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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

WDFY1 Gene

protein-coding   GIFtS: 46
GCID: GC02M224704

WD repeat and FYVE domain containing 1

(Previous name: WD40 and FYVE domain containing 1 )
  Search for WDFY1
in our new
 Human Malady Compendium 
Biological research products
for WDFY1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
WD Repeat And FYVE Domain Containing 11 2     Phosphoinositide-Binding Protein 12 3
FENS-11 2 3     Zinc Finger FYVE Domain-Containing Protein 172 3
WDF11 2 3     WD40- And FYVE Domain-Containing Protein 12 3
ZFYVE171 2 3     Phosphoinositide-Binding Protein SR12
WD40 And FYVE Domain Containing 11 2     WD Repeat And FYVE Domain-Containing Protein 12
KIAA14351 3     

External Ids:    HGNC: 204511   Entrez Gene: 575902   Ensembl: ENSG000000854497   UniProtKB: Q8IWB73   

Export aliases for WDFY1 gene to outside databases

Previous GC identifers: GC02M223461 GC02M224942 GC02M224565 GC02M224448 GC02M216592


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for WDFY1:
The FYVE domain mediates the recruitment of proteins involved in membrane trafficking and cell signaling to
phosphatidylinositol 3-phosphate (PtdIns(3)P)-containing membranes. This gene encodes a protein which contains a
single FYVE domain and multiple WD40 repeats. This protein is localized to endosomes. (provided by RefSeq, Jul 2008)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.1  NT_005403.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the WDFY1 gene promoter:
         c-Fos   AML1a   AP-1   CUTL1   C/EBPalpha   GATA-1   c-Myb   ZID   c-Jun   Ik-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidWDFY1 promoter sequence
   Search SABiosciences Chromatin IP Primers for WDFY1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat WDFY1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2q36.1   Ensembl cytogenetic band:  2q36.1   HGNC cytogenetic band: 2q36.2

WDFY1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
WDFY1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M224704:  view genomic region     (about GC identifiers)

Start:
224,720,433 bp from pter      End:
224,810,104 bp from pter
Size:
89,672 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: WDFY1_HUMAN, Q8IWB7 (See protein sequence)
Recommended Name: WD repeat and FYVE domain-containing protein 1  
Size: 410 amino acids; 46324 Da
Subunit: Binds PtdIns3P in vitro with high specificity over other phosphoinositides
Subcellular location: Early endosome
Sequence caution: Sequence=BAA92673.1; Type=Erroneous initiation;
Secondary accessions: Q53S17 Q9H9D5 Q9P2B3

Explore the universe of human proteins at neXtProt for WDFY1: NX_Q8IWB7

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8IWB7

  • WDFY1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_065881.1  
    ENSEMBL proteins: 
     ENSP00000233055   ENSP00000395416  

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    Uscn Proteins for WDFY1

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA11739631
    GO:0005769early endosome IDA11739631
    GO:0005829cytosol IDA11739631


    WDFY1 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    WDFY1 for domains           About GeneDecksing

    5/9 InterPro domains/families (see all 9):
     IPR019775 WD40_repeat_CS
     IPR001680 WD40_repeat
     IPR020472 G-protein_beta_WD-40_rep
     IPR000306 Znf_FYVE
     IPR017455 Znf_FYVE-rel

    Graphical View of Domain Structure for InterPro Entry Q8IWB7

    ProtoNet protein and cluster: Q8IWB7

    1 Blocks protein family: IPB000306 Zn-finger

    UniProtKB/Swiss-Prot: WDFY1_HUMAN, Q8IWB7
    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
    Similarity: Contains 1 FYVE-type zinc finger
    Similarity: Contains 7 WD repeats


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    miRNA
    Products:
        
    miRTarBase miRNAs that target WDFY1:
    hsa-mir-1 (MIRT001322), hsa-mir-155 (MIRT001486)

    OriGene 3'-UTR Clone: WDFY1
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    hsa-miR-1178 hsa-miR-3910 hsa-miR-579 hsa-miR-330-5p hsa-miR-509-5p hsa-miR-3942-5p hsa-miR-29c hsa-miR-29a
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:00055451-phosphatidylinositol binding IDA11739631
    GO:0008270zinc ion binding NAS11739631


    WDFY1 for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for WDFY1

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for WDFY1 (ENSP000002330554) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    ARL6IP5ENSP000002732584STRING: ENSP00000273258
    SNX2ENSP000003688314STRING: ENSP00000368831
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--


    WDFY1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for WDFY1
    Search CenterWatch for drugs/clinical trials and news about WDFY1 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for WDFY1 gene: 
    NM_020830.3  

    Unigene Cluster for WDFY1:

    WD repeat and FYVE domain containing 1
    Hs.368359  [show with all ESTs]
    Unigene Representative Sequence: BC040525
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000462702 ENST00000233055(uc002vnq.3) ENST00000491453 ENST00000493001
    ENST00000429915 ENST00000483061

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    8/30 QIAGEN miScript miRNA Assays for microRNAs that regulate WDFY1 (see all 30):
    hsa-miR-1178 hsa-miR-3910 hsa-miR-579 hsa-miR-330-5p hsa-miR-509-5p hsa-miR-3942-5p hsa-miR-29c hsa-miR-29a
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    Additional cDNA sequence: 

    AB037856.1 AF411977.1 AJ310568.1 AK022888.1 AK023415.1 BC040525.1 BC065934.1 

    7 DOTS entries:

    DT.415418  DT.91770521  DT.100034723  DT.95150414  DT.100027471  DT.120940389  DT.91770519 

    24/276 AceView cDNA sequences (see all 276):

    AF393369 AU134546 AA242945 BM786152 CA398252 BP364649 BG759326 BX115673 
    CB160619 BG777963 AA721432 AW243572 AF411977 BG177582 BQ887960 BF447259 
    AK023415 CB161324 AA411290 BF223120 BM470844 AA450337 BM692877 CB113572 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for WDFY1    About this scheme

    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:                                                                                                                  


    ECgene alternative splicing isoforms for WDFY1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    WDFY1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTATATTTAT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    WDFY1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Head MesenchymeBranchial Arch 1Cranial Neural Crest CellsNeural Crest
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See WDFY1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for WDFY1

    SOURCE GeneReport for Unigene cluster: Hs.368359
        SABiosciences Custom PCR Arrays for WDFY1
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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for WDFY1 gene from 6/19 species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves WDFY11 WD repeat and FYVE domain containing 1 81.78(n)
    91.91(a)
      424806  NM_001031310.1  NP_001026481.1 
    lizard
    (Anolis carolinensis)
    Reptilia WDFY16
    --
    89(a)
    1 ↔ 1
    3(25025591-25057346)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.114422 Transcribed sequence with moderate similarity to protein more 77.27(n)    BX732332.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.37872 Transcribed sequence with moderate similarity to protein more 77.59(n)    CA474866.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG51686
    --
    47(a)
    1 → many
    2L(10423291-10425482)
    worm
    (Caenorhabditis elegans)
    Secernentea wdfy-26
    WD repeat and FYVE domain-containing protein 2
    38(a)
    1 → many
    II(9319806-9321986)


    ENSEMBL Gene Tree for WDFY1 (if available)
    TreeFam Gene Tree for WDFY1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for WDFY1 gene
    WDFY22  HGS2  
    1 SIMAP similar gene for WDFY1 using alignment to 3 protein entries:     WDFY1_HUMAN (see all proteins):
    WDFY2

    WDFY1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1335 NCBI SNPs in WDFY1 are shown (see all 1335    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs113318831,2
    C,F,--216600047(+) TATTA-/TTTTTT 1 -- int1 trp33Minor allele frequency- T:0.33NA CSA 6
    rs1461457221,2
    --224739615(+) GAGGTA/GTCAGT 1 -- ds50010--------
    rs1873434481,2
    --224739641(+) CCACAC/TGTGTT 1 -- ds50010--------
    rs1906087351,2
    --224739662(+) ACTGAA/GCTGCT 1 -- ds50010--------
    rs1392447741,2
    --224739668(+) CTGCT-/GAGGAGAA 1 -- ds50010--------
    rs168652971,2
    C,F,--224739688(+) TTGATC/TTTGTT 1 -- ds50015Minor allele frequency- T:0.05NA WA 258
    rs6477291,2
    C,F,O,A,H,--224739702(+) ACTAGA/CTAGCT 1 -- ds500119Minor allele frequency- C:0.35NS EA NA WA CSA 1210
    rs1168241901,2
    F,--224739716(+) TGTAGT/CCAGAG 1 -- ds50011Minor allele frequency- C:0.03WA 118
    rs1828901691,2
    --224739721(+) TCAGAA/GCGCCT 1 -- ds50010--------
    rs67408771,2
    C,F,A,H,--224739762(+) CAAGCG/AGCAGA 1 -- ds500119Minor allele frequency- A:0.10NS EA NA CSA WA 2362

    HapMap Linkage Disequilibrium report for WDFY1 (224720433 - 224810104 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for WDFY1
         1 CNV: 6032

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
      --

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for WDFY1 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with WDFY1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. FENS-1 and DFCP1 are FYVE domain-containing proteins with distinct functions in the endosomal and Golgi compartments. (PubMed id 11739631)1, 2, 3 Ridley S.H.... Hawkins P.T. (2001)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. 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. (PubMed id 10718198)1, 2 Nagase T.... Ohara O. (2000)
    5. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    6. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    7. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
    8. Membrane insertion of the FYVE domain is modulated by pH. (PubMed id 19296456)2 He J.... Kutateladze T.G. (2009)
    9. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
    10. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 57590 HGNC: 20451 AceView: WDFY1andAP1S3 Ensembl:ENSG00000085449 euGenes: HUgn57590
    ECgene: WDFY1 H-InvDB: WDFY1

    (According to HUGE)
    About This Section
    HUGE: KIAA1435

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for WDFY1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for WDFY1 gene:
    Search GeneIP for patents involving WDFY1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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