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    Wdfy3 WD repeat and FYVE domain containing 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 305164, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Wdfy3provided by RGD
    Official Full Name
    WD repeat and FYVE domain containing 3provided by RGD
    Primary source
    RGD:1307097
    See related
    EnsemblRapid:ENSRNOG00000061121 AllianceGenome:RGD:1307097
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable 1-phosphatidylinositol binding activity and beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity. Predicted to be involved in aggrephagy. Predicted to be located in several cellular components, including autophagosome membrane; inclusion body; and nucleus. Predicted to be part of Atg12-Atg5-Atg16 complex. Human ortholog(s) of this gene implicated in primary autosomal dominant microcephaly 18. Orthologous to human WDFY3 (WD repeat and FYVE domain containing 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 400.4), Lung (RPKM 145.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Wdfy3 in Genome Data Viewer
    Location:
    14p22
    Exon count:
    70
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (7873946..8115002)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (7578245..7810491)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (9169409..9384835)

    Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene proliferating cell nuclear antigen, pseudogene 3 Neighboring gene TBC1 domain family member 1, pseudogene 1 Neighboring gene uncharacterized LOC134481826 Neighboring gene CDP-diacylglycerol synthase 1 Neighboring gene uncharacterized LOC108352705

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Expression profile of mouse BWF1, a protein with a BEACH domain, WD40 domain and FYVE domain. Chen GY, et al. Cell Struct Funct, 2004 Apr. PMID 15342963
    2. Molecular cloning and characterization of beta-1,4-galactosyltransferase expressed in mouse testis. Uehara K, et al. Eur J Biochem, 1997 Mar 15. PMID 9108238
    3. p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy. Clausen TH, et al. Autophagy, 2010 Apr. PMID 20168092
    4. Alfy, a novel FYVE-domain-containing protein associated with protein granules and autophagic membranes. Simonsen A, et al. J Cell Sci, 2004 Aug 15. PMID 15292400
    5. The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Filimonenko M, et al. Mol Cell, 2010 Apr 23. PMID 20417604, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables 1-phosphatidylinositol binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in aggrephagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in aggrephagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of Atg12-Atg5-Atg16 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in PML body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in autophagosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in autophagosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in inclusion body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear envelope ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    WD repeat and FYVE domain-containing protein 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001170551.4 → NP_001164022.3  WD repeat and FYVE domain-containing protein 3

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/TrEMBL
      A0A0G2K9M4
      Related
      ENSRNOP00000075052.2, ENSRNOT00000088047.3
      Conserved Domains (5) summary
      cd01201
      Location:2517 → 2640
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      cd15719
      Location:3430 → 3494
      FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
      sd00039
      Location:3067 → 3108
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:2679 → 2959
      Beach; Beige/BEACH domain
      cl29593
      Location:3028 → 3230
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086032.1 Reference GRCr8

      Range
      7873946..8115002
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039091828.2 → XP_038947756.1  WD repeat and FYVE domain-containing protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A7K7
      Related
      ENSRNOP00000087230.1, ENSRNOT00000092709.3
      Conserved Domains (5) summary
      cd01201
      Location:2535 → 2658
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      cd15719
      Location:3448 → 3512
      FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
      sd00039
      Location:3085 → 3126
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:2697 → 2977
      Beach; Beige/BEACH domain
      cl29593
      Location:3046 → 3248
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    2. XM_039091827.2 → XP_038947755.1  WD repeat and FYVE domain-containing protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A7K7
      Conserved Domains (5) summary
      cd01201
      Location:2535 → 2658
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      cd15719
      Location:3448 → 3512
      FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
      sd00039
      Location:3085 → 3126
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:2697 → 2977
      Beach; Beige/BEACH domain
      cl29593
      Location:3046 → 3248
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    3. XM_039091826.2 → XP_038947754.1  WD repeat and FYVE domain-containing protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A7K7
      Conserved Domains (5) summary
      cd01201
      Location:2535 → 2658
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      cd15719
      Location:3448 → 3512
      FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
      sd00039
      Location:3085 → 3126
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:2697 → 2977
      Beach; Beige/BEACH domain
      cl29593
      Location:3046 → 3248
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    4. XM_039091829.2 → XP_038947757.1  WD repeat and FYVE domain-containing protein 3 isoform X2

      Conserved Domains (5) summary
      cd01201
      Location:2534 → 2657
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      cd15719
      Location:3447 → 3511
      FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
      sd00039
      Location:3084 → 3125
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:2696 → 2976
      Beach; Beige/BEACH domain
      cl29593
      Location:3045 → 3247
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    5. XM_039091831.2 → XP_038947759.1  WD repeat and FYVE domain-containing protein 3 isoform X4

      Conserved Domains (5) summary
      cd01201
      Location:2516 → 2639
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      cd15719
      Location:3429 → 3493
      FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
      sd00039
      Location:3066 → 3107
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:2678 → 2958
      Beach; Beige/BEACH domain
      cl29593
      Location:3027 → 3229
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    6. XM_039091830.2 → XP_038947758.1  WD repeat and FYVE domain-containing protein 3 isoform X3

      Conserved Domains (5) summary
      cd01201
      Location:2520 → 2643
      PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
      cd15719
      Location:3433 → 3497
      FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
      sd00039
      Location:3070 → 3111
      7WD40; WD40 repeat [structural motif]
      pfam02138
      Location:2682 → 2962
      Beach; Beige/BEACH domain
      cl29593
      Location:3031 → 3233
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    7. XM_063273049.1 → XP_063129119.1  WD repeat and FYVE domain-containing protein 3 isoform X6

    8. XM_063273048.1 → XP_063129118.1  WD repeat and FYVE domain-containing protein 3 isoform X5

      UniProtKB/TrEMBL
      A0A8I6AIP5
      Related
      ENSRNOP00000093405.1, ENSRNOT00000109494.2

    9. XM_063273050.1 → XP_063129120.1  WD repeat and FYVE domain-containing protein 3 isoform X7

    Nucleotide Protein Strain
    Heading Accession and Version

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