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    Vps41 VPS41 subunit of HOPS complex [ Rattus norvegicus (Norway rat) ]

    Gene ID: 306991, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Vps41provided by RGD
    Official Full Name
    VPS41 subunit of HOPS complexprovided by RGD
    Primary source
    RGD:1560511
    See related
    EnsemblRapid:ENSRNOG00000012940 AllianceGenome:RGD:1560511
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1560511
    Summary
    Predicted to enable identical protein binding activity and microtubule binding activity. Involved in regulated exocytosis. Located in Golgi-associated vesicle. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 29. Orthologous to human VPS41 (VPS41 subunit of HOPS complex). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 557.9), Kidney (RPKM 252.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Vps41 in Genome Data Viewer
    Location:
    17q11
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (50758732..50923129, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (46063132..46227533, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (48643754..48810633, complement)

    Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene amphiphysin Neighboring gene small nucleolar RNA SNORA17 Neighboring gene POU class 6 homeobox 2 Neighboring gene uncharacterized LOC108348563 Neighboring gene uncharacterized LOC134482718

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. hVPS41 is expressed in multiple isoforms and can associate with vesicles through a RING-H2 finger motif. McVey Ward D, et al. Exp Cell Res, 2001 Jul 1. PMID 11412045
    2. The HOPS proteins hVps41 and hVps39 are required for homotypic and heterotypic late endosome fusion. Pols MS, et al. Traffic, 2013 Feb. PMID 23167963
    3. Self-assembly of VPS41 promotes sorting required for biogenesis of the regulated secretory pathway. Asensio CS, et al. Dev Cell, 2013 Nov 25. PMID 24210660, Free PMC Article
    4. Structural basis of Vps33A recruitment to the human HOPS complex by Vps16. Graham SC, et al. Proc Natl Acad Sci U S A, 2013 Aug 13. PMID 23901104, Free PMC Article
    5. Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes. Wartosch L, et al. Traffic, 2015 Jul. PMID 25783203, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 RGD

    Function Evidence Code Pubs
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables microtubule binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi vesicle transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to starvation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endosomal vesicle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endosomal vesicle fusion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endosome to lysosome transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in late endosome to lysosome transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in macroautophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein targeting to vacuole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulated exocytosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vesicle-mediated transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of AP-3 adaptor complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi-associated vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi-associated vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of HOPS complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of HOPS complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of clathrin complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in clathrin-coated vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in early endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in late endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in late endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of lysosomal HOPS complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in microtubule cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 41 homolog
    Names
    VPS41 HOPS complex subunit
    Vam2
    vacuolar protein sorting 41 homolog

    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_001399318.1 → NP_001386247.1  vacuolar protein sorting-associated protein 41 homolog

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000017
      UniProtKB/TrEMBL
      A6K987
      Related
      ENSRNOP00000095914.2, ENSRNOT00000094441.2
      Conserved Domains (3) summary
      smart00299
      Location:570 → 707
      CLH; Clathrin heavy chain repeat homology
      sd00039
      Location:136 → 168
      7WD40; WD40 repeat [structural motif]
      cd16690
      Location:786 → 840
      RING-H2_Vps41; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086035.1 Reference GRCr8

      Range
      50758732..50923129 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039095720.2 → XP_038951648.1  vacuolar protein sorting-associated protein 41 homolog isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZWM9, A0A8I6AV86
      Related
      ENSRNOP00000096552.1, ENSRNOT00000106258.2
      Conserved Domains (3) summary
      smart00299
      Location:517 → 654
      CLH; Clathrin heavy chain repeat homology
      sd00039
      Location:83 → 115
      7WD40; WD40 repeat [structural motif]
      cd16690
      Location:733 → 787
      RING-H2_Vps41; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001107355.1: Suppressed sequence

      Description
      NM_001107355.1: This RefSeq was removed because currently there is insufficient support for the transcript.
    Nucleotide Protein Strain
    Heading Accession and Version

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