FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Rab3-GEF
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General Information
Symbol
Dmel\Rab3-GEF
Species
D. melanogaster
Name
Rab3 GDP-GTP exchange factor
Annotation Symbol
CG5627
Feature Type
protein_coding_gene
FlyBase ID
FBgn0030613
Gene Model Status
Current
Stock Availability
14 publicly available
Gene Summary
Rab3 GDP-GTP exchange factor (Rab3-GEF) encodes a guanine nucleotide exchange factor (GEF) for the small GTPase encoded by Rab3. They control synaptic development and function, including the regulation of active zone protein composition at the neuromuscular junction. [Date last reviewed: 2018-10-04] (FlyBase Gene Snapshot)
All Summaries
Key Links
Genomic Location
Cytogenetic map
13A10-13A12
Sequence location
Recombination map
1-49
RefSeq locus
NC_004354 REGION:15089682..15113762
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (15 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables guanyl-nucleotide exchange factor activity
inferred from sequence or structural similarity with UniProtKB:Q8WXG6
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN000988808
(GO Reference Genome Project, 2011-)
Biological Process (8 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in cytoskeletal matrix organization at active zone
inferred from mutant phenotype
(Bae et al., 2016)
Terms Based on Predictions or Assertions (7 terms)
CV Term
Evidence
References
involved_in neurotransmitter secretion
non-traceable author statement
(Lloyd et al., 2000)
involved_in positive regulation of MAPK cascade
inferred from sequence or structural similarity with UniProtKB:Q8WXG6
(Gene Ontology Curators, 2002-)
involved_in regulation of apoptotic process
inferred from biological aspect of ancestor with PANTHER:PTN000988808
(GO Reference Genome Project, 2011-)
involved_in regulation of cell cycle
inferred from sequence or structural similarity with UniProtKB:Q8WXG6
(Gene Ontology Curators, 2002-)
involved_in regulation of extrinsic apoptotic signaling pathway via death domain receptors
inferred from sequence or structural similarity with UniProtKB:Q8WXG6
(Gene Ontology Curators, 2002-)
involved_in regulation of Rab protein signal transduction
inferred from sequence or structural similarity with UniProtKB:Q8WXG6
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN000988808
(GO Reference Genome Project, 2011-)
involved_in vesicle-mediated transport
non-traceable author statement
(Lloyd et al., 2000)
Cellular Component (6 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
located_in neuromuscular junction of somatic muscle
inferred from direct assay
(Bae et al., 2016)
located_in neuronal cell body
inferred from direct assay
(Bae et al., 2016)
located_in terminal bouton
inferred from direct assay
(Bae et al., 2016)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
is_active_in cytosol
inferred from biological aspect of ancestor with PANTHER:PTN000988808
(GO Reference Genome Project, 2011-)
located_in membrane
inferred from sequence or structural similarity with UniProtKB:Q8WXG6
(Gene Ontology Curators, 2002-)
located_in synaptic vesicle
non-traceable author statement
(Lloyd et al., 2000)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the MADD family. (Q9VXY2)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Rab3 GDP-GTP exchange factor (Rab3-GEF) encodes a guanine nucleotide exchange factor (GEF) for the small GTPase encoded by Rab3. They control synaptic development and function, including the regulation of active zone protein composition at the neuromuscular junction. [Date last reviewed: 2018-10-04]
Gene Group (FlyBase)
RAB GUANINE NUCLEOTIDE EXCHANGE FACTORS - DENN DOMAIN -
DENN domain-containing proteins are Guanine Nucleotide Exchange Factors (GEFs) for Rab family GTPases. (Adapted from FBrf0220596).
Protein Function (UniProtKB)
Guanyl-nucleotide exchange factor that regulates small GTPases (By similarity). Converts GDP-bound inactive form of Rab3 to the GTP-bound active forms (By similarity).
(UniProt, Q9VXY2)
Gene Model and Products
Number of Transcripts
10
Number of Unique Polypeptides
10

Please see the JBrowse view of Dmel\Rab3-GEF 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
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VXY2)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 6.02

Gene model reviewed during 5.54

Stop-codon suppression (UGA) postulated; FBrf0216884.

Gene model reviewed during 5.44

Gene model reviewed during 5.52

Gene model reviewed during 6.13

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Rab3-GEF-RC
FBtr0307207
NM_132773
8252
2084
Rab3-GEF-RD
FBtr0307208
NM_001258746
8390
2130
Rab3-GEF-RE
FBtr0307209
NM_001103513
8372
2124
Rab3-GEF-RF
FBtr0307210
NM_001258747
5820
1822
Rab3-GEF-RG
FBtr0330400
NM_001272630
8459
1819
Rab3-GEF-RH
FBtr0330401
NM_001272631
8285
2154
Rab3-GEF-RI
FBtr0346798
NM_001316635
8285
2095
Rab3-GEF-RJ
FBtr0452146
NM_001347809
8363
2115
Rab3-GEF-RK
FBtr0452147
NM_001347810
8459
2147
Rab3-GEF-RL
FBtr0452148
NM_001347811
6000
1882
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Rab3-GEF-PC
FBpp0298036
226.1
2084
9.53
Q9VXY2
NP_573001
AAF48424
Rab3-GEF-PD
FBpp0298037
231.0
2130
9.38
M9NGF2
NP_001245675
AFH07389
Rab3-GEF-PE
FBpp0298038
230.1
2124
9.44
A8JUX2
NP_001096983
ABW09415
Rab3-GEF-PF
FBpp0298039
199.4
1822
8.52
M9NEH3
NP_001245676
AFH07390
Rab3-GEF-PG
FBpp0303426
199.0
1819
8.64
M9PJN3
NP_001259559
AGB95401
Rab3-GEF-PH
FBpp0303427
232.8
2154
9.50
M9PEM6
NP_001259560
AGB95402
Rab3-GEF-PI
FBpp0312376
227.2
2095
9.45
A0A0S0X7U5
NP_001303564
ALI51150
Rab3-GEF-PJ
FBpp0402896
229.6
2115
9.25
NP_001334679
API61812
Rab3-GEF-PK
FBpp0402897
232.8
2147
9.16
NP_001334680
API61813
Rab3-GEF-PL
FBpp0402898
205.7
1882
8.09
NP_001334681
API61814
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
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\Rab3-GEF using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.74

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
third instar larval stage
larval ventral nerve cord
(Bae et al., 2016)
larval brain
(Bae et al., 2016)
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in neuromuscular junction of somatic muscle
inferred from direct assay
(Bae et al., 2016)
located_in neuronal cell body
inferred from direct assay
(Bae et al., 2016)
located_in terminal bouton
inferred from direct assay
(Bae et al., 2016)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Rab3-GEF in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 13 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Rab3-GEF
Transgenic constructs containing regulatory region of Rab3-GEF
Aberrations (Deficiencies and Duplications) ( 3 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (8)
Hsap\MADD
13 of 14
Yes
Yes
2  
Hsap\DENND1A
1 of 14
No
No
1  
Hsap\DENND1B
1 of 14
No
No
Hsap\DENND1C
1 of 14
No
No
Hsap\DENND2A
1 of 14
No
No
Hsap\DENND2B
1 of 14
No
No
Hsap\DENND2C
1 of 14
No
No
Hsap\DENND2D
1 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (8)
Rnor\Madd
13 of 14
Yes
Yes
Rnor\Dennd1a
1 of 14
No
No
Rnor\Dennd1b
1 of 14
No
No
Rnor\Dennd1c
1 of 14
No
No
Rnor\Dennd2a
1 of 14
No
No
Rnor\Dennd2b
1 of 14
No
Yes
Rnor\Dennd2c
1 of 14
No
No
Rnor\Dennd2d
1 of 14
No
No
Mus musculus (laboratory mouse) (8)
Mmus\Madd
12 of 14
Yes
Yes
Mmus\Denn2b
1 of 14
No
No
Mmus\Dennd1a
1 of 14
No
No
Mmus\Dennd1b
1 of 14
No
No
Mmus\Dennd1c
1 of 14
No
No
Mmus\Dennd2a
1 of 14
No
No
Mmus\Dennd2c
1 of 14
No
No
Mmus\Dennd2d
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (2)
Xtro\madd
10 of 13
Yes
Yes
Xtro\dennd2c
1 of 13
No
Yes
Danio rerio (Zebrafish) (8)
Drer\madd
13 of 14
Yes
Yes
Drer\dennd1a
1 of 14
No
No
Drer\dennd1b
1 of 14
No
No
Drer\dennd1c
1 of 14
No
No
Drer\dennd2b
1 of 14
No
Yes
Drer\dennd2c
1 of 14
No
No
Drer\dennd2da
1 of 14
No
Yes
Drer\dennd2db
1 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\aex-3
12 of 14
Yes
Yes
Cele\rme-4
1 of 14
No
No
Anopheles gambiae (African malaria mosquito) (3)
Agam\AgaP_AGAP000630
12 of 12
Yes
Yes
Agam\AgaP_AGAP005212
1 of 12
No
No
Agam\AgaP_AGAP009774
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (0)
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Rab3-GEF. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (1)
CG18659
1 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 4 )
    Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    MADD; MAP kinase activating death domain
    13 of 14
    603584
       
      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
      Interaction Browsers
      View in FlyBase Interactions Browser   View in MIST tool (external link)
      Please see the Physical Interaction reports below for full details
      protein-protein
      Physical Interaction
      Assay
      References
      Rab3-GEF - Drep2
      anti tag coimmunoprecipitation, peptide massfingerprinting
      (Andlauer et al., 2014)
      Summary of Genetic Interactions
      Interaction Browsers
      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.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      FlyBase
      External Links
      External Data
      Linkouts
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Class of Gene
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      X
      Recombination map
      1-49
      Cytogenetic map
      13A10-13A12
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      13A10-13A12
      ; Limits computationally determined from genome sequence between P{EP}hiwEP1308 and P{EP}Ahcy13EP1007
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      13A-13B
      (Lloyd et al., 2000)
      Determined by comparing Celera genomic sequence with sequence from BDGP BAC and P1 clones.
      (Lloyd et al., 2000)
      Experimentally Determined Recombination Data
      Location

      1-49

      (FlyBase, 2016)

      1-49.9

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (14)
      Genomic Clones (11)
       

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

      cDNA Clones (44)
       

      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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

      cDNA clones, fully sequenced
      BDGP DGC clones
      Other 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
      Other clones
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      Antibody Information
      Laboratory Generated Antibodies
       

      polyclonal

      (Bae et al., 2016)
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          Other Comments

          dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.

          (Kiger et al., 2003)
          Relationship to Other Genes
          Source for database merge of

          Source for merge of: rab3-GEF anon- EST:Posey246

          (Ashburner, 2004.6.30)

          Source for merge of: rab3-GEF BEST:GH21304

          (Rana, 2004.7.8)
          Additional comments
          Nomenclature History
          Source for database identify of

          Source for identity of: rab3-GEF CG5627

          (Verstreken and Bellen, 2000.9.4)

          Source for identity of: Rab3-GEF rab3-GEF

          (FlyBase, 2009-)
          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (7)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 101 )
          Sequence 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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
          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
          AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
          DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
          EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
          FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
          FlyMine - An integrated database for Drosophila genomics
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          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.
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
          Flygut - An atlas of the Drosophila adult midgut
          FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          MIST (protein-protein) - An integrated Molecular Interaction Database
          Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
          References (65)