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Aliases for WDFY3 Gene

Aliases for WDFY3 Gene

  • WD Repeat And FYVE Domain Containing 3 2 3
  • Autophagy-Linked FYVE Protein 3 4
  • ALFY 3 4
  • WD Repeat And FYVE Domain-Containing Protein 3 3
  • KIAA0993 4
  • ZFYVE25 3

External Ids for WDFY3 Gene

Previous GeneCards Identifiers for WDFY3 Gene

  • GC04M085884
  • GC04M086049
  • GC04M085947
  • GC04M085809
  • GC04M085590
  • GC04M081332

Summaries for WDFY3 Gene

Entrez Gene Summary for WDFY3 Gene

  • This gene encodes a phosphatidylinositol 3-phosphate-binding protein that functions as a master conductor for aggregate clearance by autophagy. This protein shuttles from the nuclear membrane to colocalize with aggregated proteins, where it complexes with other autophagic components to achieve macroautophagy-mediated clearance of these aggregated proteins. However, it is not necessary for starvation-induced macroautophagy. [provided by RefSeq, May 2010]

GeneCards Summary for WDFY3 Gene

WDFY3 (WD Repeat And FYVE Domain Containing 3) is a Protein Coding gene. Diseases associated with WDFY3 include chediak-higashi syndrome. GO annotations related to this gene include 1-phosphatidylinositol binding and beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity. An important paralog of this gene is LRBA.

UniProtKB/Swiss-Prot for WDFY3 Gene

  • Required for selective autophagy (aggrephagy) but not for autophagic degradation of bulk cytospol in response to starvation. Involved in the formation and degradation of cytoplasmic polyubiquitin-containing bodies (p62 bodies, ALIS/aggresome-like induced structures). May play a role as adaptor or scaffolding protein by promoting the association of the E3-like ligase ATG12-ATG5-ATG16L and LC3 to ubiquitinated target substrate. The association with GABARAP is required for its recruitment to LC3B-positive p62 bodies suggesting a role in targeting certain p62 structures for clearance. Involved in midbody ring degradation.

Gene Wiki entry for WDFY3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for WDFY3 Gene

Genomics for WDFY3 Gene

Regulatory Elements for WDFY3 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for WDFY3 Gene

Start:
84,669,537 bp from pter
End:
84,966,391 bp from pter
Size:
296,855 bases
Orientation:
Minus strand

Genomic View for WDFY3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for WDFY3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for WDFY3 Gene

Proteins for WDFY3 Gene

  • Protein details for WDFY3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IZQ1-WDFY3_HUMAN
    Recommended name:
    WD repeat and FYVE domain-containing protein 3
    Protein Accession:
    Q8IZQ1
    Secondary Accessions:
    • Q4W5K5
    • Q6P0Q5
    • Q8N1T2
    • Q8NAV6
    • Q96BS7
    • Q96D33
    • Q96N85
    • Q9Y2J7

    Protein attributes for WDFY3 Gene

    Size:
    3526 amino acids
    Molecular mass:
    395258 Da
    Quaternary structure:
    • Interacts with ATG5 and SQSTM1. Associates with the ATG12-ATG5-ATG16L complex. Interacts with GABARAP, GABARAPL1 and GABARAPL2, and weakly with MAP1LC3C.
    SequenceCaution:
    • Sequence=AAH13377.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH15214.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB71020.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=BAC04455.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for WDFY3 Gene

    Alternative splice isoforms for WDFY3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for WDFY3 Gene

Proteomics data for WDFY3 Gene at MOPED

Post-translational modifications for WDFY3 Gene

  • Ubiquitination at Lys1353
  • Modification sites at PhosphoSitePlus

Other Protein References for WDFY3 Gene

Antibody Products

No data available for DME Specific Peptides for WDFY3 Gene

Domains for WDFY3 Gene

Gene Families for WDFY3 Gene

HGNC:
  • WDR :WD repeat domain containing
  • ZFYVE :Zinc fingers, FYVE domain containing

Suggested Antigen Peptide Sequences for WDFY3 Gene

Graphical View of Domain Structure for InterPro Entry

Q8IZQ1

UniProtKB/Swiss-Prot:

WDFY3_HUMAN :
  • Q8IZQ1
Domain:
  • The LIR (LC3-interacting region) motif mediates the interaction with ATG8 family proteins
  • Contains 1 BEACH domain.
Similarity:
  • Contains 1 FYVE-type zinc finger.
  • Contains 5 WD repeats.
genes like me logo Genes that share domains with WDFY3: view

Function for WDFY3 Gene

Molecular function for WDFY3 Gene

UniProtKB/Swiss-Prot Function:
Required for selective autophagy (aggrephagy) but not for autophagic degradation of bulk cytospol in response to starvation. Involved in the formation and degradation of cytoplasmic polyubiquitin-containing bodies (p62 bodies, ALIS/aggresome-like induced structures). May play a role as adaptor or scaffolding protein by promoting the association of the E3-like ligase ATG12-ATG5-ATG16L and LC3 to ubiquitinated target substrate. The association with GABARAP is required for its recruitment to LC3B-positive p62 bodies suggesting a role in targeting certain p62 structures for clearance. Involved in midbody ring degradation.

Gene Ontology (GO) - Molecular Function for WDFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003831 beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity IEA --
GO:0005488 binding --
GO:0005515 protein binding IPI 20168092
GO:0005545 1-phosphatidylinositol binding IDA 15292400
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with WDFY3: view

Phenotypes for WDFY3 Gene

genes like me logo Genes that share phenotypes with WDFY3: view

Animal Model Products

CRISPR Products

miRNA for WDFY3 Gene

miRTarBase miRNAs that target WDFY3

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for WDFY3

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for WDFY3 Gene

Localization for WDFY3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for WDFY3 Gene

Nucleus membrane. Cytoplasm. Nucleus, PML body. Membrane; Peripheral membrane protein; Cytoplasmic side. Note=Colocalizes with autophagic structures in starved cells. Shuttles between nucleus and cytoplasm; translocation from the nucleus to cytoplasmic polyubiquitin-containing bodies upon cellular stress is dependent on SQSTM1.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for WDFY3 Gene COMPARTMENTS Subcellular localization image for WDFY3 gene
Compartment Confidence
nucleus 5
cytosol 3
mitochondrion 1
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for WDFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005635 nuclear envelope IDA 15292400
GO:0005737 cytoplasm IDA 15292400
GO:0005776 autophagic vacuole IMP 20168092
GO:0016234 inclusion body IDA 20168092
GO:0016605 PML body IDA 20168092
genes like me logo Genes that share ontologies with WDFY3: view

Pathways for WDFY3 Gene

SuperPathways for WDFY3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for WDFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016197 endosomal transport IBA --
GO:0016239 positive regulation of macroautophagy IMP 20168092
GO:0035973 aggrephagy IMP 20417604
genes like me logo Genes that share ontologies with WDFY3: view

No data available for Pathways by source for WDFY3 Gene

Transcripts for WDFY3 Gene

Unigene Clusters for WDFY3 Gene

WD repeat and FYVE domain containing 3:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for WDFY3

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for WDFY3 Gene

No ASD Table

Relevant External Links for WDFY3 Gene

GeneLoc Exon Structure for
WDFY3
ECgene alternative splicing isoforms for
WDFY3

Expression for WDFY3 Gene

mRNA expression in normal human tissues for WDFY3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues for WDFY3 Gene

This gene is overexpressed in Pancreatic juice (25.7) and Placenta (17.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for WDFY3 Gene

SOURCE GeneReport for Unigene cluster for WDFY3 Gene Hs.480116

mRNA Expression by UniProt/SwissProt for WDFY3 Gene

Q8IZQ1-WDFY3_HUMAN
Tissue specificity: Ubiquitous. Expressed in osteoclast and their mononuclear precursors (at protein level).
genes like me logo Genes that share expressions with WDFY3: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and Expression partners for WDFY3 Gene

Orthologs for WDFY3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for WDFY3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia WDFY3 35
  • 91.06 (n)
  • 97.65 (a)
WDFY3 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia WDFY3 35
  • 93.2 (n)
  • 98.1 (a)
WDFY3 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Wdfy3 35
  • 86.45 (n)
  • 96.47 (a)
Wdfy3 16
Wdfy3 36
  • 96 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia WDFY3 35
  • 99.71 (n)
  • 99.83 (a)
WDFY3 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Wdfy3 35
  • 85.03 (n)
  • 95.55 (a)
oppossum
(Monodelphis domestica)
Mammalia WDFY3 36
  • 94 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia WDFY3 36
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves WDFY3 35
  • 82.09 (n)
  • 93.19 (a)
WDFY3 36
  • 93 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia WDFY3 36
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.18129 35
wdfy3 35
  • 77.2 (n)
  • 88.42 (a)
zebrafish
(Danio rerio)
Actinopterygii Dr.17425 35
wdfy3 35
  • 73.66 (n)
  • 84.94 (a)
wdfy3 36
  • 84 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta bchs 35
  • 53.31 (n)
  • 51.64 (a)
bchs 36
  • 48 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea C26H9A.2 35
  • 48.2 (n)
  • 40.05 (a)
C26H9A.2 36
  • 37 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BPH1 38
rice
(Oryza sativa)
Liliopsida Os.23284 35
Species with no ortholog for WDFY3:
  • 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)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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)
  • wheat (Triticum aestivum)

Evolution for WDFY3 Gene

ENSEMBL:
Gene Tree for WDFY3 (if available)
TreeFam:
Gene Tree for WDFY3 (if available)

Paralogs for WDFY3 Gene

Paralogs for WDFY3 Gene

Selected SIMAP similar genes for WDFY3 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with WDFY3: view

Variants for WDFY3 Gene

Sequence variations from dbSNP and Humsavar for WDFY3 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type MAF
rs894533 -- 84,743,141(+) TAGCA(C/T)ATATA intron-variant
rs936750 -- 84,865,052(+) cctgt(C/T)taatt intron-variant
rs970208 -- 84,758,086(+) ACTCA(A/G)GATAC intron-variant
rs970209 -- 84,758,439(+) gacaa(A/G)gtctt intron-variant
rs970210 -- 84,758,458(+) gctca(A/G)gctgg intron-variant

Structural Variations from Database of Genomic Variants (DGV) for WDFY3 Gene

Variant ID Type Subtype PubMed ID
nsv527581 CNV Loss 19592680
esv1008012 CNV Insertion 20482838
nsv519588 CNV Gain 19592680
nsv879515 CNV Loss 21882294
nsv508295 CNV Loss 20534489
esv269362 CNV Insertion 20981092
nsv879516 CNV Loss 21882294

Relevant External Links for WDFY3 Gene

HapMap Linkage Disequilibrium report
WDFY3
Human Gene Mutation Database (HGMD)
WDFY3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for WDFY3 Gene

Disorders for WDFY3 Gene

MalaCards: The human disease database

MalaCards: The human disease database.

Search for WDFY3 Gene in MalaCards »

(1) Diseases for WDFY3 Gene including...

(1) University of Copenhagen DISEASES for WDFY3 Gene

Relevant External Links for WDFY3

Genetic Association Database (GAD)
WDFY3
Human Genome Epidemiology (HuGE) Navigator
WDFY3
genes like me logo Genes that share disorders with WDFY3: view

No data available for OMIM , UniProtKB/Swiss-Prot , Novoseek inferred disease relationships and Genatlas for WDFY3 Gene

Publications for WDFY3 Gene

  1. Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10231032) Nagase T. … Ohara O. (DNA Res. 1999) 2 3 4
  2. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PMID: 12168954) Nakajima D. … Nagase T. (DNA Res. 2002) 3 4
  3. p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy. (PMID: 20168092) Clausen T.H. … Johansen T. (Autophagy 2010) 3 4
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 48
  5. The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. (PMID: 20417604) Filimonenko M. … Yamamoto A. (Mol. Cell 2010) 3 4

Products for WDFY3 Gene

Sources for WDFY3 Gene

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