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

    Gene ID: 545030, updated on 9-May-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 endoplasmic reticulum and endosome. Orthologous to human WDFY4 (WDFY family member 4). [provided by Alliance of Genome Resources, Apr 2022]
    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. Dendritic cells can prime anti-tumor CD8(+) T cell responses through major histocompatibility complex cross-dressing. MacNabb BW, et al. Immunity, 2022 Jun 14. PMID 35617964, Free PMC Article
    2. 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
    3. 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
    4. 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
    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 (20) 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 
    acts_upstream_of_or_within 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 endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endosome 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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