U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Wdfy3 WD repeat and FYVE domain containing 3 [ Mus musculus (house mouse) ]

Gene ID: 72145, updated on 22-Jan-2023

Summary

Official Symbol
Wdfy3provided by MGI
Official Full Name
WD repeat and FYVE domain containing 3provided by MGI
Primary source
MGI:MGI:1096875
See related
Ensembl:ENSMUSG00000043940 AllianceGenome:MGI:1096875
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
ALFY; BWF1; Bchs; Ggtb3; ZFYVE25; D5Ertd66e; mKIAA0993; B930017C24; 2610509D04Rik
Summary
Enables beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity. Predicted to be involved in aggrephagy. Predicted to act upstream of or within autophagy. Located in cytoplasm. Is extrinsic component of autophagosome membrane. Is expressed in central nervous system; ganglia; heart; liver; and neural retina. Used to study autism spectrum disorder. 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
Ubiquitous expression in cerebellum adult (RPKM 13.9), whole brain E14.5 (RPKM 11.6) and 28 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See Wdfy3 in Genome Data Viewer
Location:
5 E5; 5 48.95 cM
Exon count:
70
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (101980819..102220081, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (101832953..102072215, complement)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 9430085M18 gene Neighboring gene predicted gene, 42134 Neighboring gene CDP-diacylglycerol synthase 1 Neighboring gene predicted gene, 42135 Neighboring gene predicted gene, 42136 Neighboring gene centromere protein N pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables 1-phosphatidylinositol binding ISO
Inferred from Sequence Orthology
more info
 
enables beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables lipid binding IEA
Inferred from Electronic Annotation
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
PubMed 
involved_in aggrephagy ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within autophagy IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
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
PubMed 
located_in cell projection IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
PubMed 
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
PubMed 
located_in nuclear envelope ISO
Inferred from Sequence Orthology
more info
PubMed 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
WD repeat and FYVE domain-containing protein 3
Names
beach domain, WD repeat and FYVE domain-containing protein 1
galactosyltransferase 3 beta 1, 4

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_172882.3NP_766470.2  WD repeat and FYVE domain-containing protein 3

    See identical proteins and their annotated locations for NP_766470.2

    Status: VALIDATED

    Source sequence(s)
    AC131915, AC158143, AC171108, AC171109
    Consensus CDS
    CCDS19473.1
    UniProtKB/Swiss-Prot
    Q6VNB8, Q8C8H7
    Related
    ENSMUSP00000052607.8, ENSMUST00000053177.14
    Conserved Domains (7) summary
    smart01026
    Location:26772958
    Beach; Beige/BEACH domain
    COG2319
    Location:30263229
    WD40; WD40 repeat [General function prediction only]
    cd01201
    Location:25162639
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34313495
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    pfam15787
    Location:14341554
    DUF4704; Domain of unknown function (DUF4704)
    sd00039
    Location:30663107
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:30483229
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    101980819..102220081 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006535220.4XP_006535283.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006535283.1

    Conserved Domains (6) summary
    cd01201
    Location:25352658
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34503514
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30853126
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26972977
    Beach; Beige/BEACH domain
    pfam15787
    Location:13921554
    DUF4704; Domain of unknown function (DUF4704)
    cl29593
    Location:30673248
    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_006535222.5XP_006535285.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006535285.1

    Conserved Domains (6) summary
    cd01201
    Location:25352658
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34503514
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30853126
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26972977
    Beach; Beige/BEACH domain
    pfam15787
    Location:13921554
    DUF4704; Domain of unknown function (DUF4704)
    cl29593
    Location:30673248
    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_030254820.2XP_030110680.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    Conserved Domains (6) summary
    cd01201
    Location:25352658
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34503514
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30853126
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26972977
    Beach; Beige/BEACH domain
    pfam15787
    Location:13921554
    DUF4704; Domain of unknown function (DUF4704)
    cl29593
    Location:30673248
    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_006535223.5XP_006535286.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006535286.1

    Conserved Domains (6) summary
    cd01201
    Location:25352658
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34503514
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30853126
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26972977
    Beach; Beige/BEACH domain
    pfam15787
    Location:13921554
    DUF4704; Domain of unknown function (DUF4704)
    cl29593
    Location:30673248
    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_036165509.1XP_036021402.1  WD repeat and FYVE domain-containing protein 3 isoform X8

    Conserved Domains (5) summary
    cd01201
    Location:24922615
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34073471
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30423083
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26542934
    Beach; Beige/BEACH domain
    cl29593
    Location:30243205
    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_006535227.5XP_006535290.1  WD repeat and FYVE domain-containing protein 3 isoform X5

    Conserved Domains (6) summary
    cd01201
    Location:25072630
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34223486
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30573098
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26692949
    Beach; Beige/BEACH domain
    pfam15787
    Location:13641526
    DUF4704; Domain of unknown function (DUF4704)
    cl29593
    Location:30393220
    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_030254821.2XP_030110681.1  WD repeat and FYVE domain-containing protein 3 isoform X7

    Conserved Domains (6) summary
    cd01201
    Location:25012624
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34163480
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30513092
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26632943
    Beach; Beige/BEACH domain
    pfam15787
    Location:13921554
    DUF4704; Domain of unknown function (DUF4704)
    cl29593
    Location:30333214
    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 ...
  8. XM_036165508.1XP_036021401.1  WD repeat and FYVE domain-containing protein 3 isoform X6

    Conserved Domains (5) summary
    cd01201
    Location:25022625
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34173481
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30523093
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26642944
    Beach; Beige/BEACH domain
    cl29593
    Location:30343215
    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 ...
  9. XM_006535225.5XP_006535288.1  WD repeat and FYVE domain-containing protein 3 isoform X3

    UniProtKB/TrEMBL
    A0A1D5RLV7
    Related
    ENSMUSP00000148521.2, ENSMUST00000212024.2
    Conserved Domains (6) summary
    cd01201
    Location:25202643
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34353499
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30703111
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26822962
    Beach; Beige/BEACH domain
    pfam15787
    Location:13921554
    DUF4704; Domain of unknown function (DUF4704)
    cl29593
    Location:30523233
    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 ...
  10. XM_006535224.5XP_006535287.1  WD repeat and FYVE domain-containing protein 3 isoform X2

    UniProtKB/TrEMBL
    G3UYW1
    Related
    ENSMUSP00000134244.2, ENSMUST00000174598.8
    Conserved Domains (6) summary
    cd01201
    Location:25342657
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34493513
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30843125
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26962976
    Beach; Beige/BEACH domain
    pfam15787
    Location:13921554
    DUF4704; Domain of unknown function (DUF4704)
    cl29593
    Location:30663247
    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 ...
  11. XM_006535226.5XP_006535289.1  WD repeat and FYVE domain-containing protein 3 isoform X4

    Conserved Domains (6) summary
    cd01201
    Location:25172640
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34323496
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30673108
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26792959
    Beach; Beige/BEACH domain
    pfam15787
    Location:13921554
    DUF4704; Domain of unknown function (DUF4704)
    cl29593
    Location:30493230
    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 ...
  12. XM_006535221.4XP_006535284.1  WD repeat and FYVE domain-containing protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006535284.1

    Conserved Domains (6) summary
    cd01201
    Location:25352658
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    cd15719
    Location:34503514
    FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins
    sd00039
    Location:30853126
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:26972977
    Beach; Beige/BEACH domain
    pfam15787
    Location:13921554
    DUF4704; Domain of unknown function (DUF4704)
    cl29593
    Location:30673248
    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 ...
  13. XM_006535228.4XP_006535291.1  WD repeat and FYVE domain-containing protein 3 isoform X9

    Conserved Domains (3) summary
    cd01201
    Location:25352658
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    pfam02138
    Location:26972968
    Beach; Beige/BEACH domain
    pfam15787
    Location:13921554
    DUF4704; Domain of unknown function (DUF4704)

RNA

  1. XR_004942568.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_028124.1: Suppressed sequence

    Description
    NM_028124.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.