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Vps39 Gene Detail
Summary
  • Symbol
    Vps39
  • Name
    VPS39 HOPS complex subunit
  • Synonyms
    A230065P22Rik, mVam6, Vam6, Vam6P
  • Feature Type
    protein coding gene
  • IDs
    MGI:2443189
    NCBI Gene: 269338
  • Gene Overview
    MyGene.info: VPS39
  • Alliance
  • Transcription Start Sites
    4 TSS
Location &
Maps
more
  • Sequence Map
    Chr2:120316461-120353137 bp, - strand
  • From Ensembl annotation of GRCm38

    View this region in JBrowse

  • Genome Browsers
  • Genetic Map
    Chromosome 2, 60.31 cM
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    276 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_2443189
protein coding gene Chr2:120316461-120353146 (-)
129S1/SvImJ MGP_129S1SvImJ_G0026364
protein coding gene Chr2:123177863-123216021 (-)
A/J MGP_AJ_G0026325
protein coding gene Chr2:118128137-118167111 (-)
AKR/J MGP_AKRJ_G0026304
protein coding gene Chr2:121426500-121466881 (-)
BALB/cJ MGP_BALBcJ_G0026338
protein coding gene Chr2:118373473-118410716 (-)
C3H/HeJ MGP_C3HHeJ_G0026084
protein coding gene Chr2:121902325-121940506 (-)
C57BL/6NJ MGP_C57BL6NJ_G0026785
protein coding gene Chr2:127193271-127230787 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0024165
protein coding gene Chr2:113147201-113189065 (-)
CAST/EiJ MGP_CASTEiJ_G0025546
protein coding gene Chr2:122215177-122253128 (-)
CBA/J MGP_CBAJ_G0026060
protein coding gene Chr2:131641358-131685664 (-)
DBA/2J MGP_DBA2J_G0026199
protein coding gene Chr2:117520465-117557316 (-)
FVB/NJ MGP_FVBNJ_G0026161
protein coding gene Chr2:116356482-116393082 (-)
LP/J MGP_LPJ_G0026300
protein coding gene Chr2:123437039-123476159 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0026180
protein coding gene Chr2:135954165-135995607 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0026840
protein coding gene Chr2:121551739-121590962 (-)
PWK/PhJ MGP_PWKPhJ_G0025282
protein coding gene Chr2:117121849-117158775 (-)
SPRET/EiJ MGP_SPRETEiJ_G0025081
protein coding gene Chr2:120742477-120779660 (-)
WSB/EiJ MGP_WSBEiJ_G0025615
protein coding gene Chr2:122389552-122427010 (-)



Homology
more
  • Human Ortholog
    VPS39, VPS39, HOPS complex subunit
  • Vertebrate Orthologs
    9
  • Human Ortholog
    VPS39, VPS39, HOPS complex subunit
    Orthology source: HomoloGene, HGNC
  • Synonyms
    hVam6p, TLP, VAM6
  • Links
    NCBI Gene ID: 23339
    neXtProt AC: NX_Q96JC1
    UniProt: Q96JC1

  • Chr Location
    15q15.1; chr15:42158701-42208331 (-)  GRCh38.p7

Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    8 phenotype references
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
  • GO References
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell death
cell differentiation
cell proliferation
cellular component organization
establishment of localization
homeostatic process
immune system process
lipid metabolic process
nucleic acid-templated transcription
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
non-membrane-bounded organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
synapse
vacuole
Click cells to view annotations.
Expression
less
  • cDNA Data
Interactions
less
Sequences &
Gene Models
less
Representative SequencesLengthStrain/SpeciesFlank
genomic ENSMUSG00000027291 Ensembl Gene Model | MGI Sequence Detail 36677 C57BL/6J ±  kb
transcript ENSMUST00000102501 Ensembl | MGI Sequence Detail 4384 Not Applicable  
polypeptide ENSMUSP00000099559 Ensembl | MGI Sequence Detail 886 Not Applicable  
For the selected sequence
Protein
Information
less
  • UniProt
    8 Sequences
  • Protein Ontology
    PR:000017339 vam6/Vps39-like protein
  • InterPro Domains
    IPR001180 Citron homology (CNH) domain
    IPR000547 Clathrin, heavy chain/VPS, 7-fold repeat
    IPR019452 Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1
    IPR019453 Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2
    IPR032914 Vam6/VPS39/TRAP1 family
    IPR036322 WD40-repeat-containing domain superfamily
Molecular
Reagents
less
  • All nucleic 100
    cDNA 100

    Microarray probesets 3
Other
Accession IDs
less
MGI:3035039
References
more
  • Summaries
    All 37
    Gene Ontology 7
    Phenotypes 8
  • Earliest
    J:109968 Roderick TH, et al., Nineteen paracentric chromosomal inversions in mice. Genetics. 1974 Jan;76(1):109-17
  • Latest
    J:265628 Gaudet P, et al., Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform. 2011 Sep;12(5):449-62

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
Citing These Resources
Funding Information
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last database update
11/06/2018
MGI 6.13
The Jackson Laboratory