Human Gene VAMP8 (ENST00000263864.10_4) from GENCODE V47lift37
  Description: vesicle associated membrane protein 8 (from RefSeq NM_003761.5)
Gencode Transcript: ENST00000263864.10_4
Gencode Gene: ENSG00000118640.11_7
Transcript (Including UTRs)
   Position: hg19 chr2:85,804,709-85,809,154 Size: 4,446 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr2:85,804,770-85,808,839 Size: 4,070 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:85,804,709-85,809,154)mRNA (may differ from genome)Protein (100 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VAMP8_HUMAN
DESCRIPTION: RecName: Full=Vesicle-associated membrane protein 8; Short=VAMP-8; AltName: Full=Endobrevin; Short=EDB;
FUNCTION: Involved in the targeting and/or fusion of transport vesicles to their target membrane. Involved for dense-granule secretion in platelets. Plays a role in regulated enzyme secretion in pancreatic acinar cells. Involved in the abscission of the midbody during cell division, which leads to completely separate daughter cells. Involved in the homotypic fusion of early and late endosomes (By similarity).
SUBUNIT: Found in a number of SNARE complexes with NAPA, SNAP23, SNAP25, STX1A, STX4, STX7, STX8 and VTI1B (By similarity). Interacts with STX8 (By similarity).
SUBCELLULAR LOCATION: Membrane; Single-pass type IV membrane protein (Probable).
TISSUE SPECIFICITY: Platelets.
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

+  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: 124.62 RPKM in Minor Salivary Gland
Total median expression: 1771.39 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 -20.5061-0.336 Picture PostScript Text
3' UTR -104.00315-0.330 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:
81665 - Calcium ATPase, transmembrane domain M
58038 - SNARE fusion complex

ModBase Predicted Comparative 3D Structure on Q9BV40
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000149 SNARE binding
GO:0005484 SNAP receptor activity
GO:0005515 protein binding
GO:0019869 chloride channel inhibitor activity

Biological Process:
GO:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent
GO:0006906 vesicle fusion
GO:0006914 autophagy
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0016240 autophagosome docking
GO:0043312 neutrophil degranulation
GO:0046718 viral entry into host cell
GO:0061024 membrane organization
GO:0070254 mucus secretion
GO:0097352 autophagosome maturation
GO:1903076 regulation of protein localization to plasma membrane
GO:1903531 negative regulation of secretion by cell
GO:1903595 positive regulation of histamine secretion by mast cell
GO:0043308 eosinophil degranulation

Cellular Component:
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005769 early endosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030665 clathrin-coated vesicle membrane
GO:0030667 secretory granule membrane
GO:0030670 phagocytic vesicle membrane
GO:0031201 SNARE complex
GO:0031901 early endosome membrane
GO:0031902 late endosome membrane
GO:0031982 vesicle
GO:0035577 azurophil granule membrane
GO:0035579 specific granule membrane
GO:0048471 perinuclear region of cytoplasm
GO:0055037 recycling endosome
GO:0055038 recycling endosome membrane
GO:0070062 extracellular exosome
GO:0070821 tertiary granule membrane
GO:0098594 mucin granule


-  Descriptions from all associated GenBank mRNAs
  LF207194 - JP 2014500723-A/14697: Polycomb-Associated Non-Coding RNAs.
KM576739 - Homo sapiens clone VAMP8-VAMP5_intrasplicedV3middle-V2 mRNA sequence.
BC001634 - Homo sapiens vesicle-associated membrane protein 8 (endobrevin), mRNA (cDNA clone MGC:1585 IMAGE:3538672), complete cds.
JD061509 - Sequence 42533 from Patent EP1572962.
AF053233 - Homo sapiens endobrevin mRNA, complete cds.
BT006700 - Homo sapiens vesicle-associated membrane protein 8 (endobrevin) mRNA, complete cds.
CR456995 - Homo sapiens full open reading frame cDNA clone RZPDo834E105D for gene VAMP5, vesicle-associated membrane protein 5 (myobrevin); complete cds, incl. stopcodon.
LF363043 - JP 2014500723-A/170546: Polycomb-Associated Non-Coding RNAs.
LF363042 - JP 2014500723-A/170545: Polycomb-Associated Non-Coding RNAs.
KM576738 - Homo sapiens clone VAMP8-VAMP5_V3middle-V2 mRNA sequence.
JD189886 - Sequence 170910 from Patent EP1572962.
JD170043 - Sequence 151067 from Patent EP1572962.
KM576737 - Homo sapiens clone VAMP8-VAMP5_V3middle2-V2 mRNA sequence.
JD063313 - Sequence 44337 from Patent EP1572962.
JD200129 - Sequence 181153 from Patent EP1572962.
JD442089 - Sequence 423113 from Patent EP1572962.
MA598620 - JP 2018138019-A/170546: Polycomb-Associated Non-Coding RNAs.
MA598619 - JP 2018138019-A/170545: Polycomb-Associated Non-Coding RNAs.
MA442771 - JP 2018138019-A/14697: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9BV40 (Reactome details) participates in the following event(s):

R-HSA-376364 Vamp8 associated secretory vesicle to plasma membrane transport
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-6798739 Exocytosis of azurophil granule membrane proteins
R-HSA-6799350 Exocytosis of specific granule membrane proteins
R-HSA-6798747 Exocytosis of tertiary granule membrane proteins
R-HSA-8867613 PICALM binds R-SNAREs
R-HSA-434362 Recruitment Of Cytoplasmic Proteins To Vesicles
R-HSA-421836 trans-Golgi Network Derived Vesicle Uncoating
R-HSA-432688 trans-Golgi Network Derived Lysosomal Vesicle Uncoating
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-421837 Clathrin derived vesicle budding
R-HSA-432722 Golgi Associated Vesicle Biogenesis
R-HSA-432720 Lysosome Vesicle Biogenesis
R-HSA-6798695 Neutrophil degranulation
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-1236974 ER-Phagosome pathway
R-HSA-168249 Innate Immune System
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-199991 Membrane Trafficking
R-HSA-1236975 Antigen processing-Cross presentation
R-HSA-168256 Immune System
R-HSA-5653656 Vesicle-mediated transport
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1280218 Adaptive Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000263864.1, ENST00000263864.2, ENST00000263864.3, ENST00000263864.4, ENST00000263864.5, ENST00000263864.6, ENST00000263864.7, ENST00000263864.8, ENST00000263864.9, NM_003761, O60625, Q53SP9, Q6IB09, Q9BV40, uc317hnb.1, uc317hnb.2, VAMP8 , VAMP8_HUMAN
UCSC ID: ENST00000263864.10_4
RefSeq Accession: NM_003761.5
Protein: Q9BV40 (aka VAMP8_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.