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

Gene ID: 435626, updated on 28-Oct-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; liver; lung; and metanephros. Orthologous to human RUFY4 (RUN and FYVE domain containing 4). [provided by Alliance of Genome Resources, Oct 2024]
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 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. RUFY4 deletion prevents pathological bone loss by blocking endo-lysosomal trafficking of osteoclasts. Kim M, et al. Bone Res, 2024 May 15. PMID 38744829, Free PMC Article
  2. 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
  3. 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
  4. Maternal RNA transcription in Dlk1-Dio3 domain is critical for proper development of the mouse placental vasculature. Zhang X, et al. Commun Biol, 2024 Mar 23. PMID 38521877, Free PMC Article
  5. Genetic determinants of micronucleus formation in vivo. Adams DJ, et al. Nature, 2024 Mar. PMID 38355793, Free PMC Article

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RUFY4 deletion prevents pathological bone loss by blocking endo-lysosomal trafficking of osteoclasts.
    Title: RUFY4 deletion prevents pathological bone loss by blocking endo-lysosomal trafficking of osteoclasts.
  2. 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
  
enables phosphatidylinositol-3-phosphate binding ISS
Inferred from Sequence or Structural Similarity
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
  
involved_in autophagosome assembly ISS
Inferred from Sequence or Structural Similarity
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
  
involved_in positive regulation of macroautophagy ISS
Inferred from Sequence or Structural Similarity
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 autophagosome ISS
Inferred from Sequence or Structural Similarity
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_001034060.4 → NP_001029232.2  RUN and FYVE domain-containing protein 4 isoform 2

    Status: VALIDATED

    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_001170641.2 → 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

    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

  3. NM_001431246.1 → NP_001418175.1  RUN and FYVE domain-containing protein 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC117757
    UniProtKB/Swiss-Prot
    B2RX43, D3YY30, Q3TYX8

  4. NM_001431247.1 → NP_001418176.1  RUN and FYVE domain-containing protein 4 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC117757

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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