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General Information
Symbol
Dmel\PDZ-GEF
Species
D. melanogaster
Name
PDZ domain-containing guanine nucleotide exchange factor
Annotation Symbol
CG9491
Feature Type
FlyBase ID
FBgn0265778
Gene Model Status
Stock Availability
Gene Summary
PDZ domain-containing guanine nucleotide exchange factor (PDZ-GEF) encodes a guanine nucleotide exchange factor for the product of Rap1. The product of PDZ-GEF contributes to ventral furrow formation, border cell migration, macrophage migration, epithelial migration and morphogenesis, eye development, ovary development, spermathecae formation, germline stem cell maintenance in the testis, adherens junction formation, and anchorage of stem cells to niche. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
Also Known As

Gef26, dizzy, dPDZ-GEF, l(2)k13720, GEF

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
2-19
RefSeq locus
NT_033779 REGION:6323767..6332789
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (22 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from physical interaction with FLYBASE:Rap1; FB:FBgn0004636
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN007734601
(assigned by GO_Central )
inferred from sequence or structural similarity with HGNC:16854
Biological Process (16 terms)
Terms Based on Experimental Evidence (14 terms)
CV Term
Evidence
References
inferred from genetic interaction with FLYBASE:Rap1; FB:FBgn0004636
inferred from mutant phenotype
inferred from mutant phenotype
involved_in hemocyte migration
inferred from mutant phenotype
inferred from mutant phenotype
involved_in MAPK cascade
inferred from genetic interaction with FLYBASE:Raf; FB:FBgn0003079
inferred from genetic interaction with FLYBASE:rl; FB:FBgn0003256
inferred from genetic interaction with FLYBASE:Dsor1; FB:FBgn0010269
involved_in oogenesis
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN007734601
(assigned by GO_Central )
inferred from sequence or structural similarity with HGNC:16854
inferred from biological aspect of ancestor with PANTHER:PTN007734601
(assigned by GO_Central )
Cellular Component (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
colocalizes_with adherens junction
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN001896698
(assigned by GO_Central )
is_active_in plasma membrane
inferred from biological aspect of ancestor with PANTHER:PTN007734601
(assigned by GO_Central )
Protein Family (UniProt)
-
Summaries
Gene Snapshot
PDZ domain-containing guanine nucleotide exchange factor (PDZ-GEF) encodes a guanine nucleotide exchange factor for the product of Rap1. The product of PDZ-GEF contributes to ventral furrow formation, border cell migration, macrophage migration, epithelial migration and morphogenesis, eye development, ovary development, spermathecae formation, germline stem cell maintenance in the testis, adherens junction formation, and anchorage of stem cells to niche. [Date last reviewed: 2019-03-14]
Gene Group (FlyBase)
RAS GUANINE NUCLEOTIDE EXCHANGE FACTORS -
RasGEFs are Guanine Nucleotide Exchange Factors (GEFs) for Ras family GTPases. The RasGEFs are characterized by a CDC25 homology domain. (Adapted from FBrf0220530).
Pathway (FlyBase)
Positive Regulators of Sevenless Signaling Pathway -
Positive regulators of Sevenless signaling up-regulate the pathway, promoting cell fate to that of an R7 photoreceptor. (Adapted from FBrf0127283 and FBrf0221727).
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
3

Please see the JBrowse view of Dmel\PDZ-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 New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VMF3)

If you don't see the viewer to the right, 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.

Comments on Gene Model

Low-frequency RNA-Seq exon junction(s) not annotated.

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.46

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0079249
6067
1573
FBtr0300038
5912
1569
FBtr0300039
5471
1422
FBtr0333242
6823
1569
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
RefSeq ID
GenBank
FBpp0078879
171.7
1573
7.48
FBpp0289315
171.1
1569
7.37
FBpp0289316
155.0
1422
7.25
FBpp0305443
171.1
1569
7.37
Polypeptides with Identical Sequences

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

1569 aa isoforms: PDZ-GEF-PB, PDZ-GEF-PD
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
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\PDZ-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
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

PDZ-GEF protein is strongly expressed in spermathecal ducts and stalks.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
colocalizes_with adherens junction
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
Stage
Tissue/Position (including subcellular localization)
Reference
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\PDZ-GEF 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
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
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 25 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 14 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of PDZ-GEF
Transgenic constructs containing regulatory region of PDZ-GEF
Aberrations (Deficiencies and Duplications) ( 8 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
cell-cell adherens junction & hub cell (with PDZ-GEF3)
cell-cell adherens junction & hub cell (with PDZ-GEF4)
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (21)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
12 of 15
Yes
Yes
2  
12 of 15
Yes
Yes
2 of 15
No
No
2 of 15
No
No
3  
2 of 15
No
No
2 of 15
No
No
2 of 15
No
Yes
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1  
1 of 15
No
No
1 of 15
No
No
1  
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
1 of 15
No
No
1  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (36)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
12 of 15
Yes
Yes
8 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
Yes
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
2 of 15
No
Yes
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
No
1 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
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
Rattus norvegicus (Norway rat) (22)
9 of 13
Yes
Yes
8 of 13
No
Yes
2 of 13
No
Yes
2 of 13
No
No
2 of 13
No
No
2 of 13
No
Yes
2 of 13
No
Yes
2 of 13
No
Yes
2 of 13
No
No
2 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
Yes
1 of 13
No
Yes
1 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (13)
2 of 12
Yes
No
2 of 12
Yes
Yes
2 of 12
Yes
No
2 of 12
Yes
No
2 of 12
Yes
Yes
2 of 12
Yes
No
2 of 12
Yes
No
2 of 12
Yes
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
Danio rerio (Zebrafish) (22)
11 of 15
Yes
Yes
10 of 15
No
Yes
6 of 15
No
Yes
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
2 of 15
No
Yes
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
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
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
Caenorhabditis elegans (Nematode, roundworm) (5)
11 of 15
Yes
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (2)
1 of 15
Yes
No
1 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (2)
1 of 12
Yes
No
1 of 12
Yes
No
Other Organism Orthologs (via OrthoDB)
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (8)
3 of 10
3 of 10
3 of 10
3 of 10
2 of 10
2 of 10
2 of 10
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Model Summary Ribbon
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 0 )
Allele
Disease
Evidence
References
Potential Models Based on Orthology ( 1 )
Modifiers Based on Experimental Evidence ( 0 )
Allele
Disease
Interaction
References
Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
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 see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
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
DroID - A comprehensive database of gene and protein interactions.
MIST (genetic) - An integrated Molecular Interaction Database
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Positive Regulators of Sevenless Signaling Pathway -
Positive regulators of Sevenless signaling up-regulate the pathway, promoting cell fate to that of an R7 photoreceptor. (Adapted from FBrf0127283 and FBrf0221727).
Metabolic Pathways
FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
External Data
Linkouts
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2L
Recombination map
2-19
Cytogenetic map
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
26C2-26C3
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
26C2-26C3
(determined by in situ hybridisation)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (8)
Genomic Clones (29)
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 GBrowse 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
    RNAi and Array Information
    Linkouts
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    Antibody Information
    Laboratory Generated Antibodies
     

    polyclonal

    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of

    Source for identity of: PDZ-GEF Gef26

    Source for identity of: Gef26 CG9491

    Source for database merge of

    Source for merge of: Gef26 PDZ-GEF

    Source for merge of: Gef26 dizzy

    Source for merge of: Gef26 l(2)k13720

    Source for merge of: PDZ-GEF GEF

    Additional comments

    FlyBase curator comment: Renamed from 'Gef26' to 'PDZ-GEF' because: i) 'Gef26' isn't very informative; ii) There are no recorded publications that use 'Gef26'; iii) the first paper to characterize the gene (FBrf0152217) called the gene 'PDZ-GEF'; iv) 'PDZ-GEF' is descriptive and popular in the literature.

    Source for identity of Gef26 CG9491 was sequence comparison ( date:011113 ).

    Other Comments

    Gef26 is required for macrophage shape and migration during embryogenesis and depends on the function of the R and mys proteins.

    Gef26 is necessary for the maintenance (formation?) of adherens junctions which anchor male germline stem cells to the hub in the testis.

    Plays a role in the development of the spermathecae.

    Mutant females show supernumerary spermathecae.

    PDZ-GEF is the first component of a conserved "inside-out" signalling pathway which changes the adhesive properties of macrophages via integrins.

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

    Retinal axons make abnormal projections to their targets in the lamina in Gef26 mutants, while the photoreceptors appear normal.

    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 54 )
    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/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.
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    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
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    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
    FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
    KEGG Genes - Molecular building blocks of life in the genomic space.
    MARRVEL_MODEL - MARRVEL (model organism gene)
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Synonyms and Secondary IDs (17)
    Reported As
    Name Synonyms
    GEF
    Gef26
    PDZ domain-containing guanine nucleotide exchange factor
    PDZ-GEF
    Secondary FlyBase IDs
    • FBgn0069356
    • FBgn0031798
    • FBgn0021873
    • FBgn0265624
    • FBgn0082671
    Datasets (8)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    Study result (8)
    Result
    Result Type
    Title
    Clustering analysis of hemocytes from non-infested third instar larvae
    Clustering analysis of hemocytes from wasp-infested third instar larvae
    Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying
    Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying
    Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying
    Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying
    Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying
    Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
    References (89)