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Wdfy4 WD repeat and FYVE domain containing 4 [ Mus musculus (house mouse) ]

Gene ID: 545030, updated on 27-Nov-2024

Summary

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Official Symbol
Wdfy4provided by MGI
Official Full Name
WD repeat and FYVE domain containing 4provided by MGI
Primary source
MGI:MGI:3584510
See related
Ensembl:ENSMUSG00000051506 AllianceGenome:MGI:3584510
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Gm18810
Summary
Acts upstream of or within with a positive effect on CD8-positive, alpha-beta T cell activation. Acts upstream of or within antigen processing and presentation and cellular response to virus. Predicted to be located in early endosome and endoplasmic reticulum. Orthologous to human WDFY4 (WDFY family member 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in spleen adult (RPKM 29.1), mammary gland adult (RPKM 6.4) and 4 other tissues See more
Orthologs
human all
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Genomic context

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See Wdfy4 in Genome Data Viewer
Location:
14 B; 14 19.44 cM
Exon count:
69
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (32681504..32915809, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (32959547..33193855, complement)

Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene V-set and transmembrane domain containing 4 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene predicted gene, 36674 Neighboring gene leucine rich repeat containing 18 Neighboring gene STARR-positive B cell enhancer ABC_E4104 Neighboring gene STARR-positive B cell enhancer ABC_E1893 Neighboring gene STARR-seq mESC enhancer starr_36348 Neighboring gene predicted gene, 25498 Neighboring gene predicted pseudogene 6340

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Deficiency in WDFY4 reduces the number of CD8(+) T cells via reactive oxygen species-induced apoptosis. Li Y, et al. Mol Immunol, 2021 Nov. PMID 34482201
  2. Lack of WDFY4 Aggravates Ovalbumin-Induced Asthma via Enhanced Th2 Cell Differentiation. Li Y, et al. Int Arch Allergy Immunol, 2021. PMID 34425575, Free PMC Article
  3. WDFY4 Is Involved in Symptoms of Systemic Lupus Erythematosus by Modulating B Cell Fate via Noncanonical Autophagy. Yuan Q, et al. J Immunol, 2018 Nov 1. PMID 30257884
  4. WDFY4 deficiency in NOD mice ameliorates autoimmune diabetes and insulitis. Ferris ST, et al. Proc Natl Acad Sci U S A, 2023 Mar 28. PMID 36940342, Free PMC Article
  5. Chikungunya Virus Evades Antiviral CD8(+) T Cell Responses To Establish Persistent Infection in Joint-Associated Tissues. Davenport BJ, et al. J Virol, 2020 Apr 16. PMID 32102875, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. WDFY4 deficiency in NOD mice ameliorates autoimmune diabetes and insulitis.
    Title: WDFY4 deficiency in NOD mice ameliorates autoimmune diabetes and insulitis.
  2. Lack of WDFY4 Aggravates Ovalbumin-Induced Asthma via Enhanced Th2 Cell Differentiation.
    Title: Lack of WDFY4 Aggravates Ovalbumin-Induced Asthma via Enhanced Th2 Cell Differentiation.
  3. Deficiency in WDFY4 reduces the number of CD8(+) T cells via reactive oxygen species-induced apoptosis.
    Title: Deficiency in WDFY4 reduces the number of CD8(+) T cells via reactive oxygen species-induced apoptosis.
  4. Genetic silencing of WDFY4 in B cells increased lipidation of LC3 independent of p62 and Beclin1, which are essential proteins of canonical autophagy. In vivo and in vitro data suggest that WDFY4 facilitates noncanonical autophagic activity. These findings provide a novel functional link underlying the mechanism of systemic lupus erythematosus in which WDFY4 influences B cell fate via noncanonical autophagy.
    Title: WDFY4 Is Involved in Symptoms of Systemic Lupus Erythematosus by Modulating B Cell Fate via Noncanonical Autophagy.
  5. Wdfy4 (-/-) mice failed to prime virus-specific CD8(+) T cells in vivo or induce tumor rejection, revealing a critical role for cross-presentation in antiviral and antitumor immunity.
    Title: WDFY4 is required for cross-presentation in response to viral and tumor antigens.
Submit: New GeneRIF Correction

Variation

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Alleles

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Process Evidence Code Pubs
acts_upstream_of_or_within_positive_effect CD8-positive, alpha-beta T cell activation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in antigen processing and presentation IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within antigen processing and presentation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in autophagy IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cellular response to virus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in early endosome IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
WD repeat- and FYVE domain-containing protein 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)

  1. NM_001146022.2 → NP_001139494.1  WD repeat- and FYVE domain-containing protein 4

    Status: PROVISIONAL

    Source sequence(s)
    AC133585, AC154206, AC154239, AC165262
    Consensus CDS
    CCDS49441.1
    UniProtKB/TrEMBL
    E9PV60
    Related
    ENSMUSP00000057556.9, ENSMUST00000061753.15
    Conserved Domains (4) summary
    cd01201
    Location:2227 → 2348
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    sd00039
    Location:2777 → 2820
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:2379 → 2660
    Beach; Beige/BEACH domain
    cl29593
    Location:2742 → 2940
    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

  1. NC_000080.7 Reference GRCm39 C57BL/6J

    Range
    32681504..32915809 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011245119.4 → XP_011243421.1  WD repeat- and FYVE domain-containing protein 4 isoform X2

    Conserved Domains (4) summary
    cd01201
    Location:2385 → 2506
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    sd00039
    Location:2935 → 2978
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:2537 → 2818
    Beach; Beige/BEACH domain
    cl29593
    Location:2900 → 3098
    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_011245118.4 → XP_011243420.1  WD repeat- and FYVE domain-containing protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011243420.1

    UniProtKB/Swiss-Prot
    E9Q2M9
    Conserved Domains (4) summary
    cd01201
    Location:2386 → 2507
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    sd00039
    Location:2936 → 2979
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:2538 → 2819
    Beach; Beige/BEACH domain
    cl29593
    Location:2901 → 3099
    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_036158761.1 → XP_036014654.1  WD repeat- and FYVE domain-containing protein 4 isoform X1

    UniProtKB/Swiss-Prot
    E9Q2M9
    Conserved Domains (4) summary
    cd01201
    Location:2386 → 2507
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    sd00039
    Location:2936 → 2979
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:2538 → 2819
    Beach; Beige/BEACH domain
    cl29593
    Location:2901 → 3099
    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_006519277.5 → XP_006519340.1  WD repeat- and FYVE domain-containing protein 4 isoform X1

    See identical proteins and their annotated locations for XP_006519340.1

    UniProtKB/Swiss-Prot
    E9Q2M9
    Conserved Domains (4) summary
    cd01201
    Location:2386 → 2507
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    sd00039
    Location:2936 → 2979
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:2538 → 2819
    Beach; Beige/BEACH domain
    cl29593
    Location:2901 → 3099
    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_006519278.5 → XP_006519341.1  WD repeat- and FYVE domain-containing protein 4 isoform X1

    See identical proteins and their annotated locations for XP_006519341.1

    UniProtKB/Swiss-Prot
    E9Q2M9
    Conserved Domains (4) summary
    cd01201
    Location:2386 → 2507
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    sd00039
    Location:2936 → 2979
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:2538 → 2819
    Beach; Beige/BEACH domain
    cl29593
    Location:2901 → 3099
    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_006519279.5 → XP_006519342.1  WD repeat- and FYVE domain-containing protein 4 isoform X1

    See identical proteins and their annotated locations for XP_006519342.1

    UniProtKB/Swiss-Prot
    E9Q2M9
    Related
    ENSMUSP00000117068.4, ENSMUST00000130509.10
    Conserved Domains (4) summary
    cd01201
    Location:2386 → 2507
    PH_BEACH; Pleckstrin homology domain in BEACH domain containing proteins
    sd00039
    Location:2936 → 2979
    7WD40; WD40 repeat [structural motif]
    pfam02138
    Location:2538 → 2819
    Beach; Beige/BEACH domain
    cl29593
    Location:2901 → 3099
    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 ...
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
E9Q2M9.2 GenPept UniProtKB/Swiss-Prot:E9Q2M9

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