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VAMP3 vesicle associated membrane protein 3 [ Homo sapiens (human) ]

Gene ID: 9341, updated on 9-Dec-2018

Summary

Official Symbol
VAMP3provided by HGNC
Official Full Name
vesicle associated membrane protein 3provided by HGNC
Primary source
HGNC:HGNC:12644
See related
Ensembl:ENSG00000049245 MIM:603657
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CEB
Summary
Synaptobrevins/VAMPs, syntaxins, and the 25-kD synaptosomal-associated protein are the main components of a protein complex involved in the docking and/or fusion of synaptic vesicles with the presynaptic membrane. This gene is a member of the vesicle-associated membrane protein (VAMP)/synaptobrevin family. Because of its high homology to other known VAMPs, its broad tissue distribution, and its subcellular localization, the protein encoded by this gene was shown to be the human equivalent of the rodent cellubrevin. In platelets the protein resides on a compartment that is not mobilized to the plasma membrane on calcium or thrombin stimulation. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in fat (RPKM 43.9), lung (RPKM 35.7) and 25 other tissues See more
Orthologs

Genomic context

See VAMP3 in Genome Data Viewer
Location:
1p36.23
Exon count:
5
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (7771269..7781432)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (7831329..7841492)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene calmodulin binding transcription activator 1 Neighboring gene uncharacterized LOC105376691 Neighboring gene uncharacterized LOC105376689 Neighboring gene period circadian regulator 3 Neighboring gene urotensin 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study of periodontal pathogen colonization.
NHGRI GWA Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef impairs the recruitment of VAMP3-positive endosomes at the site of phagocytosis PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Antigen processing-Cross presentation, organism-specific biosystem (from REACTOME)
    Antigen processing-Cross presentation, organism-specific biosystemMHC class I molecules generally present peptide antigens derived from proteins synthesized by the cell itself to CD8+ T cells. However, in some circumstances, antigens from extracellular environment ...
  • Arf6 trafficking events, organism-specific biosystem (from Pathway Interaction Database)
    Arf6 trafficking events, organism-specific biosystem
    Arf6 trafficking events
  • Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystemRecruitment of plasma membrane-localized cargo into clathrin-coated endocytic vesicles is mediated by interaction with a variety of clathrin-interacting proteins collectively called CLASPs (clathrin-...
  • Class I MHC mediated antigen processing & presentation, organism-specific biosystem (from REACTOME)
    Class I MHC mediated antigen processing & presentation, organism-specific biosystemMajor histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular b...
  • Clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Clathrin-mediated endocytosis, organism-specific biosystemClathrin-mediated endocytosis (CME) is one of a number of process that control the uptake of material from the plasma membrane, and leads to the formation of clathrin-coated vesicles (Pearse et al, 1...
  • ER-Phagosome pathway, organism-specific biosystem (from REACTOME)
    ER-Phagosome pathway, organism-specific biosystemThe other TAP-dependent cross-presentation mechanism in phagocytes is the endoplasmic reticulum (ER)-phagosome model. Desjardins proposed that ER is recruited to the cell surface, where it fuses wit...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystem (from REACTOME)
    Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystemThe mammalian Golgi complex, a central hub of both anterograde and retrograde trafficking, is a ribbon of stacked cisterna with biochemically distinct compartments (reviewed in Glick and Nakano, 2009...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Phagosome, organism-specific biosystem (from KEGG)
    Phagosome, organism-specific biosystemPhagocytosis is the process of taking in relatively large particles by a cell, and is a central mechanism in the tissue remodeling, inflammation, and defense against infectious agents. A phagosome is...
  • Phagosome, conserved biosystem (from KEGG)
    Phagosome, conserved biosystemPhagocytosis is the process of taking in relatively large particles by a cell, and is a central mechanism in the tissue remodeling, inflammation, and defense against infectious agents. A phagosome is...
  • Retrograde transport at the Trans-Golgi-Network, organism-specific biosystem (from REACTOME)
    Retrograde transport at the Trans-Golgi-Network, organism-specific biosystemThe trans-Golgi network is the docking site for retrograde cargo from the endolysosomal system and the plasma membrane. Typical cargo includes recycling resident TGN proteins such as TGOLN2 (also kn...
  • SNARE interactions in vesicular transport, organism-specific biosystem (from KEGG)
    SNARE interactions in vesicular transport, organism-specific biosystem
    SNARE interactions in vesicular transport
  • SNARE interactions in vesicular transport, conserved biosystem (from KEGG)
    SNARE interactions in vesicular transport, conserved biosystem
    SNARE interactions in vesicular transport
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
syntaxin-1 binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
Golgi to plasma membrane protein transport IEA
Inferred from Electronic Annotation
more info
 
SNARE complex assembly IEA
Inferred from Electronic Annotation
more info
 
antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent TAS
Traceable Author Statement
more info
 
calcium ion regulated exocytosis IEA
Inferred from Electronic Annotation
more info
 
cellular response to interferon-gamma IEA
Inferred from Electronic Annotation
more info
 
exocytosis TAS
Traceable Author Statement
more info
PubMed 
membrane fusion TAS
Traceable Author Statement
more info
PubMed 
membrane organization TAS
Traceable Author Statement
more info
 
NOT mucus secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of secretion by cell IDA
Inferred from Direct Assay
more info
PubMed 
NOT positive regulation of immunoglobulin secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of receptor recycling ISS
Inferred from Sequence or Structural Similarity
more info
 
protein-containing complex assembly TAS
Traceable Author Statement
more info
PubMed 
NOT regulation of histamine secretion by mast cell IMP
Inferred from Mutant Phenotype
more info
PubMed 
retrograde transport, endosome to Golgi IDA
Inferred from Direct Assay
more info
PubMed 
substrate adhesion-dependent cell spreading ISS
Inferred from Sequence or Structural Similarity
more info
 
vesicle docking involved in exocytosis TAS
Traceable Author Statement
more info
PubMed 
vesicle-mediated transport ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
SNARE complex IDA
Inferred from Direct Assay
more info
PubMed 
apical plasma membrane IEA
Inferred from Electronic Annotation
more info
 
cell junction IEA
Inferred from Electronic Annotation
more info
 
cell surface IEA
Inferred from Electronic Annotation
more info
 
clathrin-coated vesicle IDA
Inferred from Direct Assay
more info
PubMed 
clathrin-coated vesicle membrane TAS
Traceable Author Statement
more info
 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane TAS
Traceable Author Statement
more info
PubMed 
integral component of synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
PubMed 
neuron projection IEA
Inferred from Electronic Annotation
more info
 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
phagocytic vesicle membrane TAS
Traceable Author Statement
more info
 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
recycling endosome IDA
Inferred from Direct Assay
more info
PubMed 
recycling endosome membrane TAS
Traceable Author Statement
more info
 
secretory granule IEA
Inferred from Electronic Annotation
more info
 
trans-Golgi network membrane TAS
Traceable Author Statement
more info
 
transport vesicle TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
vesicle-associated membrane protein 3
Names
VAMP-3
cellubrevin
synaptobrevin-3

NCBI Reference Sequences (RefSeq)

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)

  1. NM_004781.4NP_004772.1  vesicle-associated membrane protein 3

    See identical proteins and their annotated locations for NP_004772.1

    Status: REVIEWED

    Source sequence(s)
    BC003570, BC005941
    Consensus CDS
    CCDS88.1
    UniProtKB/Swiss-Prot
    Q15836
    UniProtKB/TrEMBL
    Q6FGG2
    Related
    ENSP00000054666.6, ENST00000054666.10
    Conserved Domains (1) summary
    cd15870
    Location:1375
    R-SNARE_VAMP2; SNARE motif of VAMP2

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    7771269..7781432
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002841.2XP_016858330.1  vesicle-associated membrane protein 3 isoform X1

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