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    Rufy4 RUN and FYVE domain containing 4 [ Mus musculus (house mouse) ]

    Gene ID: 435626, updated on 7-May-2024

    Summary

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    Official Symbol
    Rufy4provided by MGI
    Official Full Name
    RUN and FYVE domain containing 4provided by MGI
    Primary source
    MGI:MGI:3588214
    See related
    Ensembl:ENSMUSG00000061815 AllianceGenome:MGI:3588214
    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
    F930048N03Rik
    Summary
    Predicted to enable phosphatidylinositol-3-phosphate binding activity. Involved in cellular response to interleukin-4. Predicted to be located in cytoplasmic vesicle. Predicted to be active in autophagosome. Is expressed in heart. Orthologous to human RUFY4 (RUN and FYVE domain containing 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in placenta adult (RPKM 1.7), kidney adult (RPKM 0.9) and 18 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Rufy4 in Genome Data Viewer
    Location:
    1 C3; 1 38.38 cM
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (74163768..74187389)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (74124433..74148230)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene tensin 1 Neighboring gene predicted gene, 39664 Neighboring gene STARR-positive B cell enhancer ABC_E11074 Neighboring gene VISTA enhancer mm1630 Neighboring gene predicted gene, 31637 Neighboring gene C-X-C motif chemokine receptor 2 Neighboring gene C-X-C motif chemokine receptor 1

    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. RUN and FYVE domain-containing protein 4 enhances autophagy and lysosome tethering in response to Interleukin-4. Terawaki S, et al. J Cell Biol, 2015 Sep 28. PMID 26416964, Free PMC Article
    2. Rufy3, a protein specifically expressed in neurons, interacts with actin-bundling protein Fascin to control the growth of axons. Wei Z, et al. J Neurochem, 2014 Sep. PMID 24720729
    3. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. Diez-Roux G, et al. PLoS Biol, 2011 Jan 18. PMID 21267068, Free PMC Article
    4. Antisense transcription in the mammalian transcriptome. Katayama S, et al. Science, 2005 Sep 2. PMID 16141073
    5. High-efficiency full-length cDNA cloning. Carninci P, et al. Methods Enzymol, 1999. PMID 10349636

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RUFY4 is therefore the first molecule characterized to date that promotes autophagy and influences endosome dynamics in a subset of immune cells.
      Title: RUN and FYVE domain-containing protein 4 enhances autophagy and lysosome tethering in response to Interleukin-4.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (5) 

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol-3-phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3-phosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to interleukin-4 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cellular response to interleukin-4 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of macroautophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of macroautophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in autophagosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    RUN 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_001034060.3 → NP_001029232.2  RUN and FYVE domain-containing protein 4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site and and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC117757
      Consensus CDS
      CCDS15039.1
      UniProtKB/Swiss-Prot
      Q3TYX8
      Related
      ENSMUSP00000079062.5, ENSMUST00000080167.11
      Conserved Domains (4) summary
      cd15745
      Location:428 → 470
      FYVE_RUFY4; FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins
      pfam03938
      Location:332 → 410
      OmpH; Outer membrane protein (OmpH-like)
      cl02689
      Location:10 → 79
      RUN; RUN domain
      cl12013
      Location:302 → 403
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    2. NM_001170641.1 → NP_001164112.1  RUN and FYVE domain-containing protein 4 isoform 1

      See identical proteins and their annotated locations for NP_001164112.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC117757
      Consensus CDS
      CCDS48289.1
      UniProtKB/Swiss-Prot
      B2RX43, D3YY30, Q3TYX8
      Related
      ENSMUSP00000115873.2, ENSMUST00000127134.2
      Conserved Domains (4) summary
      cd15745
      Location:512 → 554
      FYVE_RUFY4; FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins
      pfam03938
      Location:416 → 494
      OmpH; Outer membrane protein (OmpH-like)
      cl02689
      Location:41 → 163
      RUN; RUN domain
      cl12013
      Location:386 → 487
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    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_000067.7 Reference GRCm39 C57BL/6J

      Range
      74163768..74187389
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006496129.3 → XP_006496192.1  RUN and FYVE domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_006496192.1

      Conserved Domains (3) summary
      cd15745
      Location:544 → 586
      FYVE_RUFY4; FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins
      pfam03938
      Location:448 → 524
      OmpH; Outer membrane protein (OmpH-like)
      cl02689
      Location:41 → 163
      RUN; RUN domain

    2. XM_006496132.3 → XP_006496195.1  RUN and FYVE domain-containing protein 4 isoform X3

      Conserved Domains (2) summary
      cd15745
      Location:495 → 537
      FYVE_RUFY4; FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins
      cl02689
      Location:41 → 163
      RUN; RUN domain

    3. XM_006496131.3 → XP_006496194.1  RUN and FYVE domain-containing protein 4 isoform X2

      Conserved Domains (3) summary
      cd15745
      Location:541 → 583
      FYVE_RUFY4; FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins
      pfam03938
      Location:445 → 521
      OmpH; Outer membrane protein (OmpH-like)
      cl02689
      Location:41 → 163
      RUN; RUN domain

    4. XM_006496130.3 → XP_006496193.1  RUN and FYVE domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_006496193.1

      Conserved Domains (3) summary
      cd15745
      Location:544 → 586
      FYVE_RUFY4; FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins
      pfam03938
      Location:448 → 524
      OmpH; Outer membrane protein (OmpH-like)
      cl02689
      Location:41 → 163
      RUN; RUN domain

    5. XM_006496133.4 → XP_006496196.1  RUN and FYVE domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_006496196.1

      Conserved Domains (3) summary
      cd15745
      Location:544 → 586
      FYVE_RUFY4; FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins
      pfam03938
      Location:448 → 524
      OmpH; Outer membrane protein (OmpH-like)
      cl02689
      Location:41 → 163
      RUN; RUN domain

    6. XM_006496134.1 → XP_006496197.1  RUN and FYVE domain-containing protein 4 isoform X4

      Conserved Domains (2) summary
      cd15745
      Location:371 → 413
      FYVE_RUFY4; FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins
      pfam03938
      Location:275 → 351
      OmpH; Outer membrane protein (OmpH-like)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3TYX8.3 GenPept UniProtKB/Swiss-Prot:Q3TYX8

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