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

Gene ID: 306991, updated on 10-Jul-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
Enables protein self-association. Involved in regulated exocytosis. Located in Golgi-associated vesicle. Human ortholog(s) of this gene implicated in autosomal recessive cerebellar ataxia. Orthologous to human VPS41 (VPS41 subunit of HOPS complex). [provided by Alliance of Genome Resources, Apr 2022]
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 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
    A0A8I5ZWM9, 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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