Vamp2 vesicle-associated membrane protein 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Vamp2provided by RGD
Official Full Name: vesicle-associated membrane protein 2provided by RGD
Primary source: RGD:3949
See related: EnsemblRapid:ENSRNOG00000006989 AllianceGenome:RGD:3949
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: SYB; Syb2; RATVAMPB; RATVAMPIR
Summary: Enables several functions, including calcium-dependent protein binding activity; syntaxin-1 binding activity; and transmembrane transporter binding activity. Involved in several processes, including SNARE complex assembly; regulation of delayed rectifier potassium channel activity; and synaptic vesicle exocytosis. Located in neuron projection terminus; plasma membrane; and secretory vesicle. Part of several cellular components, including synaptobrevin 2-SNAP-25-syntaxin-1a complex; synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex; and synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex. Is active in postsynaptic cytosol; postsynaptic density; and synaptic vesicle membrane. Orthologous to human VAMP2 (vesicle associated membrane protein 2). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 228.6), Adrenal (RPKM 56.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q24

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (54292423..54296657)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (53793581..53797815)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (55675171..55679405)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The vSNAREs VAMP2 and VAMP4 control recycling and intracellular sorting of post-synaptic receptors in neuronal dendrites.
Title: The vSNAREs VAMP2 and VAMP4 control recycling and intracellular sorting of post-synaptic receptors in neuronal dendrites.
Interneuronal exchange and functional integration of synaptobrevin via extracellular vesicles.
Title: Interneuronal exchange and functional integration of synaptobrevin via extracellular vesicles.
PI(4,5)P2-dependent regulation of exocytosis by amisyn, the vertebrate-specific competitor of synaptobrevin 2.
Title: PI(4,5)P(2)-dependent regulation of exocytosis by amisyn, the vertebrate-specific competitor of synaptobrevin 2.
By using in-cell NMR spectroscopy study described the dynamic membrane association of rat VAMP2 SNARE motif in mammalian cells, and the structural change of VAMP2 upon the change of intracellular lipis. In contrast to the non-raft region, the membrane region of cholesterol-rich lipid raft markedly weakens the membrane association of VAMP2 SNARE motif, which releases the SNARE motif and facilitates the SNARE assembly.
Title: Different regions of synaptic vesicle membrane regulate VAMP2 conformation for the SNARE assembly.
The chemistry of formation of Synaptobrevin-2 oligomers.
Title: Oligomerisation of Synaptobrevin-2 Studied by Native Mass Spectrometry and Chemical Cross-Linking.
our findings show an intimate interaction between the dynamics of the VAMP2 transmembrane domains via the central glycine and the fluidity of the lipid membrane. In turn, this interaction influences greatly the likelihood and speed of fusion pore opening and expansion.
Title: A Central Small Amino Acid in the VAMP2 Transmembrane Domain Regulates the Fusion Pore in Exocytosis.
The ternary complex of syntaxin1:SNAP25:Munc18-1binds synaptobrevin with fast kinetics, resulting in the rapid formation of a fully zippered SNARE complex to which Munc18-1 remains tethered by the N-terminal domain of syntaxin1.
Title: An activated Q-SNARE/SM protein complex as a possible intermediate in SNARE assembly.
Syp1 clears Syb2 from the presynaptic active zone to prevent short-term depression.
Title: Synaptophysin 1 Clears Synaptobrevin 2 from the Presynaptic Active Zone to Prevent Short-Term Depression.
These effects weaken the integrity of the outer membrane layer and are attributed mainly to the highly charged linker and juxtamembrane regions of sybII
Title: Synaptobrevin transmembrane domain determines the structure and dynamics of the SNARE motif and the linker region.
miR-206 regulates lung surfactant secretion by limiting the availability of VAMP-2 protein.
Title: MicroRNA-206 regulates surfactant secretion by targeting VAMP-2.

Submit: New GeneRIF Correction See all GeneRIFs (55)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

d10mit8 (e-PCR)
- UniSTS:120629

Vamp2 (e-PCR), detects polymorphism
- UniSTS:120629

D10Arb7 (e-PCR), detects polymorphism
- UniSTS:226263

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables SNAP receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables SNARE binding	IDA Inferred from Direct Assay more info	PubMed
enables SNARE binding	IPI Inferred from Physical Interaction more info	PubMed
enables SNARE binding	ISO Inferred from Sequence Orthology more info
enables calcium-dependent protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables calmodulin binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables lipid binding	EXP Inferred from Experiment more info	PubMed
enables molecular adaptor activity	EXP Inferred from Experiment more info	PubMed
enables myosin binding	IPI Inferred from Physical Interaction more info	PubMed
enables phospholipid binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables syntaxin binding	IEA Inferred from Electronic Annotation more info
enables syntaxin binding	ISO Inferred from Sequence Orthology more info
enables syntaxin-1 binding	IBA Inferred from Biological aspect of Ancestor more info
enables syntaxin-1 binding	IDA Inferred from Direct Assay more info	PubMed
enables syntaxin-1 binding	IPI Inferred from Physical Interaction more info	PubMed
enables syntaxin-1 binding	ISO Inferred from Sequence Orthology more info
enables transmembrane transporter binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within Golgi to plasma membrane protein transport	ISO Inferred from Sequence Orthology more info
involved_in SNARE complex assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in SNARE complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within calcium-ion regulated exocytosis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to insulin stimulus	ISO Inferred from Sequence Orthology more info
involved_in eosinophil degranulation	IEA Inferred from Electronic Annotation more info
involved_in eosinophil degranulation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of localization in cell	ISO Inferred from Sequence Orthology more info
involved_in exocytic insertion of neurotransmitter receptor to postsynaptic membrane	ISO Inferred from Sequence Orthology more info
involved_in hormone secretion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within long-term synaptic potentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within membrane fusion	ISO Inferred from Sequence Orthology more info
NOT involved_in mucus secretion	ISO Inferred from Sequence Orthology more info
NOT involved_in natural killer cell degranulation	ISO Inferred from Sequence Orthology more info
NOT involved_in neutrophil degranulation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of intracellular protein transport	ISO Inferred from Sequence Orthology more info
involved_in protein-containing complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulated exocytosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of delayed rectifier potassium channel activity	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of exocytosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of exocytosis	TAS Traceable Author Statement more info	PubMed
NOT involved_in regulation of histamine secretion by mast cell	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic vesicle recycling	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of vesicle-mediated transport	ISO Inferred from Sequence Orthology more info
involved_in response to glucose	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic vesicle docking	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle endocytosis	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle endocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in synaptic vesicle exocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic vesicle exocytosis	IEP Inferred from Expression Pattern more info	PubMed
involved_in synaptic vesicle exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within synaptic vesicle exocytosis	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle exocytosis	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle exocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle fusion	IEA Inferred from Electronic Annotation more info
involved_in vesicle fusion	ISO Inferred from Sequence Orthology more info
involved_in vesicle fusion	ISS Inferred from Sequence or Structural Similarity more info
involved_in vesicle-mediated transport	IEA Inferred from Electronic Annotation more info
involved_in vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle-mediated transport in synapse	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SNARE complex	IDA Inferred from Direct Assay more info	PubMed
part_of SNARE complex	IEA Inferred from Electronic Annotation more info
part_of SNARE 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 clathrin-coated vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic vesicle	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic vesicle membrane	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in neuron projection terminus	IDA Inferred from Direct Assay more info	PubMed
located_in 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	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic cytosol	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
located_in secretory granule	IDA Inferred from Direct Assay more info	PubMed
located_in secretory granule	ISO Inferred from Sequence Orthology more info
NOT located_in secretory granule membrane	ISO Inferred from Sequence Orthology more info
located_in storage vacuole	ISO Inferred from Sequence Orthology more info
located_in synapse	ISO Inferred from Sequence Orthology more info
located_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle	ISO Inferred from Sequence Orthology more info
is_active_in synaptic vesicle membrane	EXP Inferred from Experiment more info	PubMed
is_active_in synaptic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in synaptic vesicle membrane	ISO Inferred from Sequence Orthology more info
located_in synaptic vesicle membrane	NAS Non-traceable Author Statement more info	PubMed
part_of synaptobrevin 2-SNAP-25-syntaxin-1a complex	IDA Inferred from Direct Assay more info	PubMed
part_of synaptobrevin 2-SNAP-25-syntaxin-1a complex	IMP Inferred from Mutant Phenotype more info	PubMed
part_of synaptobrevin 2-SNAP-25-syntaxin-1a complex	ISO Inferred from Sequence Orthology more info
part_of synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex	IDA Inferred from Direct Assay more info	PubMed
part_of synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex	IDA Inferred from Direct Assay more info	PubMed
located_in terminal bouton	HDA more info	PubMed
located_in trans-Golgi network	ISO Inferred from Sequence Orthology more info
located_in vesicle	ISO Inferred from Sequence Orthology more info
part_of voltage-gated potassium channel complex	IDA Inferred from Direct Assay more info	PubMed
located_in zymogen granule membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: vesicle-associated membrane protein 2

Names: Synaptobrevin 2 (vesicle-associated membrane protein VAMP-2); VAMP-2; Vesicle-associated membrane protein (synaptobrevin 2); synaptobrevin-2

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_001429986.1 → NP_001416915.1 vesicle-associated membrane protein 2 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010
NM_012663.3 → NP_036795.1 vesicle-associated membrane protein 2 isoform 1

See identical proteins and their annotated locations for NP_036795.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

P63045

UniProtKB/TrEMBL

A6HFN5

Related

ENSRNOP00000054114.5, ENSRNOT00000057295.5

Conserved Domains (1) summary

cd15870
Location:30 → 92

R-SNARE_VAMP2; SNARE motif of VAMP2