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

Gene ID: 305164, updated on 3-Apr-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
Ensembl: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; inclusion body; and nucleus. Predicted to be extrinsic component of autophagosome membrane. 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, Apr 2022]
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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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, ENSRNOT00000088047.2
    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
    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

  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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