Vps16 VSP16 CORVET/HOPS core subunit [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Vps16provided by MGI
Official Full Name: VSP16 CORVET/HOPS core subunitprovided by MGI
Primary source: MGI:MGI:2136772
See related: Ensembl:ENSMUSG00000027411 AllianceGenome:MGI:2136772
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: mVPS16; 1810074M16Rik
Summary: Enables actin binding activity. Acts upstream of or within viral entry into host cell. Located in actin filament; clathrin-coated vesicle; and early endosome membrane. Part of AP-3 adaptor complex and CORVET complex. Human ortholog(s) of this gene implicated in dystonia. Orthologous to human VPS16 (VPS16 core subunit of CORVET and HOPS complexes). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thymus adult (RPKM 21.6), CNS E14 (RPKM 19.5) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 F1; 2 63.22 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (130265744..130286189)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (130424320..130444269)

Chromosome 2 - NC_000068.8 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?

mVps16p has potential roles in membrane trafficking
Title: Identification of mouse Vps16 and biochemical characterization of mammalian class C Vps complex.
Vps16p is highly expressed in neurons of various brain areas and developmental stages tested; it colocalizes with microtubule associated protein 2, but not glial fibrillary acidic protein.
Title: Expression of the mammalian homologue of vacuolar protein sorting 16 (Vps16p) in the mouse and rat brain.

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Variation

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Alleles

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

Endonuclease-mediated (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables actin binding	IBA Inferred from Biological aspect of Ancestor more info
enables actin binding	IDA Inferred from Direct Assay more info	PubMed
enables actin filament binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in autophagosome maturation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within autophagy	IEA Inferred from Electronic Annotation more info
involved_in endosomal transport	IBA Inferred from Biological aspect of Ancestor 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
acts_upstream_of_or_within protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within symbiont entry into host cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vacuole fusion, non-autophagic	IBA Inferred from Biological aspect of Ancestor more info
involved_in vacuole organization	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 CORVET complex	IDA Inferred from Direct Assay more info	PubMed
part_of HOPS complex	IBA Inferred from Biological aspect of Ancestor more info
part_of HOPS complex	ISO Inferred from Sequence Orthology more info
located_in actin filament	IDA Inferred from Direct Assay more info	PubMed
located_in axon	ISO Inferred from Sequence Orthology more info
located_in clathrin-coated vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome	ISO Inferred from Sequence Orthology more info
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome	ISO Inferred from Sequence Orthology more info
located_in late endosome	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
is_active_in presynapse	ISO Inferred from Sequence Orthology more info
located_in recycling endosome	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 16 homolog

Names: vacuolar protein sorting 16

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_001362651.1 → NP_001349580.1 vacuolar protein sorting-associated protein 16 homolog isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

BX890605

Conserved Domains (2) summary

pfam04841
Location:1 → 131

Vps16_N; Vps16, N-terminal region

pfam04840
Location:228 → 543

Vps16_C; Vps16, C-terminal region
NM_030559.3 → NP_085036.3 vacuolar protein sorting-associated protein 16 homolog isoform 1

See identical proteins and their annotated locations for NP_085036.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AK032558, AK049872, BX890605, BY123989

Consensus CDS

CCDS38242.1

UniProtKB/TrEMBL

G3X8X7, Q8BWV2

Related

ENSMUSP00000028900.10, ENSMUST00000028900.11

Conserved Domains (2) summary

pfam04841
Location:4 → 420

Vps16_N; Vps16, N-terminal region

pfam04840
Location:517 → 835

Vps16_C; Vps16, C-terminal region

RNA

NR_156013.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice junction in the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BX890605
NR_156014.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an alternate internal segment and uses an alternate splice junction in the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BX890605

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

130265744..130286189

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006500430.4 → XP_006500493.1 vacuolar protein sorting-associated protein 16 homolog isoform X1

UniProtKB/TrEMBL

Q8BWV2

Conserved Domains (2) summary

pfam04841
Location:4 → 420

Vps16_N; Vps16, N-terminal region

pfam04840
Location:517 → 832

Vps16_C; Vps16, C-terminal region
XM_036162728.1 → XP_036018621.1 vacuolar protein sorting-associated protein 16 homolog isoform X2

Conserved Domains (2) summary

pfam04841
Location:1 → 131

Vps16_N; Vps16, N-terminal region

pfam04840
Location:228 → 546

Vps16_C; Vps16, C-terminal region