U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 269338, updated on 5-Mar-2024

Summary

Official Symbol
Vps39provided by MGI
Official Full Name
VPS39 HOPS complex subunitprovided by MGI
Primary source
MGI:MGI:2443189
See related
Ensembl:ENSMUSG00000027291 AllianceGenome:MGI:2443189
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
Vam6; Vam6P; mVam6; A230065P22Rik
Summary
Predicted to be involved in endocytic recycling; lysosomal transport; and vesicle fusion. Predicted to act upstream of or within protein transport. Part of AP-3 adaptor complex. Is expressed in several structures, including brain; genitourinary system; gut; quadriceps femoris muscle; and trigeminal nerve. Orthologous to human VPS39 (VPS39 subunit of HOPS complex). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E18 (RPKM 15.5), whole brain E14.5 (RPKM 15.5) and 28 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See Vps39 in Genome Data Viewer
Location:
2 E5; 2 60.31 cM
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_02 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)

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 CapStarr-seq enhancer MGSCv37_chr2:120178706-120178815 Neighboring gene transmembrane protein 87A Neighboring gene STARR-positive B cell enhancer ABC_E10133 Neighboring gene STARR-positive B cell enhancer ABC_E9071 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)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
 
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
 
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
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
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
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 

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
    UniProtKB/TrEMBL
    Q3URK7, Q8BY36
    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
    UniProtKB/TrEMBL
    Q3TC98, Q3URK7, Q8BY36
    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, Q922I3
    UniProtKB/TrEMBL
    Q3URK7, Q3USV9, Q8BY36
    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/TrEMBL
    Q3URK7, Q5KU38, Q8BY36
    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:588735
    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: 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
    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