Vapa vesicle-associated membrane protein, associated protein A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Vapaprovided by MGI
Official Full Name: vesicle-associated membrane protein, associated protein Aprovided by MGI
Primary source: MGI:MGI:1353561
See related: Ensembl:ENSMUSG00000024091 AllianceGenome:MGI:1353561
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: 33kDa; VAP-A; VAP33; VAMP-A; VAP-33
Summary: Predicted to enable several functions, including FFAT motif binding activity; microtubule binding activity; and protein dimerization activity. Predicted to be involved in several processes, including endoplasmic reticulum-plasma membrane tethering; modulation by host of viral genome replication; and sphingomyelin biosynthetic process. Located in endoplasmic reticulum and microtubule cytoskeleton. Orthologous to human VAPA (VAMP associated protein A). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in duodenum adult (RPKM 108.3), adrenal adult (RPKM 93.7) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 17 E1.1; 17 34.9 cM

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (65887048..65925441, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (65580053..65616462, complement)

Chromosome 17 - NC_000083.7 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?

CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.
Title: CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.
ORP/Osh mediate cross-talk between ER-plasma membrane contact site components and plasma membrane SNAREs.
Title: ORP/Osh mediate cross-talk between ER-plasma membrane contact site components and plasma membrane SNAREs.
the VAP-interacting membrane-associated phosphatidylinositol (PtdIns) transfer proteins PYK2 N-terminal domain-interacting receptor 2 (Nir2) and Nir3 specifically associate with Kv2.1 complexes.
Title: Neuronal ER-plasma membrane junctions organized by Kv2-VAP pairing recruit Nir proteins and affect phosphoinositide homeostasis.
There was colocalization of Kv2.1 and Kv2.2 with endogenous VAPA at ER-PM junctions in mouse brain neurons. Expression of Kv2.1 recruits VAPA to ER-PM junctions. Knocking out VAPA expression disrupts Kv2.1 clustering.The domains of VAPs and Kv2.1 necessary and sufficient for their association at ER-PM junctions were identified.
Title: Identification of VAPA and VAPB as Kv2 Channel-Interacting Proteins Defining Endoplasmic Reticulum-Plasma Membrane Junctions in Mammalian Brain Neurons.
VAP-33 expression in dendritic cell sarcoma was related to vesicle transportation during antigen processing in dendritic cells.
Title: [Expression and function of VAP-33 in murine dendritic cell sarcoma].
These data suggest that VAPA could be involved in prestin's transportation inside outer hair cells (OHCs) and may facilitate the targeting of this abundant OHC protein to the plasma membrane.
Title: Interaction between the motor protein prestin and the transporter protein VAPA.
Vapa regulates partitioning of Osbp between the endoplasmic retiuculum and the Golgi apparatus.
Title: VAMP-associated protein-A regulates partitioning of oxysterol-binding protein-related protein-9 between the endoplasmic reticulum and Golgi apparatus.

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Variation

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Alleles

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

Endonuclease-mediated (3)

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:234503

RH76596 (e-PCR)
- UniSTS:87126

RH125582 (e-PCR)
- UniSTS:162396

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables FFAT motif binding	IEA Inferred from Electronic Annotation more info
enables FFAT motif binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables microtubule binding	IEA Inferred from Electronic Annotation more info
enables microtubule binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables protein heterodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables protein-membrane adaptor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in COPII-coated vesicle budding	IEA Inferred from Electronic Annotation more info
involved_in COPII-coated vesicle budding	ISO Inferred from Sequence Orthology more info
involved_in ceramide transport	ISO Inferred from Sequence Orthology more info
involved_in cholesterol transport	IEA Inferred from Electronic Annotation more info
involved_in cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	ISO Inferred from Sequence Orthology more info
involved_in endoplasmic reticulum-plasma membrane tethering	IEA Inferred from Electronic Annotation more info
involved_in endoplasmic reticulum-plasma membrane tethering	ISO Inferred from Sequence Orthology more info
involved_in negative regulation by host of viral genome replication	IEA Inferred from Electronic Annotation more info
involved_in negative regulation by host of viral genome replication	ISO Inferred from Sequence Orthology more info
involved_in neuron projection development	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in neuron projection development	ISS Inferred from Sequence or Structural Similarity more info
involved_in phospholipid transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation by host of viral genome replication	IEA Inferred from Electronic Annotation more info
involved_in positive regulation by host of viral genome replication	ISO Inferred from Sequence Orthology more info
involved_in protein localization to endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
involved_in protein localization to endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
involved_in sphingomyelin biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in sterol transport	ISO Inferred from Sequence Orthology more info
involved_in viral release from host cell	IEA Inferred from Electronic Annotation more info
involved_in viral release from host cell	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi membrane	ISO Inferred from Sequence Orthology more info
located_in bicellular tight junction	IEA Inferred from Electronic Annotation more info
colocalizes_with bicellular tight junction	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	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
located_in nuclear membrane	IEA Inferred from Electronic Annotation more info
located_in nuclear membrane	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
colocalizes_with perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in vesicle	IEA Inferred from Electronic Annotation more info
located_in vesicle	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: vesicle-associated membrane protein-associated protein A

Names: 33 kDa VAMP-associated protein; VAMP-associated protein A; synaptobrevin-associated protein of 33kDa

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_001355402.1 → NP_001342331.1 vesicle-associated membrane protein-associated protein A isoform 1

Status: VALIDATED

Source sequence(s)

AC166058, CT030729

UniProtKB/TrEMBL

A0A3B2W837

Related

ENSMUSP00000156845.2, ENSMUST00000232686.2

Conserved Domains (1) summary

pfam00635
Location:14 → 118

Motile_Sperm; MSP (Major sperm protein) domain
NM_013933.3 → NP_038961.2 vesicle-associated membrane protein-associated protein A isoform 2

See identical proteins and their annotated locations for NP_038961.2

Status: VALIDATED

Source sequence(s)

AK167381, BM899396

Consensus CDS

CCDS37677.1

UniProtKB/Swiss-Prot

Q3TJM1, Q9QY77, Q9WV55

Related

ENSMUSP00000024897.9, ENSMUST00000024897.10

Conserved Domains (1) summary

pfam00635
Location:14 → 118

Motile_Sperm; MSP (Major sperm protein) domain

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_000083.7 Reference GRCm39 C57BL/6J

Range

65887048..65925441 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036160637.1 → XP_036016530.1 vesicle-associated membrane protein-associated protein A isoform X2

Conserved Domains (1) summary

pfam00635
Location:14 → 118

Motile_Sperm; MSP (Major sperm protein) domain
XM_017317500.3 → XP_017172989.1 vesicle-associated membrane protein-associated protein A isoform X1

UniProtKB/TrEMBL

A0A3B2W837

Conserved Domains (1) summary

pfam00635
Location:14 → 118

Motile_Sperm; MSP (Major sperm protein) domain