Human Gene VAMP2 (ENST00000316509.11_13) from GENCODE V47lift37
  Description: vesicle associated membrane protein 2, transcript variant 1 (from RefSeq NM_014232.3)
Gencode Transcript: ENST00000316509.11_13
Gencode Gene: ENSG00000220205.10_17
Transcript (Including UTRs)
   Position: hg19 chr17:8,062,467-8,066,266 Size: 3,800 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr17:8,064,173-8,066,197 Size: 2,025 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:8,062,467-8,066,266)mRNA (may differ from genome)Protein (116 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
ReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VAMP2_HUMAN
DESCRIPTION: RecName: Full=Vesicle-associated membrane protein 2; Short=VAMP-2; AltName: Full=Synaptobrevin-2;
FUNCTION: Involved in the targeting and/or fusion of transport vesicles to their target membrane.
SUBUNIT: Part of the SNARE core complex containing SNAP25, VAMP2 and STX1A. This complex binds to CPLX1. Interacts with BVES and STX4 (By similarity). Interacts with VAPA and VAPB.
INTERACTION: O55012:Picalm (xeno); NbExp=2; IntAct=EBI-520113, EBI-915601; O94806:PRKD3; NbExp=7; IntAct=EBI-520113, EBI-1255366;
SUBCELLULAR LOCATION: Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Single-pass type IV membrane protein. Cell junction, synapse, synaptosome. Note=Neuronal synaptic vesicles.
TISSUE SPECIFICITY: Nervous system and skeletal muscle.
SIMILARITY: Belongs to the synaptobrevin family.
SIMILARITY: Contains 1 v-SNARE coiled-coil homology domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: VAMP2
Diseases sorted by gene-association score: tetanus (21), infant botulism (2), primary bacterial infectious disease (2), attention deficit-hyperactivity disorder (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.00 RPKM in (null)
Total median expression: 0.00 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -15.5069-0.225 Picture PostScript Text
3' UTR -530.101706-0.311 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001388 - Synaptobrevin
IPR016444 - Synaptobrevin_met/fun

Pfam Domains:
PF00957 - Synaptobrevin

SCOP Domains:
58038 - SNARE fusion complex
57997 - Tropomyosin

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3FIE - X-ray 3FII - X-ray 3RK2 - X-ray MuPIT 3RK3 - X-ray MuPIT 3RL0 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P63027
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000149 SNARE binding
GO:0005484 SNAP receptor activity
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0005543 phospholipid binding
GO:0017075 syntaxin-1 binding
GO:0019905 syntaxin binding
GO:0043621 protein self-association
GO:0048306 calcium-dependent protein binding

Biological Process:
GO:0006887 exocytosis
GO:0006906 vesicle fusion
GO:0009749 response to glucose
GO:0014047 glutamate secretion
GO:0015031 protein transport
GO:0016079 synaptic vesicle exocytosis
GO:0016192 vesicle-mediated transport
GO:0017156 calcium ion regulated exocytosis
GO:0017157 regulation of exocytosis
GO:0032869 cellular response to insulin stimulus
GO:0043001 Golgi to plasma membrane protein transport
GO:0043308 eosinophil degranulation
GO:0060291 long-term synaptic potentiation
GO:0060627 regulation of vesicle-mediated transport
GO:0061024 membrane organization
GO:0061025 membrane fusion
GO:0065003 macromolecular complex assembly
GO:0090316 positive regulation of intracellular protein transport
GO:1902259 regulation of delayed rectifier potassium channel activity
GO:0043312 neutrophil degranulation
GO:0043320 natural killer cell degranulation
GO:0070254 mucus secretion
GO:1903593 regulation of histamine secretion by mast cell

Cellular Component:
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030136 clathrin-coated vesicle
GO:0030141 secretory granule
GO:0030665 clathrin-coated vesicle membrane
GO:0030667 secretory granule membrane
GO:0030672 synaptic vesicle membrane
GO:0031201 SNARE complex
GO:0031410 cytoplasmic vesicle
GO:0031982 vesicle
GO:0042589 zymogen granule membrane
GO:0043005 neuron projection
GO:0043231 intracellular membrane-bounded organelle
GO:0044306 neuron projection terminus
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm
GO:0060203 clathrin-sculpted glutamate transport vesicle membrane
GO:0061202 clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane
GO:0070032 synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex
GO:0070033 synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex
GO:0070044 synaptobrevin 2-SNAP-25-syntaxin-1a complex
GO:0070083 clathrin-sculpted monoamine transport vesicle membrane
GO:0008076 voltage-gated potassium channel complex


-  Descriptions from all associated GenBank mRNAs
  LF209120 - JP 2014500723-A/16623: Polycomb-Associated Non-Coding RNAs.
JD305573 - Sequence 286597 from Patent EP1572962.
AL050223 - Homo sapiens mRNA; cDNA DKFZp586L1323 (from clone DKFZp586L1323).
LF326295 - JP 2014500723-A/133798: Polycomb-Associated Non-Coding RNAs.
JD176104 - Sequence 157128 from Patent EP1572962.
JD339600 - Sequence 320624 from Patent EP1572962.
JD283471 - Sequence 264495 from Patent EP1572962.
LF326294 - JP 2014500723-A/133797: Polycomb-Associated Non-Coding RNAs.
JD269490 - Sequence 250514 from Patent EP1572962.
JD219872 - Sequence 200896 from Patent EP1572962.
LF326293 - JP 2014500723-A/133796: Polycomb-Associated Non-Coding RNAs.
JD234511 - Sequence 215535 from Patent EP1572962.
JD278813 - Sequence 259837 from Patent EP1572962.
JD353549 - Sequence 334573 from Patent EP1572962.
JD240933 - Sequence 221957 from Patent EP1572962.
JD292494 - Sequence 273518 from Patent EP1572962.
JD429566 - Sequence 410590 from Patent EP1572962.
JD099967 - Sequence 80991 from Patent EP1572962.
JD452150 - Sequence 433174 from Patent EP1572962.
BC002737 - Homo sapiens vesicle-associated membrane protein 2 (synaptobrevin 2), mRNA (cDNA clone MGC:3377 IMAGE:3628842), complete cds.
BC019608 - Homo sapiens vesicle-associated membrane protein 2 (synaptobrevin 2), mRNA (cDNA clone MGC:24865 IMAGE:4508990), complete cds.
BC033870 - Homo sapiens vesicle-associated membrane protein 2 (synaptobrevin 2), mRNA (cDNA clone MGC:45137 IMAGE:5203115), complete cds.
AK021522 - Homo sapiens cDNA FLJ11460 fis, clone HEMBA1001569, highly similar to SYNAPTOBREVIN 2.
AK225777 - Homo sapiens mRNA for vesicle-associated membrane protein 2 variant, clone: FCC132D12.
JD477702 - Sequence 458726 from Patent EP1572962.
JD541758 - Sequence 522782 from Patent EP1572962.
JD366065 - Sequence 347089 from Patent EP1572962.
JD519496 - Sequence 500520 from Patent EP1572962.
LF326292 - JP 2014500723-A/133795: Polycomb-Associated Non-Coding RNAs.
JD127255 - Sequence 108279 from Patent EP1572962.
JD556029 - Sequence 537053 from Patent EP1572962.
JD254905 - Sequence 235929 from Patent EP1572962.
JD555724 - Sequence 536748 from Patent EP1572962.
JD503389 - Sequence 484413 from Patent EP1572962.
LF326291 - JP 2014500723-A/133794: Polycomb-Associated Non-Coding RNAs.
AK289555 - Homo sapiens cDNA FLJ76510 complete cds, highly similar to Homo sapiens vesicle-associated membrane protein 2 (synaptobrevin 2), mRNA.
LF326290 - JP 2014500723-A/133793: Polycomb-Associated Non-Coding RNAs.
JD459361 - Sequence 440385 from Patent EP1572962.
JD306491 - Sequence 287515 from Patent EP1572962.
JD120739 - Sequence 101763 from Patent EP1572962.
JD440633 - Sequence 421657 from Patent EP1572962.
JD192681 - Sequence 173705 from Patent EP1572962.
HQ448696 - Synthetic construct Homo sapiens clone IMAGE:100072140; CCSB004137_02 vesicle-associated membrane protein 2 (synaptobrevin 2) (VAMP2) gene, encodes complete protein.
KJ892235 - Synthetic construct Homo sapiens clone ccsbBroadEn_01629 VAMP2 gene, encodes complete protein.
AJ225044 - Homo sapiens mRNA for vesicle associated membrane protein 2 (VAMP2).
AB464344 - Synthetic construct DNA, clone: pF1KB6771, Homo sapiens VAMP2 gene for vesicle-associated membrane protein 2, without stop codon, in Flexi system.
LF326289 - JP 2014500723-A/133792: Polycomb-Associated Non-Coding RNAs.
JD114232 - Sequence 95256 from Patent EP1572962.
MA561872 - JP 2018138019-A/133798: Polycomb-Associated Non-Coding RNAs.
MA561871 - JP 2018138019-A/133797: Polycomb-Associated Non-Coding RNAs.
MA561870 - JP 2018138019-A/133796: Polycomb-Associated Non-Coding RNAs.
MA561869 - JP 2018138019-A/133795: Polycomb-Associated Non-Coding RNAs.
MA561868 - JP 2018138019-A/133794: Polycomb-Associated Non-Coding RNAs.
MA561867 - JP 2018138019-A/133793: Polycomb-Associated Non-Coding RNAs.
MA561866 - JP 2018138019-A/133792: Polycomb-Associated Non-Coding RNAs.
MA444697 - JP 2018138019-A/16623: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_botulinPathway - Blockade of Neurotransmitter Relase by Botulinum Toxin

Reactome (by CSHL, EBI, and GO)

Protein P63027 (Reactome details) participates in the following event(s):

R-HSA-194796 BoNT/B LC cleaves target cell VAMP2
R-HSA-5228578 TeNT LC cleaves target cell VAMP2
R-HSA-5250606 BoNT/D LC cleaves target cell VAMP2
R-HSA-5250892 BoNT/F LC cleaves target cell VAMP2
R-HSA-5250962 BoNT/G LC cleaves target cell VAMP2
R-HSA-376369 Vamp2 associated secretory vesicle to plasma membrane transport
R-HSA-264615 Loading of acetylcholine in synaptic vesicle
R-HSA-372505 Acetylcholine synaptic vesicle docking and priming
R-HSA-210430 release of L-Glutamate at the synapse
R-HSA-372529 Release of acetylcholine at the synapse
R-HSA-374899 Release of noradrenaline at the synapse
R-HSA-380869 Release of docked dopamine loaded synaptic vesicle
R-HSA-380901 Release of docked serotonin loaded synaptic vesicle
R-HSA-888589 Release of GABA at the synapse
R-HSA-8867613 PICALM binds R-SNAREs
R-HSA-210426 Glutamate synaptic vesicle docking and priming
R-HSA-210444 L-Glutamate loading of synaptic vesicle
R-HSA-421833 Vamp And trans-Golgi Network AP-1 Binding Coupled With Cargo Capture
R-HSA-432712 Vamp And trans-Golgi Network AP-1 Binding Coupled With Cargo Capture On Lysosome Vesicle Destined Golgi Membrane
R-HSA-434362 Recruitment Of Cytoplasmic Proteins To Vesicles
R-HSA-421836 trans-Golgi Network Derived Vesicle Uncoating
R-HSA-374922 Noradrenalin synaptic vesicle docking and priming
R-HSA-380574 Dopamine synaptic vesicle docking and priming
R-HSA-380905 Serotonin loaded synaptic vesicle docking and priming
R-HSA-432688 trans-Golgi Network Derived Lysosomal Vesicle Uncoating
R-HSA-917744 GABA loaded synaptic vesicle Docking and Priming
R-HSA-421831 trans-Golgi Network Coat Assembly
R-HSA-432706 trans-Golgi Network Lysosome Vesicle Destined Membrane Coat Assembly
R-HSA-421835 trans-Golgi Network Vesicle Scission
R-HSA-432707 trans-Golgi Network Lysosomal Vesicle Scission
R-HSA-8867756 CLASP proteins and cargo are recruited to the nascent clathrin-coated pit
R-HSA-8868071 Clathrin recruits PIK3C2A
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8867754 F- and N- BAR domain proteins bind the clathrin-coated pit
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-8868072 Clathrin-associated PIK3C2A phosphorylates PI(4)P to PI(3,4)P2
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-5250958 Toxicity of botulinum toxin type B (BoNT/B)
R-HSA-5250982 Toxicity of tetanus toxin (TeNT)
R-HSA-5250955 Toxicity of botulinum toxin type D (BoNT/D)
R-HSA-5250981 Toxicity of botulinum toxin type F (BoNT/F)
R-HSA-5250989 Toxicity of botulinum toxin type G (BoNT/G)
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-422356 Regulation of insulin secretion
R-HSA-1445148 Translocation of GLUT4 to the plasma membrane
R-HSA-168799 Neurotoxicity of clostridium toxins
R-HSA-264642 Acetylcholine Neurotransmitter Release Cycle
R-HSA-210500 Glutamate Neurotransmitter Release Cycle
R-HSA-181430 Norepinephrine Neurotransmitter Release Cycle
R-HSA-212676 Dopamine Neurotransmitter Release Cycle
R-HSA-181429 Serotonin Neurotransmitter Release Cycle
R-HSA-888590 GABA synthesis, release, reuptake and degradation
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-163685 Energy Metabolism
R-HSA-432722 Golgi Associated Vesicle Biogenesis
R-HSA-432720 Lysosome Vesicle Biogenesis
R-HSA-199991 Membrane Trafficking
R-HSA-5339562 Uptake and actions of bacterial toxins
R-HSA-112310 Neurotransmitter release cycle
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-264876 Insulin processing
R-HSA-1430728 Metabolism
R-HSA-5653656 Vesicle-mediated transport
R-HSA-5663205 Infectious disease
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-2980736 Peptide hormone metabolism
R-HSA-1643685 Disease
R-HSA-112316 Neuronal System
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000316509.1, ENST00000316509.10, ENST00000316509.2, ENST00000316509.3, ENST00000316509.4, ENST00000316509.5, ENST00000316509.6, ENST00000316509.7, ENST00000316509.8, ENST00000316509.9, NM_014232, P19065, P63027, Q9BUC2, SYB2, uc317qap.1, uc317qap.2, VAMP2 , VAMP2_HUMAN
UCSC ID: ENST00000316509.11_13
RefSeq Accession: NM_014232.3
Protein: P63027 (aka VAMP2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.