Mouse Gene Vamp1 (ENSMUST00000032487.13) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus vesicle-associated membrane protein 1 (Vamp1), transcript variant 1, mRNA. (from RefSeq NM_009496)
Gencode Transcript: ENSMUST00000032487.13
Gencode Gene: ENSMUSG00000030337.16
Transcript (Including UTRs)
   Position: mm10 chr6:125,215,551-125,222,306 Size: 6,756 Total Exon Count: 5 Strand: +
Coding Region
   Position: mm10 chr6:125,215,726-125,220,066 Size: 4,341 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:125,215,551-125,222,306)mRNA (may differ from genome)Protein (118 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: VAMP1_MOUSE
DESCRIPTION: RecName: Full=Vesicle-associated membrane protein 1; Short=VAMP-1; AltName: Full=Synaptobrevin-1;
FUNCTION: Involved in the targeting and/or fusion of transport vesicles to their target membrane.
SUBUNIT: Interacts with VAPA and VAPB (By similarity).
SUBCELLULAR LOCATION: Isoform 1: Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Single-pass type IV membrane protein (By similarity). Cell junction, synapse, synaptosome (By similarity).
SUBCELLULAR LOCATION: Isoform 2: Cytoplasmic vesicle membrane; Single-pass type IV membrane protein (By similarity). Cell junction, synapse, synaptosome (By similarity).
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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -51.70175-0.295 Picture PostScript Text
3' UTR -766.202240-0.342 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

ModBase Predicted Comparative 3D Structure on Q62442
FrontTopSide
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
 RGDEnsembl   
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005484 SNAP receptor activity
GO:0019905 syntaxin binding

Biological Process:
GO:0006887 exocytosis
GO:0016192 vesicle-mediated transport
GO:0035493 SNARE complex assembly

Cellular Component:
GO:0005739 mitochondrion
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030659 cytoplasmic vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0031201 SNARE complex
GO:0031410 cytoplasmic vesicle
GO:0035579 specific granule membrane
GO:0043005 neuron projection
GO:0045202 synapse
GO:0070821 tertiary granule membrane


-  Descriptions from all associated GenBank mRNAs
  AK018783 - Mus musculus adult male cerebellum cDNA, RIKEN full-length enriched library, clone:1500035D08 product:vesicle-associated membrane protein 1, full insert sequence.
AK037711 - Mus musculus 16 days neonate thymus cDNA, RIKEN full-length enriched library, clone:A130039J07 product:vesicle-associated membrane protein 1, full insert sequence.
AK078156 - Mus musculus adult male medulla oblongata cDNA, RIKEN full-length enriched library, clone:6330583M24 product:vesicle-associated membrane protein 1, full insert sequence.
AK013893 - Mus musculus 12 days embryo head cDNA, RIKEN full-length enriched library, clone:3010005E14 product:vesicle-associated membrane protein 1, full insert sequence.
BC057587 - Mus musculus vesicle-associated membrane protein 1, mRNA (cDNA clone MGC:67110 IMAGE:6415847), complete cds.
BC049902 - Mus musculus vesicle-associated membrane protein 1, mRNA (cDNA clone MGC:54750 IMAGE:4500872), complete cds.
U61751 - Mus musculus vesicle-associated membrane protein VAMP-1 mRNA, complete cds.
AF007167 - Mus musculus vesicle associated membrane protein 1 (mVAMP-1) mRNA, complete cds.
X83886 - M.musculus thymus-specific mRNA (275 bp).

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu04130 - SNARE interactions in vesicular transport

-  Other Names for This Gene
  Alternate Gene Symbols: NM_009496, Q62442, Q6PFF3, Q810K6, Syb1, uc009dtx.1, uc009dtx.2, VAMP1_MOUSE
UCSC ID: uc009dtx.2
RefSeq Accession: NM_009496
Protein: Q62442 (aka VAMP1_MOUSE)
CCDS: CCDS20546.1, CCDS39637.1

-  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.