WDFY1 Gene (Protein Coding)

WD Repeat And FYVE Domain Containing 1

GC02M223855
GIFtS:
34
The protein encoded by this gene is a phosphatidylinositol 3-phosphate binding protein, which contains a FYVE zinc finger domain and multiple WD-40 repeat domains. When exogenously expressed, it localizes to early endosomes. Mutagenesis analysis demonstrates that this endosomal localization is mediated by the FYVE domain. [provided by RefSeq, Jan 2015] See more...

Aliases for WDFY1 Gene

Aliases for WDFY1 Gene

  • WD Repeat And FYVE Domain Containing 1 2 3 5
  • FYVE Domain-Containing Protein Localized To Endosomes 1 3 4
  • WD Repeat And FYVE Domain-Containing Protein 1 3 4
  • Zinc Finger FYVE Domain-Containing Protein 17 3 4
  • WD40- And FYVE Domain-Containing Protein 1 3 4
  • ZFYVE17 3 4
  • FENS-1 3 4
  • FENS1 3 4
  • WDF1 3 4
  • Phosphoinositide-Binding Protein SR1 3
  • Phosphoinositide-Binding Protein 1 4
  • WD40 And FYVE Domain Containing 1 2
  • KIAA1435 4

External Ids for WDFY1 Gene

Previous GeneCards Identifiers for WDFY1 Gene

  • GC02M223461
  • GC02M224704
  • GC02M224942
  • GC02M224565
  • GC02M224448
  • GC02M216592

Summaries for WDFY1 Gene

Entrez Gene Summary for WDFY1 Gene

  • The protein encoded by this gene is a phosphatidylinositol 3-phosphate binding protein, which contains a FYVE zinc finger domain and multiple WD-40 repeat domains. When exogenously expressed, it localizes to early endosomes. Mutagenesis analysis demonstrates that this endosomal localization is mediated by the FYVE domain. [provided by RefSeq, Jan 2015]

GeneCards Summary for WDFY1 Gene

WDFY1 (WD Repeat And FYVE Domain Containing 1) is a Protein Coding gene. Diseases associated with WDFY1 include Schizophrenia 19. Gene Ontology (GO) annotations related to this gene include 1-phosphatidylinositol binding. An important paralog of this gene is WDFY2.

UniProtKB/Swiss-Prot Summary for WDFY1 Gene

  • Positively regulates TLR3- and TLR4-mediated signaling pathways by bridging the interaction between TLR3 or TLR4 and TICAM1. Promotes TLR3/4 ligand-induced activation of transcription factors IRF3 and NF-kappa-B, as well as the production of IFN-beta and inflammatory cytokines (PubMed:25736436).

Additional gene information for WDFY1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for WDFY1 Gene

Genomics for WDFY1 Gene

GeneHancer (GH) Regulatory Elements for WDFY1 Gene

Promoters and enhancers for WDFY1 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
GH02J223942 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 530 +0.9 885 3.4 EP300 RXRA HNRNPK ZBTB40 TCF12 SIN3A NRF1 POLR2G USF1 SP1 WDFY1 ENSG00000286239 ENSG00000228446 AP1S3 MRPL44 RF00994-559
GH02J223946 Promoter 0.3 Ensembl 500.7 -1.1 -1113 0.2 ENSG00000286239 WDFY1 lnc-MRPL44-2
GH02J223956 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 36.3 -12.7 -12658 3.9 EP300 RXRA ZBTB40 ZNF217 ZSCAN5C TCF12 SIN3A NRF1 USF1 POLR2G MRPL44 lnc-WDFY1-4 piR-41482 WDFY1 ENSG00000228446 SCG2
GH02J223832 Enhancer 0.7 Ensembl 53.1 +112.4 112386 1.6 RBAK ZNF623 ZNF510 ZNF341 ZNF266 NFIC ZBTB11 ZNF426 KLF9 ZNF189 WDFY1 ENSG00000228446 MRPL44 AP1S3 RF00017-3434 piR-50444-270 ENSG00000286239
GH02J223893 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 22 +49.4 49420 4.8 SP1 FOS ZNF639 EP300 JUND RELA MEF2C RCOR1 REST TRIM22 WDFY1 MRPL44 lnc-AP1S3-2 lnc-WDFY1-1 ENSG00000286239
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around WDFY1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for WDFY1

Top Transcription factor binding sites by QIAGEN in the WDFY1 gene promoter:
  • AML1a
  • AP-1
  • c-Fos
  • c-Jun
  • c-Myb
  • C/EBPalpha
  • CUTL1
  • GATA-1
  • Ik-1
  • ZID

Genomic Locations for WDFY1 Gene

Genomic Locations for WDFY1 Gene
chr2:223,855,716-223,945,387
(GRCh38/hg38)
Size:
89,672 bases
Orientation:
Minus strand
chr2:224,720,433-224,810,104
(GRCh37/hg19)
Size:
89,672 bases
Orientation:
Minus strand

Genomic View for WDFY1 Gene

Genes around WDFY1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
WDFY1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for WDFY1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for WDFY1 Gene

Proteins for WDFY1 Gene

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  • Protein details for WDFY1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IWB7-WDFY1_HUMAN
    Recommended name:
    WD repeat and FYVE domain-containing protein 1
    Protein Accession:
    Q8IWB7
    Secondary Accessions:
    • Q53S17
    • Q9H9D5
    • Q9P2B3

    Protein attributes for WDFY1 Gene

    Size:
    410 amino acids
    Molecular mass:
    46324 Da
    Quaternary structure:
    • Binds PtdIns3P in vitro with high specificity over other phosphoinositides. Interacts (via WD repeat 2) with tyrosine-phosphorylated TLR3 (via TIR domain) in response to poly(I:C) (PubMed:25736436). Interacts with TICAM1 in response to poly(I:C) (By similarity). Interacts with TLR4 in response to LPS (By similarity).
    SequenceCaution:
    • Sequence=BAA92673.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

neXtProt entry for WDFY1 Gene

Protein Expression for WDFY1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for WDFY1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for WDFY1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for WDFY1 Gene

Domains & Families for WDFY1 Gene

Gene Families for WDFY1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for WDFY1 Gene

Blocks:
  • Zn-finger, FYVE type
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for WDFY1 Gene

GenScript: Design optimal peptide antigens:
  • WD repeat and FYVE domain containing 1, isoform CRA_a (Q53S17_HUMAN)
  • Zinc finger FYVE domain-containing protein 17 (WDFY1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IWB7

UniProtKB/Swiss-Prot:

WDFY1_HUMAN :
  • The FYVE-type zinc finger domain mediates interactions with phosphatidylinositol 3-phosphate in membranes of early endosomes and penetrates bilayers. The FYVE domain insertion into PtdIns(3)P-enriched membranes is substantially increased in acidic conditions. The FYVE domain is required for its function in regulating TLR3 signaling (PubMed:25736436).
Domain:
  • The FYVE-type zinc finger domain mediates interactions with phosphatidylinositol 3-phosphate in membranes of early endosomes and penetrates bilayers. The FYVE domain insertion into PtdIns(3)P-enriched membranes is substantially increased in acidic conditions. The FYVE domain is required for its function in regulating TLR3 signaling (PubMed:25736436).
genes like me logo Genes that share domains with WDFY1: view

Function for WDFY1 Gene

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Molecular function for WDFY1 Gene

UniProtKB/Swiss-Prot Function:
Positively regulates TLR3- and TLR4-mediated signaling pathways by bridging the interaction between TLR3 or TLR4 and TICAM1. Promotes TLR3/4 ligand-induced activation of transcription factors IRF3 and NF-kappa-B, as well as the production of IFN-beta and inflammatory cytokines (PubMed:25736436).

Phenotypes From GWAS Catalog for WDFY1 Gene

Gene Ontology (GO) - Molecular Function for WDFY1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25736436
GO:0005545 1-phosphatidylinositol binding IDA 11739631
GO:0008270 zinc ion binding NAS 11739631
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with WDFY1: view
genes like me logo Genes that share phenotypes with WDFY1: view

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No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for WDFY1 Gene

Localization for WDFY1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for WDFY1 Gene

Early endosome.

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 WDFY1 gene
Compartment Confidence
nucleus 5
endosome 5
cytosol 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for WDFY1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 11739631
GO:0005768 endosome IEA --
GO:0005769 early endosome IEA,IDA 11739631
GO:0005829 cytosol IDA 11739631
genes like me logo Genes that share ontologies with WDFY1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for WDFY1 Gene

Pathways & Interactions for WDFY1 Gene

PathCards logo

SuperPathways for WDFY1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for WDFY1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034141 positive regulation of toll-like receptor 3 signaling pathway IMP 25736436
GO:0034145 positive regulation of toll-like receptor 4 signaling pathway IMP 25736436
genes like me logo Genes that share ontologies with WDFY1: view

No data available for Pathways by source and SIGNOR curated interactions for WDFY1 Gene

Drugs & Compounds for WDFY1 Gene

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  1. Drug
No Compound Related Data Available

Transcripts for WDFY1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for WDFY1 Gene

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

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for WDFY1 Gene

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

Relevant External Links for WDFY1 Gene

GeneLoc Exon Structure for
WDFY1

Expression for WDFY1 Gene

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  1. Primer
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for WDFY1 Gene

mRNA expression in normal human tissues for WDFY1 Gene
mRNA expression by BioGPS for WDFY1 GenemRNA expression by GTEx for WDFY1 Gene

Protein differential expression in normal tissues from HIPED for WDFY1 Gene

This gene is overexpressed in Urinary Bladder (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for WDFY1 Gene



Protein tissue co-expression partners for WDFY1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for WDFY1

SOURCE GeneReport for Unigene cluster for WDFY1 Gene:

Hs.368359

Evidence on tissue expression from TISSUES for WDFY1 Gene

  • Nervous system(4.6)
  • Skin(4.5)
genes like me logo Genes that share expression patterns with WDFY1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for WDFY1 Gene

Orthologs for WDFY1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for WDFY1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia WDFY1 31 30
  • 99.27 (n)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia WDFY1 31
  • 94 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia WDFY1 31
  • 92 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia WDFY1 31 30
  • 90.98 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia WDFY1 31 30
  • 89.35 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Wdfy1 17 31 30
  • 88.86 (n)
chicken
(Gallus gallus)
 Aves WDFY1 31 30
  • 81.78 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia WDFY1 31
  • 90 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia wdfy1 30
  • 73.12 (n)
Str.11442 30
zebrafish
(Danio rerio)
 Actinopterygii wdfy1 31 30
  • 75.16 (n)
 OneToOne
Dr.3787 30
fruit fly
(Drosophila melanogaster)
 Insecta CG5168 31
  • 45 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea wdfy-2 31
  • 38 (a)
 OneToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes VPS27 31
  • 8 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.4999 31
  • 51 (a)
 OneToMany
Species where no ortholog for WDFY1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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)
  • 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)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for WDFY1 Gene

ENSEMBL:
Gene Tree for WDFY1 (if available)
TreeFam:
Gene Tree for WDFY1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for WDFY1: view image

Paralogs for WDFY1 Gene

Paralogs for WDFY1 Gene

(1) SIMAP similar genes for WDFY1 Gene using alignment to 3 proteins:

  • WDFY1_HUMAN
  • C9JJ54_HUMAN
  • L8E905_HUMAN
genes like me logo Genes that share paralogs with WDFY1: view

Variants for WDFY1 Gene

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Additional dbSNP identifiers (rs#s) for WDFY1 Gene

Structural Variations from Database of Genomic Variants (DGV) for WDFY1 Gene

Variant ID Type Subtype PubMed ID
nsv214769 CNV deletion 16902084
nsv834555 CNV loss 17160897

Variation tolerance for WDFY1 Gene

Residual Variation Intolerance Score: 32.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.03; 21.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for WDFY1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
WDFY1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for WDFY1 Gene

Disorders for WDFY1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for WDFY1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
schizophrenia 19
  • sczd19
- elite association - COSMIC cancer census association via MalaCards
Search WDFY1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for WDFY1

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with WDFY1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for WDFY1 Gene

Publications for WDFY1 Gene

  1. FENS-1 and DFCP1 are FYVE domain-containing proteins with distinct functions in the endosomal and Golgi compartments. (PMID: 11739631) Ridley SH … Hawkins PT (Journal of cell science 2001) 2 3 4 54
  2. WDFY1 mediates TLR3/4 signaling by recruiting TRIF. (PMID: 25736436) Hu YH … Liu Y (EMBO reports 2015) 3 4 54
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  5. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4 54

ExternalLinks

View latest publications for WDFY1 gene in Mastermind

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