General Information
Symbol
Dmel\Syb
Species
D. melanogaster
Name
Synaptobrevin
Annotation Symbol
CG12210
Feature Type
FlyBase ID
FBgn0003660
Gene Model Status
Stock Availability
Gene Snapshot
In progress.Contributions welcome.
Also Known As
VAMP
Genomic Location
Cytogenetic map
Sequence location
2R:10,249,435..10,252,417 [-]
Recombination map
2-62
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
Belongs to the synaptobrevin family. (P18489)
Protein Domains/Motifs
Molecular Function (see GO section for details)
Experimental Evidence
-
Predictions / Assertions
Summaries
Gene Group Membership
R-SNAREs -
R-SNAREs are members of the SNARE (soluble N-ethylmaleimide-sensitive factor-attachment protein (SNAP) receptor) family that mediate vesicle-fusion. SNAREs are cytoplasmic, membrane-anchored proteins that contain a 60 amino acid SNARE domain. Three Q-SNAREs domains from the target membrane and one R-SNARE domain from the vesicle interact to form a four-helix bundle that pulls the two membranes in close proximity and promotes fusion. After fusion, the complexes are dissembled by NSF (N-ethylmaleimide-sensitive factor) and SNAPs (Soluble NSF Attachment Proteins). R-SNAREs are named from their contribution of a conserved arginine (R) residue to the helix bundle. (Adapted from PMID:15893389 and FBrf0216182).
UniProt Contributed Function Data
Unknown, but synaptobrevins are presumed to be involved in targeting and fusion of synaptic vesicles with the presynaptic membrane as well as in neurotransmitter release.
(UniProt, P18489)
Phenotypic Description from the Red Book (Lindsley and Zimm 1992)
Syb: Synaptobrevin
Encodes a 20 kd polypeptide that is recognized by antibodies to rat synaptobrevin. Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles from mammalian brain; it is highly homologous to Torpedo VAMP-1. Signal from Drosophila heads exceeds that from rat brain suggesting that it is an abundant protein in flies.
Gene Model and Products
Number of Transcripts
5
Number of Unique Polypeptides
4

Please see the GBrowse view of Dmel\Syb or the JBrowse view of Dmel\Syb for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model
Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.
Gene model reviewed during 5.49
Low-frequency RNA-Seq exon junction(s) not annotated.
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0088362
852
129
FBtr0088363
1139
132
FBtr0273274
921
152
FBtr0273275
1070
109
FBtr0339455
814
129
Additional Transcript Data and Comments
Reported size (kB)
0.9, 0.85 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0087450
14.1
129
7.56
FBpp0087451
14.9
132
5.90
FBpp0271782
16.7
152
6.54
FBpp0271783
12.2
109
6.84
FBpp0308541
14.1
129
7.56
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

129 aa isoforms: Syb-PA, Syb-PE
Additional Polypeptide Data and Comments
Reported size (kDa)
152, 132 (aa)
152 (aa); 20 (kD observed); 16.585 (kD predicted)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Syb using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (7 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from sequence or structural similarity
non-traceable author statement
Biological Process (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
non-traceable author statement
inferred from sequence or structural similarity
inferred from electronic annotation with InterPro:IPR001388
(assigned by InterPro )
non-traceable author statement
inferred from sequence or structural similarity
Cellular Component (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR001388
(assigned by InterPro )
non-traceable author statement
non-traceable author statement
inferred from sequence or structural similarity
Expression Data
Transcript Expression
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Syb in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 9 )
Transgenic Constructs ( 9 )
Deletions and Duplications ( 13 )
Summary of Phenotypes
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (11)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
10 of 15
Yes
Yes
 
10 of 15
Yes
No
 
8 of 15
No
Yes
 
5 of 15
No
Yes
4 of 15
No
Yes
2 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (10)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
9 of 15
Yes
No
8 of 15
No
Yes
8 of 15
No
Yes
5 of 15
No
Yes
4 of 15
No
Yes
2 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (10)
8 of 13
Yes
No
7 of 13
No
No
7 of 13
No
Yes
4 of 13
No
Yes
2 of 13
No
Yes
2 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (6)
6 of 12
Yes
Yes
5 of 12
No
No
5 of 12
No
No
4 of 12
No
Yes
1 of 12
No
No
1 of 12
No
Yes
Danio rerio (Zebrafish) (13)
10 of 15
Yes
Yes
10 of 15
Yes
No
8 of 15
No
Yes
7 of 15
No
Yes
4 of 15
No
Yes
3 of 15
No
Yes
2 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (10)
11 of 15
Yes
Yes
4 of 15
No
Yes
4 of 15
No
Yes
3 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (14)
1 of 9
Yes
No
1 of 9
Yes
No
1 of 9
Yes
No
1 of 9
Yes
No
1 of 9
Yes
No
1 of 9
Yes
No
1 of 9
Yes
No
1 of 9
Yes
No
1 of 9
Yes
No
1 of 9
Yes
No
1 of 9
Yes
No
1 of 9
Yes
No
1 of 9
Yes
Yes
1 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (4)
9 of 15
Yes
Yes
8 of 15
No
Yes
3 of 15
No
Yes
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
6 of 12
Yes
Yes
1 of 12
No
No
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190J6J )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150HUN )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Mayetiola destructor
Hessian fly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0P1H )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bombyx mori
Silkmoth
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0NPK )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0MPE )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Human Disease Model Data
FlyBase Human Disease Model Reports
    Alleles Reported to Model Human Disease (Disease Ontology)
    Download
    Models ( 0 )
    Allele
    Disease
    Evidence
    References
    Interactions ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments ( 0 )
     
    Human Orthologs (via DIOPT v7.1)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please look at the Interaction Group reports for full details of the physical interactions
    protein-protein
    Interacting group
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    Pathways
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map
    2-62
    Cytogenetic map
    Sequence location
    2R:10,249,435..10,252,417 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    46F8-46F8
    Limits computationally determined from genome sequence between P{lacW}Hr46k10308 and P{PZ}lola00349&P{EP}lolaEP952
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    46F9-46F10
    (determined by in situ hybridisation)
    46E-46F
    (determined by in situ hybridisation)
    Complementation data from unspecified deficiency chromosomes.
    Determined by comparing Celera genomic sequence with sequence from BDGP BAC and P1 clones.
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (11)
    Genomic Clones (3)
     

    Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

    cDNA Clones (55)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequences
    BDGP DGC clones
    Drosophila Genomics Resource Center cDNA clones

    For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

    cDNA Clones, End Sequenced (ESTs)
    BDGP DGC clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    Antibody Information
    Laboratory Generated Antibodies
     
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for database merge of
    Source for merge of: Syb l(2)46El
    Source for merge of: Syb l(2)46CFq
    Additional comments
    Other Comments
    The Syb gene product is essential for transmission and is required for calcium-dependent vesicle fusion.
    Syb gene comprises 5 exons, alternative splicing generates 2 transcripts, the ratio of these transcripts is highly regulated during development. Syb expression pattern suggests Syb may have a general role in membrane trafficking and perhaps a role in the secretion of digestive enzymes.
    Complementation group identified in an EMS and DEB screen to isolate deficiencies that uncover Jra.
    Initial characterisation of the Syb gene function reveals that overexpression of a cytosolic form of Syb is lethal.
    Identification: First isolated from a Drosophila cDNA library using a bovine cDNA probe.
    Encodes a 20kD polypeptide that is recognized by antibodies to rat synaptobrevin.
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 56 )
    Crossreferences
    NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
    GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
    GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
    RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
    UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
    UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
    Other crossreferences
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    InterPro - A database of protein families, domains and functional sites
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
    DPiM - Drosophila Protein interaction map
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Flygut - An atlas of the Drosophila adult midgut
    FlyMine - An integrated database for Drosophila genomics
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Synonyms and Secondary IDs (19)
    Reported As
    Symbol Synonym
    l(2)46CFq
    l(2)46El
    synaptobrevin
    Secondary FlyBase IDs
    • FBgn0005620
    • FBgn0019711
    • FBgn0023032
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (144)