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Aliases for WDFY3 Gene

Aliases for WDFY3 Gene

  • WD Repeat And FYVE Domain Containing 3 2 3 5
  • 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. GO annotations related to this gene include binding and beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity. An important paralog of this gene is WDFY4.

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 CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for WDFY3 Gene

Genomics for WDFY3 Gene

Regulatory Elements for WDFY3 Gene

Enhancers for WDFY3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04G084937 0.9 Ensembl ENCODE 12 +27.8 27801 3.1 JUN BHLHE40 JUND SMARCA4 ZNF600 FOS HNF4A SP7 WDFY3-AS2 WDFY3 WDFY3-AS1 RNU6-469P
GH04G084391 0.4 FANTOM5 4.6 +574.6 574629 0.4 ZNF133 WDFY3 ENSG00000248749 GC04P084474
GH04G084877 0.8 FANTOM5 1.7 +90.2 90192 0.1 CTCF ATF1 ZBTB21 YY1 ZNF335 FOXK2 CREM ZNF362 BHLHE40 TRIM22 WDFY3 RNU6-469P WDFY3-AS1
GH04G084965 1.1 ENCODE 0.7 -0.1 -120 2.9 PKNOX1 ARNT ARID4B SIN3A ZNF2 YY1 FOS ZNF263 SP3 SP5 WDFY3-AS2 WDFY3 GC04P085101
GH04G084994 0.6 ENCODE 0.3 -28.0 -27963 0.7 ZNF146 RFX1 HCFC1 ZNF341 ZNF143 PRDM10 FOXJ2 ETS1 THAP11 WDFY3-AS2 WDFY3 GC04P085101
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around WDFY3 on UCSC Golden Path with GeneCards custom track

Promoters for WDFY3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000170201 -9 2801 PKNOX1 ARNT ARID4B SIN3A ZNF2 YY1 FOS ZNF263 SP3 SP5

Genomic Location for WDFY3 Gene

Chromosome:
4
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

Genes around WDFY3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
WDFY3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for WDFY3 Gene

  • Ubiquitination at Lys1353
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for WDFY3 Gene

Domains & Families for WDFY3 Gene

Suggested Antigen Peptide Sequences for WDFY3 Gene

Graphical View of Domain Structure for InterPro Entry

Q8IZQ1

UniProtKB/Swiss-Prot:

WDFY3_HUMAN :
  • The LIR (LC3-interacting region) motif mediates the interaction with ATG8 family proteins.
Domain:
  • The LIR (LC3-interacting region) motif mediates the interaction with ATG8 family proteins.
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:0005515 protein binding IPI 18083104
GO:0005545 1-phosphatidylinositol binding IDA 15292400
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with WDFY3: view
genes like me logo Genes that share phenotypes with WDFY3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for WDFY3

CRISPR Products

miRNA for WDFY3 Gene

miRTarBase miRNAs that target WDFY3

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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
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 WDFY3 gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytosol 5
mitochondrion 1
peroxisome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for WDFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA --
GO:0005635 nuclear envelope IDA 15292400
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IDA 15292400
GO:0005776 autophagosome IMP 20168092
genes like me logo Genes that share ontologies with WDFY3: view

Pathways & Interactions for WDFY3 Gene

SuperPathways for WDFY3 Gene

No Data Available

Pathways by source for WDFY3 Gene

1 GeneTex pathway for WDFY3 Gene

Gene Ontology (GO) - Biological Process for WDFY3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006914 autophagy IEA --
GO:0035973 aggrephagy IMP 20168092
genes like me logo Genes that share ontologies with WDFY3: view

No data available for SIGNOR curated interactions for WDFY3 Gene

Drugs & Compounds for WDFY3 Gene

No Compound Related Data Available

Transcripts for WDFY3 Gene

Unigene Clusters for WDFY3 Gene

WD repeat and FYVE domain containing 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for WDFY3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for WDFY3 Gene

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

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for WDFY3 Gene



NURSA nuclear receptor signaling pathways regulating expression of WDFY3 Gene:

WDFY3

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).

Evidence on tissue expression from TISSUES for WDFY3 Gene

  • Liver(5)
  • Blood(4.9)
  • Nervous system(4.8)
  • Kidney(4.4)
  • Intestine(4.2)
genes like me logo Genes that share expression patterns with WDFY3: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia WDFY3 34 35
  • 99.71 (n)
oppossum
(Monodelphis domestica)
Mammalia WDFY3 35
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia WDFY3 34 35
  • 93.2 (n)
cow
(Bos Taurus)
Mammalia WDFY3 34 35
  • 91.06 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia WDFY3 35
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Wdfy3 34 16 35
  • 86.45 (n)
rat
(Rattus norvegicus)
Mammalia Wdfy3 34
  • 85.03 (n)
chicken
(Gallus gallus)
Aves WDFY3 34 35
  • 82.09 (n)
lizard
(Anolis carolinensis)
Reptilia WDFY3 35
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia wdfy3 34
  • 77.2 (n)
Str.18129 34
zebrafish
(Danio rerio)
Actinopterygii wdfy3 34 35
  • 73.66 (n)
Dr.17425 34
fruit fly
(Drosophila melanogaster)
Insecta bchs 34 35
  • 53.31 (n)
worm
(Caenorhabditis elegans)
Secernentea C26H9A.2 34 35
  • 48.2 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BPH1 37
rice
(Oryza sativa)
Liliopsida Os.23284 34
Species where no ortholog for WDFY3 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)
  • 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

(6) 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
rs193920758 Uncertain significance 84,677,403(-) TGTCT(C/G)CTGCA intron-variant
rs193920805 Uncertain significance 84,801,842(-) ACTTG(A/C)CGTGG reference, missense
rs878853167 Uncertain significance 84,696,003(-) ATTGG(-/TTGG)GTTCA reference, frameshift-variant
rs1000008372 -- 84,863,044(+) TTCCT(C/T)TTATA intron-variant
rs1000010736 -- 84,905,126(+) AGGTC(A/C)GGAGT intron-variant

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

Variant ID Type Subtype PubMed ID
esv1008012 CNV insertion 20482838
esv3326890 CNV insertion 20981092
esv3601226 CNV loss 21293372
esv3601227 CNV loss 21293372
esv3601228 CNV loss 21293372
nsv1139277 CNV deletion 24896259
nsv508295 CNV deletion 20534489
nsv519588 CNV gain 19592680
nsv527581 CNV loss 19592680

Variation tolerance for WDFY3 Gene

Residual Variation Intolerance Score: 0.0964% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.15; 51.59% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for WDFY3 Gene

Human Gene Mutation Database (HGMD)
WDFY3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
WDFY3

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

Disorders for WDFY3 Gene

Relevant External Links for WDFY3

Genetic Association Database (GAD)
WDFY3
Human Genome Epidemiology (HuGE) Navigator
WDFY3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
WDFY3

No disorders were found for WDFY3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot 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 64
  2. Structural determinants in GABARAP required for the selective binding and recruitment of ALFY to LC3B-positive structures. (PMID: 24668264) Lystad A.H. … Simonsen A. (EMBO Rep. 2014) 3 4 64
  3. TRAF6 mediates ubiquitination of KIF23/MKLP1 and is required for midbody ring degradation by selective autophagy. (PMID: 24128730) Isakson P. … Simonsen A. (Autophagy 2013) 3 4 64
  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 46 64
  5. 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 64

Products for WDFY3 Gene

Sources for WDFY3 Gene

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