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    Vps39 VPS39 HOPS complex subunit [ Mus musculus (house mouse) ]

    Gene ID: 269338, updated on 23-Jun-2021

    Summary

    Official Symbol
    Vps39provided by MGI
    Official Full Name
    VPS39 HOPS complex subunitprovided by MGI
    Primary source
    MGI:MGI:2443189
    See related
    Ensembl:ENSMUSG00000027291
    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
    Va; mVa; Vam6; Vam6P; mVam6; AW743070; A230065P22Rik
    Expression
    Ubiquitous expression in CNS E18 (RPKM 15.5), whole brain E14.5 (RPKM 15.5) and 28 other tissues See more
    Orthologs
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    Genomic context

    See Vps39 in Genome Data Viewer
    Location:
    2; 2 E5
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (120146942..120183618, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (120316461..120353142, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (120142197..120178869, complement)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene predicted gene, 52560 Neighboring gene phospholipase A2, group IVD Neighboring gene phospholipase A2, group IVF Neighboring gene transmembrane protein 87A Neighboring gene glucosidase, alpha; neutral C Neighboring gene RIKEN cDNA 4931402G19 gene Neighboring gene calpain 3

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2) 

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    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 autophagosome-lysosome fusion ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in autophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in autophagy ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in endocytic recycling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in endosomal vesicle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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 intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in late endosome to lysosome transport ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in vesicle-mediated transport 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 HOPS complex ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in endosome IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    vam6/Vps39-like protein
    Names
    vacuolar protein sorting 39

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001363053.1NP_001349982.1  vam6/Vps39-like protein isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL844608
      Conserved Domains (4) summary
      pfam10366
      Location:426528
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:738846
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl02434
      Location:46257
      CNH; CNH domain
      cl26078
      Location:627712
      Clathrin; Region in Clathrin and VPS
    2. NM_001363054.1NP_001349983.1  vam6/Vps39-like protein isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL844608
      Conserved Domains (4) summary
      pfam10366
      Location:325427
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:637744
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl02434
      Location:2156
      CNH; CNH domain
      cl26078
      Location:526612
      Clathrin; Region in Clathrin and VPS
    3. NM_147153.4NP_671495.1  vam6/Vps39-like protein isoform 1

      See identical proteins and their annotated locations for NP_671495.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AB028844, AK140041, AW060607, BM249306
      Consensus CDS
      CCDS38210.1
      UniProtKB/Swiss-Prot
      Q8R5L3
      UniProtKB/TrEMBL
      Q3USV9, Q5KU38
      Related
      ENSMUSP00000099559.4, ENSMUST00000102501.10
      Conserved Domains (4) summary
      pfam10366
      Location:460562
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:772880
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl02434
      Location:20291
      CNH; CNH domain
      cl26078
      Location:661746
      Clathrin; Region in Clathrin and VPS
    4. NM_178851.4NP_849182.1  vam6/Vps39-like protein isoform 2

      See identical proteins and their annotated locations for NP_849182.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AB028844, AK038824, AK140041, AW060607, BM249306, BY125125
      Consensus CDS
      CCDS16619.1
      UniProtKB/Swiss-Prot
      Q8R5L3
      UniProtKB/TrEMBL
      Q5KU38
      Related
      ENSMUSP00000028752.8, ENSMUST00000028752.8
      Conserved Domains (4) summary
      pfam10366
      Location:449551
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:761869
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl02434
      Location:20280
      CNH; CNH domain
      cl26078
      Location:650735
      Clathrin; Region in Clathrin and VPS

    RNA

    1. NR_027618.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon and contains another alternate exon compared to variant 1. The second alternate exon causes a frameshift such that the protein is severely truncated at the C-terminus. This transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is therefore not thought to encode a protein.
      Source sequence(s)
      AB028844, AK140041, AW060607, BB655861, BM249306, BY125125
      Related
      ENSMUST00000129857.8

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

    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
      120146942..120183618 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030251658.1XP_030107518.1  vam6/Vps39-like protein isoform X1

      Conserved Domains (3) summary
      pfam10366
      Location:81183
      Vps39_1; Vacuolar sorting protein 39 domain 1
      pfam10367
      Location:393501
      Vps39_2; Vacuolar sorting protein 39 domain 2
      cl26078
      Location:282367
      Clathrin; Region in Clathrin and VPS
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