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    Rufy3 RUN and FYVE domain containing 3 [ Mus musculus (house mouse) ]

    Gene ID: 52822, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Rufy3provided by MGI
    Official Full Name
    RUN and FYVE domain containing 3provided by MGI
    Primary source
    MGI:MGI:106484
    See related
    Ensembl:ENSMUSG00000029291 AllianceGenome:MGI:106484
    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
    Ripx; Rpipx; D5Bwg0860e; 2810428M05Rik; 6330416M07Rik
    Summary
    Involved in several processes, including positive regulation of axon extension; positive regulation of intracellular protein transport; and regulation of establishment of cell polarity. Acts upstream of or within positive regulation of axonogenesis. Located in growth cone and perikaryon. Is expressed in several structures, including alimentary system; eye; genitourinary system; hemolymphoid system; and nervous system. Orthologous to human RUFY3 (RUN and FYVE domain containing 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in CNS E18 (RPKM 20.6), whole brain E14.5 (RPKM 18.1) and 18 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Rufy3 in Genome Data Viewer
    Location:
    5 E1; 5 43.77 cM
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (88711305..88799276)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (88564505..88651417)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene immunoglobulin joining chain Neighboring gene STARR-positive B cell enhancer ABC_E6343 Neighboring gene STARR-seq mESC enhancer starr_13570 Neighboring gene STARR-positive B cell enhancer ABC_E2748 Neighboring gene predicted gene, 42107 Neighboring gene UTP3 small subunit processome component Neighboring gene STARR-seq mESC enhancer starr_13573 Neighboring gene STARR-seq mESC enhancer starr_13574 Neighboring gene STARR-seq mESC enhancer starr_13575 Neighboring gene STARR-seq mESC enhancer starr_13576 Neighboring gene STARR-seq mESC enhancer starr_13577 Neighboring gene G-rich RNA sequence binding factor 1 Neighboring gene MOB kinase activator 1B Neighboring gene predicted gene 15682

    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. Perspectives of stem cell therapy in Duchenne muscular dystrophy. Meregalli M, et al. FEBS J, 2013 Sep. PMID 23206279
    2. Rufy3 is an adapter protein for small GTPases that activates a Rac guanine nucleotide exchange factor to control neuronal polarity. Honda A, et al. J Biol Chem, 2017 Dec 22. PMID 29089386, Free PMC Article
    3. Crystal structure of the RUN domain of the RAP2-interacting protein x. Kukimoto-Niino M, et al. J Biol Chem, 2006 Oct 20. PMID 16928684
    4. Neuronally Enriched RUFY3 Is Required for Caspase-Mediated Axon Degeneration. Hertz NT, et al. Neuron, 2019 Aug 7. PMID 31221560, Free PMC Article
    5. 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

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RUFY3, a neuronally enriched protein, is essential for caspase-mediated degeneration of TRKA+ sensory axons in vitro and in vivo. Deletion of Rufy3 protects axons from degeneration, even in the presence of activated CASP3 . Dephosphorylation of RUFY3 at residue S34 appears required for axon degeneration.
      Title: Neuronally Enriched RUFY3 Is Required for Caspase-Mediated Axon Degeneration.
    2. Rufy3 is a physiological adapter for Rap2 and activates Tiam2/STEF in glycoprotein M6A-regulated neuronal polarity and axon growth.
      Title: Rufy3 is an adapter protein for small GTPases that activates a Rac guanine nucleotide exchange factor to control neuronal polarity.
    3. We propose that Rufy3 may control mouse neuron axon development
      Title: Rufy3, a protein specifically expressed in neurons, interacts with actin-bundling protein Fascin to control the growth of axons.
    4. the putative Rap2 binding site of the RPIPx RUN domain interacts with the extended segment in a segment-swapping manner
      Title: Crystal structure of the RUN domain of the RAP2-interacting protein x.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (4)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0871

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in actin filament organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of axonogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of axonogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of axon extension IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of axonogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of intracellular protein transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of axonogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of establishment of cell polarity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in anchoring junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in dendrite ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endomembrane system IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in filopodium ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in filopodium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in growth cone IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in growth cone ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in growth cone ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in lamellipodium ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lamellipodium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in neuronal cell body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in perikaryon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perikaryon ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perikaryon ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    protein RUFY3
    Names
    rap2 interacting protein x
    singar
    singar1
    single axon-regulated protein 1

    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_001289774.2 → NP_001276703.1  protein RUFY3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC121541
      Consensus CDS
      CCDS80324.1
      UniProtKB/TrEMBL
      A0A0G2JFT8
      Related
      ENSMUSP00000143302.2, ENSMUST00000198965.5
      Conserved Domains (5) summary
      cd15744
      Location:611 → 657
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam01442
      Location:324 → 497
      Apolipoprotein; Apolipoprotein A1/A4/E domain
      pfam02759
      Location:153 → 276
      RUN; RUN domain
      pfam10212
      Location:323 → 372
      TTKRSYEDQ; Predicted coiled-coil domain-containing protein
      cl23720
      Location:390 → 499
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    2. NM_001289775.2 → NP_001276704.1  protein RUFY3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC121541
      Consensus CDS
      CCDS80323.1
      UniProtKB/Swiss-Prot
      Q9D394
      Related
      ENSMUSP00000143770.2, ENSMUST00000196894.5
      Conserved Domains (4) summary
      pfam01442
      Location:324 → 496
      Apolipoprotein; Apolipoprotein A1/A4/E domain
      pfam02759
      Location:153 → 276
      RUN; RUN domain
      pfam10212
      Location:323 → 372
      TTKRSYEDQ; Predicted coiled-coil domain-containing protein
      cl23720
      Location:390 → 518
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    3. NM_001289776.2 → NP_001276705.1  protein RUFY3 isoform 3

      See identical proteins and their annotated locations for NP_001276705.1

      Status: VALIDATED

      Source sequence(s)
      AC121541
      Consensus CDS
      CCDS80325.1
      UniProtKB/Swiss-Prot
      Q9D394
      Related
      ENSMUSP00000143209.2, ENSMUST00000196686.2
      Conserved Domains (2) summary
      pfam02759
      Location:121 → 244
      RUN; RUN domain
      pfam10212
      Location:291 → 340
      TTKRSYEDQ; Predicted coiled-coil domain-containing protein

    4. NM_001289777.2 → NP_001276706.1  protein RUFY3 isoform 3

      See identical proteins and their annotated locations for NP_001276706.1

      Status: VALIDATED

      Source sequence(s)
      AC121541
      Consensus CDS
      CCDS80325.1
      UniProtKB/Swiss-Prot
      Q9D394
      Related
      ENSMUSP00000143115.2, ENSMUST00000199312.5
      Conserved Domains (2) summary
      pfam02759
      Location:121 → 244
      RUN; RUN domain
      pfam10212
      Location:291 → 340
      TTKRSYEDQ; Predicted coiled-coil domain-containing protein

    5. NM_001359208.2 → NP_001346137.1  protein RUFY3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC121541
      Consensus CDS
      CCDS19403.1
      UniProtKB/Swiss-Prot
      Q3U348, Q3UF96, Q6PE64, Q8VD10, Q9D394
      Conserved Domains (2) summary
      pfam02759
      Location:103 → 224
      RUN; RUN domain
      cl25732
      Location:258 → 464
      SMC_N; RecF/RecN/SMC N terminal domain

    6. NM_001359209.2 → NP_001346138.1  protein RUFY3 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC121541
      Conserved Domains (3) summary
      TIGR02168
      Location:243 → 502
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15744
      Location:561 → 607
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:103 → 224
      RUN; RUN domain

    7. NM_001429017.1 → NP_001415946.1  protein RUFY3 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC121541

    8. NM_001429018.1 → NP_001415947.1  protein RUFY3 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC121541

    9. NM_001429019.1 → NP_001415948.1  protein RUFY3 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC121541

    10. NM_001429020.1 → NP_001415949.1  protein RUFY3 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC121541

    11. NM_001429021.1 → NP_001415950.1  protein RUFY3 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC121541

    12. NM_001429022.1 → NP_001415951.1  protein RUFY3 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC121541

    13. NM_001429023.1 → NP_001415952.1  protein RUFY3 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC121541

    14. NM_001429024.1 → NP_001415953.1  protein RUFY3 isoform 11

      Status: VALIDATED

      Source sequence(s)
      AC121541

    15. NM_001429025.1 → NP_001415954.1  protein RUFY3 isoform 12

      Status: VALIDATED

      Source sequence(s)
      AC121541

    16. NM_001429026.1 → NP_001415955.1  protein RUFY3 isoform 12

      Status: VALIDATED

      Source sequence(s)
      AC121541

    17. NM_027530.4 → NP_081806.1  protein RUFY3 isoform 4

      See identical proteins and their annotated locations for NP_081806.1

      Status: VALIDATED

      Source sequence(s)
      AC121541
      Consensus CDS
      CCDS19403.1
      UniProtKB/Swiss-Prot
      Q3U348, Q3UF96, Q6PE64, Q8VD10, Q9D394
      Related
      ENSMUSP00000031229.7, ENSMUST00000031229.11
      Conserved Domains (2) summary
      pfam02759
      Location:103 → 224
      RUN; RUN domain
      cl25732
      Location:258 → 464
      SMC_N; RecF/RecN/SMC N terminal domain

    RNA

    1. NR_190568.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC121541

    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_000071.7 Reference GRCm39 C57BL/6J

      Range
      88711305..88799276
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006535115.5 → XP_006535178.1  protein RUFY3 isoform X5

      Conserved Domains (3) summary
      TIGR02168
      Location:179 → 438
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15744
      Location:497 → 543
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:39 → 160
      RUN; RUN domain

    2. XM_036165294.1 → XP_036021187.1  protein RUFY3 isoform X7

      Conserved Domains (2) summary
      COG1196
      Location:192 → 400
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam02759
      Location:39 → 160
      RUN; RUN domain

    3. XM_006535109.4 → XP_006535172.1  protein RUFY3 isoform X1

      Conserved Domains (3) summary
      COG1196
      Location:340 → 570
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd15744
      Location:629 → 675
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:171 → 292
      RUN; RUN domain

    4. XM_036165293.1 → XP_036021186.1  protein RUFY3 isoform X6

      Conserved Domains (2) summary
      COG1196
      Location:326 → 532
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam02759
      Location:171 → 292
      RUN; RUN domain

    5. XM_036165295.1 → XP_036021188.1  protein RUFY3 isoform X7

      Conserved Domains (2) summary
      COG1196
      Location:192 → 400
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam02759
      Location:39 → 160
      RUN; RUN domain

    6. XM_006535116.5 → XP_006535179.1  protein RUFY3 isoform X5

      Conserved Domains (3) summary
      TIGR02168
      Location:179 → 438
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15744
      Location:497 → 543
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:39 → 160
      RUN; RUN domain

    7. XM_006535112.2 → XP_006535175.1  protein RUFY3 isoform X2

      See identical proteins and their annotated locations for XP_006535175.1

      Conserved Domains (3) summary
      TIGR02168
      Location:261 → 520
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15744
      Location:579 → 625
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:121 → 242
      RUN; RUN domain

    8. XM_006535111.2 → XP_006535174.1  protein RUFY3 isoform X2

      Conserved Domains (3) summary
      TIGR02168
      Location:261 → 520
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15744
      Location:579 → 625
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:121 → 242
      RUN; RUN domain

    9. XM_017320983.3 → XP_017176472.1  protein RUFY3 isoform X3

      Conserved Domains (3) summary
      TIGR02168
      Location:243 → 502
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15744
      Location:561 → 607
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:103 → 224
      RUN; RUN domain

    10. XM_006535114.4 → XP_006535177.1  protein RUFY3 isoform X4

      Conserved Domains (3) summary
      TIGR02168
      Location:213 → 472
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd15744
      Location:531 → 577
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:73 → 194
      RUN; RUN domain

    RNA

    1. XR_389285.4 RNA Sequence

    2. XR_001784724.3 RNA Sequence

    3. XR_004942538.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9D394.1 GenPept UniProtKB/Swiss-Prot:Q9D394

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