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

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. Located in cytoplasm. 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, Dec 2024]
Expression: Ubiquitous expression in cerebellum adult (RPKM 13.9), whole brain E14.5 (RPKM 11.6) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 5 E5; 5 48.95 cM

Exon count:: 70

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	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_000071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A genome-wide CRISPR screen identifies WDFY3 as a regulator of macrophage efferocytosis.
Title: A genome-wide CRISPR screen identifies WDFY3 as a regulator of macrophage efferocytosis.
WDFY3 mutation alters laminar position and morphology of cortical neurons.
Title: WDFY3 mutation alters laminar position and morphology of cortical neurons.
Wdfy3 regulates glycophagy, mitophagy, and synaptic plasticity.
Title: Wdfy3 regulates glycophagy, mitophagy, and synaptic plasticity.
Examining aggregates through the eyes of WDFY3/Alfy.
Title: Examining aggregates through the eyes of WDFY3/Alfy.
Although the heterozygous depletion of the autophagy adaptor protein Alfy/Wdfy3 has no consequence in control mice, it significantly accelerates age of onset and progression of Huntington's disease pathogenesis. Alfy depletion in mice accelerates the aberrant accumulation of this pathological hallmark shared across adult-onset neurodegenerative diseases.
Title: Huntington's Disease Pathogenesis Is Modified In Vivo by Alfy/Wdfy3 and Selective Macroautophagy.
Wdfy3 plays an essential role in cardiac development, which may be mediated by modulation of Notch1 signalling.
Title: WD40 repeat and FYVE domain containing 3 is essential for cardiac development.
These findings support a critical role for Wdfy3 in mitochondrial homeostasis with implications for neuron differentiation, neurodevelopment and age-dependent neurodegeneration.
Title: Beyond autophagy: a novel role for autism-linked Wdfy3 in brain mitophagy.
Data provide a novel association between WDFY3 and the RANKL-induced osteoclastogenesis pathway via the modulation of TRAF6.
Title: Autophagy-linked FYVE containing protein WDFY3 interacts with TRAF6 and modulates RANKL-induced osteoclastogenesis.
The authors report that this evolutionarily conserved protein is required for the formation of axonal tracts throughout the brain and spinal cord, including the formation of the major forebrain commissures.
Title: Autophagy linked FYVE (Alfy/WDFY3) is required for establishing neuronal connectivity in the mammalian brain.
Alfy translocalization likely is involved in the pathogenesis of amyotrophic lateral sclerosis.
Title: Autophagy-linked FYVE protein (Alfy) promotes autophagic removal of misfolded proteins involved in amyotrophic lateral sclerosis (ALS).

Submit: New GeneRIF Correction See all GeneRIFs (12)

Variation

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Alleles

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

Chemically induced (ENU) (2) 1 citation
Endonuclease-mediated (2)
Gene trapped (1) 1 citation
Targeted (4) 1 citation
Transposon induced (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW319683 (e-PCR)
- UniSTS:179212

Ggtb3 (e-PCR), detects polymorphism
- UniSTS:143199

D10Mit157.2 (e-PCR), detects polymorphism
- UniSTS:126061

RH126231 (e-PCR)
- UniSTS:162939

D1S3690 (e-PCR)
- UniSTS:474268

NoName (e-PCR)
- UniSTS:235236

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 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
involved_in aggrephagy	ISS Inferred from Sequence or Structural Similarity 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 PML body	ISS Inferred from Sequence or Structural Similarity 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 axon	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	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 inclusion body	ISS Inferred from Sequence or Structural Similarity 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 perikaryon	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

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

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)

NM_172882.3 → NP_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:2677 → 2958

Beach; Beige/BEACH domain

COG2319
Location:3026 → 3229

WD40; WD40 repeat [General function prediction only]

cd01201
Location:2516 → 2639

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3431 → 3495

FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins

pfam15787
Location:1434 → 1554

DUF4704; Domain of unknown function (DUF4704)

sd00039
Location:3066 → 3107

7WD40; WD40 repeat [structural motif]

cl02567
Location:3048 → 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 ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000071.7 Reference GRCm39 C57BL/6J

Range

101980819..102220081 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006535220.4 → XP_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:2535 → 2658

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3450 → 3514

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

pfam15787
Location:1392 → 1554

DUF4704; Domain of unknown function (DUF4704)

cl29593
Location:3067 → 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 ...
XM_006535222.5 → XP_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:2535 → 2658

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3450 → 3514

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

pfam15787
Location:1392 → 1554

DUF4704; Domain of unknown function (DUF4704)

cl29593
Location:3067 → 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 ...
XM_030254820.2 → XP_030110680.1 WD repeat and FYVE domain-containing protein 3 isoform X1

Conserved Domains (6) summary

cd01201
Location:2535 → 2658

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3450 → 3514

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

pfam15787
Location:1392 → 1554

DUF4704; Domain of unknown function (DUF4704)

cl29593
Location:3067 → 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 ...
XM_006535223.5 → XP_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:2535 → 2658

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3450 → 3514

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

pfam15787
Location:1392 → 1554

DUF4704; Domain of unknown function (DUF4704)

cl29593
Location:3067 → 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 ...
XM_036165509.1 → XP_036021402.1 WD repeat and FYVE domain-containing protein 3 isoform X8

Conserved Domains (5) summary

cd01201
Location:2492 → 2615

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3407 → 3471

FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins

sd00039
Location:3042 → 3083

7WD40; WD40 repeat [structural motif]

pfam02138
Location:2654 → 2934

Beach; Beige/BEACH domain

cl29593
Location:3024 → 3205

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 ...
XM_006535227.5 → XP_006535290.1 WD repeat and FYVE domain-containing protein 3 isoform X5

Conserved Domains (6) summary

cd01201
Location:2507 → 2630

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3422 → 3486

FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins

sd00039
Location:3057 → 3098

7WD40; WD40 repeat [structural motif]

pfam02138
Location:2669 → 2949

Beach; Beige/BEACH domain

pfam15787
Location:1364 → 1526

DUF4704; Domain of unknown function (DUF4704)

cl29593
Location:3039 → 3220

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 ...
XM_030254821.2 → XP_030110681.1 WD repeat and FYVE domain-containing protein 3 isoform X7

Conserved Domains (6) summary

cd01201
Location:2501 → 2624

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3416 → 3480

FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins

sd00039
Location:3051 → 3092

7WD40; WD40 repeat [structural motif]

pfam02138
Location:2663 → 2943

Beach; Beige/BEACH domain

pfam15787
Location:1392 → 1554

DUF4704; Domain of unknown function (DUF4704)

cl29593
Location:3033 → 3214

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 ...
XM_036165508.1 → XP_036021401.1 WD repeat and FYVE domain-containing protein 3 isoform X6

Conserved Domains (5) summary

cd01201
Location:2502 → 2625

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3417 → 3481

FYVE_WDFY3; FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins

sd00039
Location:3052 → 3093

7WD40; WD40 repeat [structural motif]

pfam02138
Location:2664 → 2944

Beach; Beige/BEACH domain

cl29593
Location:3034 → 3215

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 ...
XM_006535225.5 → XP_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:2520 → 2643

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3435 → 3499

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

pfam15787
Location:1392 → 1554

DUF4704; Domain of unknown function (DUF4704)

cl29593
Location:3052 → 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 ...
XM_006535224.5 → XP_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:2534 → 2657

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3449 → 3513

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

pfam15787
Location:1392 → 1554

DUF4704; Domain of unknown function (DUF4704)

cl29593
Location:3066 → 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 ...
XM_006535226.5 → XP_006535289.1 WD repeat and FYVE domain-containing protein 3 isoform X4

Conserved Domains (6) summary

cd01201
Location:2517 → 2640

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3432 → 3496

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

pfam15787
Location:1392 → 1554

DUF4704; Domain of unknown function (DUF4704)

cl29593
Location:3049 → 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 ...
XM_006535221.4 → XP_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:2535 → 2658

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

cd15719
Location:3450 → 3514

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

pfam15787
Location:1392 → 1554

DUF4704; Domain of unknown function (DUF4704)

cl29593
Location:3067 → 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 ...
XM_006535228.4 → XP_006535291.1 WD repeat and FYVE domain-containing protein 3 isoform X9

Conserved Domains (3) summary

cd01201
Location:2535 → 2658

PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins

pfam02138
Location:2697 → 2968

Beach; Beige/BEACH domain

pfam15787
Location:1392 → 1554

DUF4704; Domain of unknown function (DUF4704)

RNA

XR_004942568.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_028124.1: Suppressed sequence

Description

NM_028124.1: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.