Vps41 VPS41 HOPS complex subunit [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Vps41provided by MGI
Official Full Name: VPS41 HOPS complex subunitprovided by MGI
Primary source: MGI:MGI:1929215
See related: Ensembl:ENSMUSG00000041236 AllianceGenome:MGI:1929215
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: Vam2; mVam2
Summary: Enables microtubule binding activity. Predicted to be involved in several processes, including cellular response to starvation; endosomal vesicle fusion; and vacuolar transport. Located in early endosome; late endosome membrane; and microtubule cytoskeleton. Part of HOPS complex. Is expressed in embryo; extraembryonic component; and primitive endoderm. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 29. Orthologous to human VPS41 (VPS41 subunit of HOPS complex). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in frontal lobe adult (RPKM 8.5), cortex adult (RPKM 8.2) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 13 A2; 13 6.75 cM

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (18901462..19050981)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (18717292..18866811)

Chromosome 13 - NC_000079.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

VPS41-mediated incomplete autophagy aggravates cadmium-induced apoptosis in mouse hepatocytes.
Title: VPS41-mediated incomplete autophagy aggravates cadmium-induced apoptosis in mouse hepatocytes.
Pancreatic beta-Cell-Specific Deletion of VPS41 Causes Diabetes Due to Defects in Insulin Secretion.
Title: Pancreatic β-Cell-Specific Deletion of VPS41 Causes Diabetes Due to Defects in Insulin Secretion.
Lack of Coxiella burnetii targeting to degradative compartments involves an antagonistic engagement of TLR4 by lipopolysaccharides, lack of p38alpha-MAPK-driven phosphorylation, and block in recruitment of the Vps41 to lipopolysaccharide-containing vesicles.
Title: Impaired stimulation of p38α-MAPK/Vps41-HOPS by LPS from pathogenic Coxiella burnetii prevents trafficking to microbicidal phagolysosomes.
It was found that Vam2, which interacts with BMP type I receptor, is required for the spatiotemporal modulation of BMP signaling, via sequestration of the receptor complex in the late stages of the endocytic pathway.
Title: Spatial restriction of bone morphogenetic protein signaling in mouse gastrula through the mVam2-dependent endocytic pathway.

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Variation

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Alleles

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

Gene trapped (1)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI317346 (e-PCR)
- UniSTS:160272

NoName (e-PCR)
- UniSTS:236594

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables microtubule binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi vesicle transport	ISO Inferred from Sequence Orthology more info
involved_in autophagy	IEA Inferred from Electronic Annotation more info
involved_in cellular response to starvation	IBA Inferred from Biological aspect of Ancestor 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 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
involved_in macroautophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein targeting to vacuole	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein targeting to vacuole	IEA Inferred from Electronic Annotation more info
involved_in regulated exocytosis	ISO Inferred from Sequence Orthology more info
involved_in vesicle-mediated transport	ISO Inferred from Sequence Orthology more info
involved_in vesicle-mediated transport	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of AP-3 adaptor complex	IEA Inferred from Electronic Annotation more info
part_of AP-3 adaptor complex	ISO Inferred from Sequence Orthology more info
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in Golgi-associated vesicle	ISO Inferred from Sequence Orthology more info
part_of HOPS complex	IBA Inferred from Biological aspect of Ancestor more info
part_of HOPS complex	IPI Inferred from Physical Interaction more info	PubMed
part_of HOPS complex	ISO Inferred from Sequence Orthology more info
part_of HOPS complex	ISS Inferred from Sequence or Structural Similarity more info
part_of clathrin complex	IEA Inferred from Electronic Annotation more info
part_of clathrin complex	ISO Inferred from Sequence Orthology more info
located_in clathrin-coated vesicle	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated vesicle	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	ISO Inferred from Sequence Orthology more info
is_active_in late endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome	ISO Inferred from Sequence Orthology more info
located_in late endosome membrane	IDA Inferred from Direct Assay more info	PubMed
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
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in microtubule cytoskeleton	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 41 homolog

Names: VAM2 homolog; vacuolar protein sorting 41

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_172120.4 → NP_742118.3 vacuolar protein sorting-associated protein 41 homolog

See identical proteins and their annotated locations for NP_742118.3

Status: VALIDATED

Source sequence(s)

AB028843, AI851542

Consensus CDS

CCDS26257.1

UniProtKB/Swiss-Prot

Q05AE9, Q3TPS1, Q5KU39, Q80V99, Q8BKK6, Q8CG01, Q8CJC3

Related

ENSMUSP00000072729.5, ENSMUST00000072961.6

Conserved Domains (3) summary

smart00299
Location:570 → 707

CLH; Clathrin heavy chain repeat homology

pfam00637
Location:574 → 709

Clathrin; Region in Clathrin and VPS

sd00039
Location:87 → 131

7WD40; WD40 repeat [structural motif]

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_000079.7 Reference GRCm39 C57BL/6J

Range

18901462..19050981

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006516641.3 → XP_006516704.1 vacuolar protein sorting-associated protein 41 homolog isoform X1

UniProtKB/TrEMBL

Q3TS83

Conserved Domains (2) summary

smart00299
Location:413 → 550

CLH; Clathrin heavy chain repeat homology

cd16690
Location:629 → 683

RING-H2_Vps41; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins