -112.0 -111975 4.3 RNF2 SP1 CREB1 GATAD2A PRDM10 ZNF629 REST TFE3 LEF1 IKZF1 TMEM116 ERP29 lnc-NAA25-5 RPL6 MAPKAPK5 HECTD4 ADAM1A NAA25 HSPA8P14 TRAFD1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRAFD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRAFD1

Top Transcription factor binding sites by QIAGEN in the TRAFD1 gene promoter:
  • Brachyury
  • FOXO3
  • FOXO3a
  • FOXO3b
  • HTF
  • NF-kappaB
  • NF-kappaB1
  • p53
  • Sp1
  • STAT1

Genomic Locations for TRAFD1 Gene

Genomic Locations for TRAFD1 Gene
chr12:112,125,538-112,153,604
(GRCh38/hg38)
Size:
28,067 bases
Orientation:
Plus strand
chr12:112,563,305-112,591,408
(GRCh37/hg19)
Size:
28,104 bases
Orientation:
Plus strand

Genomic View for TRAFD1 Gene

Genes around TRAFD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRAFD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRAFD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRAFD1 Gene

Proteins for TRAFD1 Gene

  • Protein details for TRAFD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O14545-TRAD1_HUMAN
    Recommended name:
    TRAF-type zinc finger domain-containing protein 1
    Protein Accession:
    O14545
    Secondary Accessions:
    • A8K5L6
    • B4DI89

    Protein attributes for TRAFD1 Gene

    Size:
    582 amino acids
    Molecular mass:
    64841 Da
    Quaternary structure:
    • Interacts with MAVS, TICAM1, TRAF1, TRAF2, TRAF3 (By similarity). Interacts with TRAF6.

    Three dimensional structures from OCA and Proteopedia for TRAFD1 Gene

    Alternative splice isoforms for TRAFD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRAFD1 Gene

Post-translational modifications for TRAFD1 Gene

  • Ubiquitination at Lys283 and Lys485
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TRAFD1 Gene

Domains & Families for TRAFD1 Gene

Gene Families for TRAFD1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for TRAFD1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TRAFD1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55063, highly similar to Homo sapiens TRAF-type zinc finger domain containing 1 (TRAFD1), mRNA (B4DI89_HUMAN)
  • Protein FLN29 (TRAD1_HUMAN)
genes like me logo Genes that share domains with TRAFD1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for TRAFD1 Gene

Function for TRAFD1 Gene

Molecular function for TRAFD1 Gene

UniProtKB/Swiss-Prot 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).

Phenotypes From GWAS Catalog for TRAFD1 Gene

Gene Ontology (GO) - Molecular Function for TRAFD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17500595
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with TRAFD1: view
genes like me logo Genes that share phenotypes with TRAFD1: view

Animal Models for TRAFD1 Gene

MGI Knock Outs for TRAFD1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRAFD1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TRAFD1 Gene

Localization for TRAFD1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TRAFD1 gene
Compartment Confidence
nucleus 3
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRAFD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IBA 21873635
genes like me logo Genes that share ontologies with TRAFD1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for TRAFD1 Gene

Pathways & Interactions for TRAFD1 Gene

PathCards logo

SuperPathways for TRAFD1 Gene

genes like me logo Genes that share pathways with TRAFD1: view

Pathways by source for TRAFD1 Gene

1 BioSystems pathway for TRAFD1 Gene

Gene Ontology (GO) - Biological Process for TRAFD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007005 mitochondrion organization IBA 21873635
GO:0045824 negative regulation of innate immune response ISS --
genes like me logo Genes that share ontologies with TRAFD1: view

No data available for SIGNOR curated interactions for TRAFD1 Gene

Drugs & Compounds for TRAFD1 Gene

No Compound Related Data Available

Transcripts for TRAFD1 Gene

mRNA/cDNA for TRAFD1 Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRAFD1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TRAFD1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c · 8d ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15
SP1: - - - -
SP2: - - -
SP3: - -
SP4: - -
SP5: - -
SP6: - - -

Relevant External Links for TRAFD1 Gene

GeneLoc Exon Structure for
TRAFD1

Expression for TRAFD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRAFD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TRAFD1 Gene

This gene is overexpressed in Fetal Brain (16.3), Fetal ovary (10.6), Peripheral blood mononuclear cells (9.4), Monocytes (8.1), and Testis (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRAFD1 Gene



Protein tissue co-expression partners for TRAFD1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRAFD1

SOURCE GeneReport for Unigene cluster for TRAFD1 Gene:

Hs.5148

Evidence on tissue expression from TISSUES for TRAFD1 Gene

  • Nervous system(4.9)
  • Skin(4.5)
  • Liver(4.3)
  • Blood(2.2)
  • Spleen(2.1)
  • Lymph node(2)
genes like me logo Genes that share expression patterns with TRAFD1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRAFD1 Gene

Orthologs for TRAFD1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TRAFD1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TRAFD1 30 31
  • 99.43 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TRAFD1 30 31
  • 88.6 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TRAFD1 30 31
  • 86.38 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Trafd1 30
  • 81.88 (n)
Mouse
(Mus musculus)
Mammalia Trafd1 30 17 31
  • 81.16 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia TRAFD1 31
  • 49 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TRAFD1 31
  • 48 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TRAFD1 30 31
  • 58.13 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TRAFD1 31
  • 33 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii zgc:162228 30
  • 51.92 (n)
TRAFD1 31
  • 31 (a)
OneToOne
Species where no ortholog for TRAFD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for TRAFD1 Gene

ENSEMBL:
Gene Tree for TRAFD1 (if available)
TreeFam:
Gene Tree for TRAFD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRAFD1: view image

Paralogs for TRAFD1 Gene

Paralogs for TRAFD1 Gene

(2) SIMAP similar genes for TRAFD1 Gene using alignment to 7 proteins:

  • TRAD1_HUMAN
  • B4DI89_HUMAN
  • F8VNX8_HUMAN
  • F8VVF3_HUMAN
  • F8VWK2_HUMAN
  • L8E7W3_HUMAN
  • S4R2Z9_HUMAN
genes like me logo Genes that share paralogs with TRAFD1: view

Variants for TRAFD1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRAFD1 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
788439 Benign: not provided 112,142,141(+) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for TRAFD1 Gene

Structural Variations from Database of Genomic Variants (DGV) for TRAFD1 Gene

Variant ID Type Subtype PubMed ID
nsv483114 CNV gain 15286789

Variation tolerance for TRAFD1 Gene

Residual Variation Intolerance Score: 36.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.44; 42.99% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRAFD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRAFD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRAFD1 Gene

Disorders for TRAFD1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for TRAFD1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
choroid plexus meningioma
  • choroid meningioma
diabetes mellitus, insulin-dependent, 19
  • iddm19
central nervous system tuberculosis
  • intracranial tuberculoma
type 1 diabetes mellitus 18
  • diabetes mellitus, insulin-dependent, 18
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TRAFD1

genes like me logo Genes that share disorders with TRAFD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TRAFD1 Gene

Publications for TRAFD1 Gene

  1. FLN29, a novel interferon- and LPS-inducible gene acting as a negative regulator of toll-like receptor signaling. (PMID: 16221674) Mashima R … Yoshimura A (The Journal of biological chemistry 2005) 2 3 4
  2. TRAFD1 (FLN29) Interacts with Plekhm1 and Regulates Osteoclast Acidification and Resorption. (PMID: 25992615) Witwicka H … Odgren PR (PloS one 2015) 2 3
  3. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. (PMID: 19862010) Ganesh SK … Lin JP (Nature genetics 2009) 3 41
  4. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. (PMID: 17554300) Wellcome Trust Case Control Consortium (Nature 2007) 3 41
  5. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PMID: 16964243) Beausoleil SA … Gygi SP (Nature biotechnology 2006) 3 4

Products for TRAFD1 Gene

  • Signalway Proteins for TRAFD1

Sources for TRAFD1 Gene