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

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. Part of AP-3 adaptor complex. Is expressed in several structures, including adipose tissue; alimentary system; genitourinary system; hemolymphoid system; and nervous system. Orthologous to human VPS39 (VPS39 subunit of HOPS complex). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in CNS E18 (RPKM 15.5), whole brain E14.5 (RPKM 15.5) and 28 other tissues See more
Orthologs: human all
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Genomic context

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_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Vam6 reduces iNKT cell function in tumor via modulating AMPK/mTOR pathways.
Title: Vam6 reduces iNKT cell function in tumor via modulating AMPK/mTOR pathways.
SGPL1 stimulates VPS39 recruitment to the mitochondria in MICU1 deficient cells.
Title: SGPL1 stimulates VPS39 recruitment to the mitochondria in MICU1 deficient cells.
our data indicate that TRAP1 and VPS39 are nonredundant and essentially required for early embryonic development
Title: The TGF-β signaling modulators TRAP1/TGFBRAP1 and VPS39/Vam6/TLP are essential for early embryonic development.
although only TBC1D15/Rab7-GAP altered Rab7-GTP levels, both Rab7-GAP and mVps39 regulate lysosomal morphology and play a role in maintaining growth factor dependence
Title: Differential effects of TBC1D15 and mammalian Vps39 on Rab7 activation state, lysosomal morphology, and growth factor dependence.
Antibodies to VAMP and SNAP inhibited sperm-zona pellucida interaction, suggesting their possible involvement in sperm membrane vesiculation.
Title: Spatio-temporal organization of Vam6P and SNAP on mouse spermatozoa and their involvement in sperm-zona pellucida interactions.

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Variation

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Alleles

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

Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:234502

G36394 (e-PCR)
- UniSTS:25608

AW743070 (e-PCR)
- UniSTS:207390

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 autophagosome-lysosome fusion	ISS Inferred from Sequence or Structural Similarity 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	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
involved_in endosomal vesicle fusion	ISO Inferred from Sequence Orthology more info
involved_in endosome to lysosome transport	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
involved_in late endosome to lysosome transport	ISO Inferred from Sequence Orthology 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 late endosome	ISO Inferred from Sequence Orthology more info
located_in late endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in late endosome membrane	IEA Inferred from Electronic Annotation 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
part_of lysosomal HOPS complex	ISS Inferred from Sequence or Structural Similarity more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: vam6/Vps39-like protein

Names: vacuolar protein sorting 39

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)

NM_001363053.1 → NP_001349982.1 vam6/Vps39-like protein isoform 3

Status: VALIDATED

Source sequence(s)

AL844608

UniProtKB/TrEMBL

Q3URK7, Q8BY36

Conserved Domains (4) summary

pfam10366
Location:426 → 528

Vps39_1; Vacuolar sorting protein 39 domain 1

pfam10367
Location:738 → 846

Vps39_2; Vacuolar sorting protein 39 domain 2

cl02434
Location:46 → 257

CNH; CNH domain

cl26078
Location:627 → 712

Clathrin; Region in Clathrin and VPS
NM_001363054.1 → NP_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:325 → 427

Vps39_1; Vacuolar sorting protein 39 domain 1

pfam10367
Location:637 → 744

Vps39_2; Vacuolar sorting protein 39 domain 2

cl02434
Location:2 → 156

CNH; CNH domain

cl26078
Location:526 → 612

Clathrin; Region in Clathrin and VPS
NM_147153.4 → NP_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:460 → 562

Vps39_1; Vacuolar sorting protein 39 domain 1

pfam10367
Location:772 → 880

Vps39_2; Vacuolar sorting protein 39 domain 2

cl02434
Location:20 → 291

CNH; CNH domain

cl26078
Location:661 → 746

Clathrin; Region in Clathrin and VPS
NM_178851.4 → NP_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:449 → 551

Vps39_1; Vacuolar sorting protein 39 domain 1

pfam10367
Location:761 → 869

Vps39_2; Vacuolar sorting protein 39 domain 2

cl02434
Location:20 → 280

CNH; CNH domain

cl26078
Location:588 → 735

Clathrin; Region in Clathrin and VPS

RNA

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

NC_000068.8 Reference GRCm39 C57BL/6J

Range

120146942..120183618 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (3) summary

pfam10366
Location:81 → 183

Vps39_1; Vacuolar sorting protein 39 domain 1

pfam10367
Location:393 → 501

Vps39_2; Vacuolar sorting protein 39 domain 2

cl26078
Location:282 → 367

Clathrin; Region in Clathrin and VPS