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Vps16 VSP16 CORVET/HOPS core subunit [ Mus musculus (house mouse) ]

Gene ID: 80743, updated on 5-Mar-2024

Summary

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Official Symbol
Vps16provided by MGI
Official Full Name
VSP16 CORVET/HOPS core subunitprovided by MGI
Primary source
MGI:MGI:2136772
See related
Ensembl:ENSMUSG00000027411 AllianceGenome:MGI:2136772
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
mVPS16; 1810074M16Rik
Summary
Enables actin binding activity. Acts upstream of or within viral entry into host cell. Located in actin filament; clathrin-coated vesicle; and early endosome membrane. Part of AP-3 adaptor complex and CORVET complex. Human ortholog(s) of this gene implicated in dystonia. Orthologous to human VPS16 (VPS16 core subunit of CORVET and HOPS complexes). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 21.6), CNS E14 (RPKM 19.5) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
2 F1; 2 63.22 cM
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (130265744..130286189)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (130424320..130444269)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 1700020A23 gene Neighboring gene transmembrane 239 Neighboring gene PC-esterase domain containing 1A Neighboring gene STARR-positive B cell enhancer ABC_E11708 Neighboring gene predicted gene, 52562 Neighboring gene protein tyrosine phosphatase receptor type A Neighboring gene VISTA enhancer mm1313 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:130358070-130358271 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:130366029-130366233 Neighboring gene RIKEN cDNA 4930473A02 gene Neighboring gene STARR-positive B cell enhancer ABC_E7863

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. Expression of the mammalian homologue of vacuolar protein sorting 16 (Vps16p) in the mouse and rat brain. Kim BY, et al. Neurosci Lett, 2004 Jan 30. PMID 14732470
  2. Homozygous mutation of VPS16 gene is responsible for an autosomal recessive adolescent-onset primary dystonia. Cai X, et al. Sci Rep, 2016 May 12. PMID 27174565, Free PMC Article
  3. Identification of mouse Vps16 and biochemical characterization of mammalian class C Vps complex. Kim BY, et al. Biochem Biophys Res Commun, 2003 Nov 21. PMID 14623309
  4. Mammalian CORVET is required for fusion and conversion of distinct early endosome subpopulations. Perini ED, et al. Traffic, 2014 Dec. PMID 25266290
  5. Clathrin-dependent mechanisms modulate the subcellular distribution of class C Vps/HOPS tether subunits in polarized and nonpolarized cells. Zlatic SA, et al. Mol Biol Cell, 2011 May 15. PMID 21411634, Free PMC Article

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. mVps16p has potential roles in membrane trafficking
    Title: Identification of mouse Vps16 and biochemical characterization of mammalian class C Vps complex.
  2. Vps16p is highly expressed in neurons of various brain areas and developmental stages tested; it colocalizes with microtubule associated protein 2, but not glial fibrillary acidic protein.
    Title: Expression of the mammalian homologue of vacuolar protein sorting 16 (Vps16p) in the mouse and rat brain.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC7352

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables actin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables actin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables actin filament 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 autophagosome maturation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within autophagy IEA
Inferred from Electronic Annotation
more info
  
involved_in endosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endosome to lysosome transport ISO
Inferred from Sequence Orthology
more info
  
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within protein transport IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within symbiont entry into host cell IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in vacuole fusion, non-autophagic IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in vacuole organization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of AP-3 adaptor complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of CORVET complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of HOPS complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of HOPS complex ISO
Inferred from Sequence Orthology
more info
  
located_in actin filament IDA
Inferred from Direct Assay
more info
 PubMed 
located_in axon ISO
Inferred from Sequence Orthology
more info
  
located_in clathrin-coated vesicle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in early endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in early endosome ISO
Inferred from Sequence Orthology
more info
  
located_in early endosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endosome ISO
Inferred from Sequence Orthology
more info
  
located_in late endosome ISO
Inferred from Sequence Orthology
more info
  
located_in lysosome ISO
Inferred from Sequence Orthology
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in neuronal cell body ISO
Inferred from Sequence Orthology
more info
  
is_active_in presynapse ISO
Inferred from Sequence Orthology
more info
  
located_in recycling endosome ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
vacuolar protein sorting-associated protein 16 homolog
Names
vacuolar protein sorting 16

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_001362651.1 → NP_001349580.1  vacuolar protein sorting-associated protein 16 homolog isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    BX890605
    Conserved Domains (2) summary
    pfam04841
    Location:1 → 131
    Vps16_N; Vps16, N-terminal region
    pfam04840
    Location:228 → 543
    Vps16_C; Vps16, C-terminal region

  2. NM_030559.3 → NP_085036.3  vacuolar protein sorting-associated protein 16 homolog isoform 1

    See identical proteins and their annotated locations for NP_085036.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AK032558, AK049872, BX890605, BY123989
    Consensus CDS
    CCDS38242.1
    UniProtKB/TrEMBL
    G3X8X7, Q8BWV2
    Related
    ENSMUSP00000028900.10, ENSMUST00000028900.11
    Conserved Domains (2) summary
    pfam04841
    Location:4 → 420
    Vps16_N; Vps16, N-terminal region
    pfam04840
    Location:517 → 835
    Vps16_C; Vps16, C-terminal region

RNA

  1. NR_156013.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice junction in the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BX890605

  2. NR_156014.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate internal segment and uses an alternate splice junction in the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BX890605

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_000068.8 Reference GRCm39 C57BL/6J

    Range
    130265744..130286189
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006500430.4 → XP_006500493.1  vacuolar protein sorting-associated protein 16 homolog isoform X1

    UniProtKB/TrEMBL
    Q8BWV2
    Conserved Domains (2) summary
    pfam04841
    Location:4 → 420
    Vps16_N; Vps16, N-terminal region
    pfam04840
    Location:517 → 832
    Vps16_C; Vps16, C-terminal region

  2. XM_036162728.1 → XP_036018621.1  vacuolar protein sorting-associated protein 16 homolog isoform X2

    Conserved Domains (2) summary
    pfam04841
    Location:1 → 131
    Vps16_N; Vps16, N-terminal region
    pfam04840
    Location:228 → 546
    Vps16_C; Vps16, C-terminal region

RNA

  1. XR_004940782.1 RNA Sequence

  2. XR_003953753.2 RNA Sequence

  3. XR_374543.4 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q920Q4.3 GenPept UniProtKB/Swiss-Prot:Q920Q4

Gene LinkOut

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