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General Information
Symbol
Dmel\stumps
Species
D. melanogaster
Name
stumps
Annotation Symbol
CG31317
Feature Type
FlyBase ID
FBgn0020299
Gene Model Status
Stock Availability
Gene Snapshot
stumps (stumps) encodes a fibroblast growth factor (FGF) scaffolding protein. Upon FGF receptor activation, it mediates the recruitment of the phosphatase encoded by csw, which is essential for the activation of the MAPK pathway. [Date last reviewed: 2019-06-13]
Also Known As
dof, hbr, heartbroken, Downstream of FGF, downstream of FGF receptor
Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:14,577,217..14,608,079 [+]
Recombination map
3-55
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Pathway (FlyBase)
Fibroblast Growth Factor Receptor Signaling Pathway Core Components -
Fibroblast Growth Factor Receptor (FGFR) signaling pathway is initiated by the binding of secreted FGFs - bnl or ths/pyr to receptor tyrosine kinases btl or htl, respectively, to initiate signaling primarily via the canonical Ras/Raf/MAP kinase (ERK) cascade. (Adapted from FBrf0221038).
Summary (Interactive Fly)
novel signal transduction protein functioning downstream of two FGF receptors - mutations are associated with defects in the migration and later specification of mesodermal and tracheal cells wgvia stabilization of the negative elongation factor complex - promotes anaphase-promoting complex/cyclosome function during cell cycle exit - acts to generate neuroblast cortical polarity - acts to prevent phenotypic variation
Gene Model and Products
Number of Transcripts
5
Number of Unique Polypeptides
5

Please see the GBrowse view of Dmel\stumps or the JBrowse view of Dmel\stumps 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
Gene model reviewed during 5.47
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 6.03
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0082959
3787
1012
FBtr0112893
4679
1211
FBtr0334955
3822
1029
FBtr0334956
4594
1220
FBtr0334957
3643
973
Additional Transcript Data and Comments
Reported size (kB)
4.043, 3.733 (longest cDNA)
5.5, 4.4 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0082418
112.9
1012
6.63
FBpp0111806
134.7
1211
7.64
FBpp0306970
114.8
1029
6.69
FBpp0306971
135.8
1220
7.56
FBpp0306972
108.8
973
6.83
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
1144, 1012 (aa)
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\stumps 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 (13 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002701890
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000417769
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN002701890
(assigned by GO_Central )
Biological Process (9 terms)
Terms Based on Experimental Evidence (9 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN002701890
(assigned by GO_Central )
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
organism

Comment: maternally deposited

anterior endoderm anlage

Comment: anlage in statu nascendi

head mesoderm anlage

Comment: anlage in statu nascendi

mesoderm anlage

Comment: anlage in statu nascendi

trunk mesoderm anlage

Comment: anlage in statu nascendi

Additional Descriptive Data
stumps transcripts are first detected on the ventral side of the embryo in the late syncytial embryo in a region slightly narrower than the mesodermal primordium. During germ band extension, they disappear from the mesoderm. They are observed in tracheal placodes by stage 9/10. As the trachea differentiate, staining disappears in the primary branches and is observed in the secondary branches. stumps transcripts are expressed transiently in the anterior midgut primordium, in parts of the posterior midgut primordium, in a subset of heart cells and in a group of migrating visceral mesoderm cells. Expression is also observed in some glial cells. Later in development expression is observed in parts of the imaginal discs and the brain. The two stumps transcripts appear to be co-expressed everywhere except in the anterior midgut primordium in which only transcript II is expressed.
Transcripts are expressed in ventral cells of the blastoderm embryo. The posterior border coincides with the posterior limit of the ventral furrow. Anteriorly, expression extends up to the anterior pole. Expression continues in the mesoderm. Expression is observed in the tracheal system and in parts of the visceral mesoderm in later embryos.
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
Prior to stage 11 stumps protein is widely expressed in the embryonic mesoderm. In early stage 11 expression is refined to the dorsal part of the mesoderm and undergoes dynamic modulation in a subset of dorsal cells including the eve-expressing muscle and heart progenitors. stumps protein can also be detected in the ectodermally derived tracheal pits at this stage.
Protein was detected in both htl and btl expressing adepithelial cells in third instar wing discs.
Marker for
 
Subcellular Localization
CV Term
Evidence
References
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\stumps 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
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 25 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 17 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of stumps
Transgenic constructs containing regulatory region of stumps
Deletions and Duplications ( 7 )
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
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
7 of 15
Yes
Yes
4 of 15
No
Yes
 
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
5 of 15
Yes
Yes
4 of 15
No
Yes
Rattus norvegicus (Norway rat) (2)
5 of 13
Yes
Yes
3 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (1)
2 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
5 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG0919013M )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
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) ( EOG091500W1 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W00PB )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X00NT )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0125 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (0)
No records found.
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 ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 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?
    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
    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.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    Fibroblast Growth Factor Receptor Signaling Pathway Core Components -
    Fibroblast Growth Factor Receptor (FGFR) signaling pathway is initiated by the binding of secreted FGFs - bnl or ths/pyr to receptor tyrosine kinases btl or htl, respectively, to initiate signaling primarily via the canonical Ras/Raf/MAP kinase (ERK) cascade. (Adapted from FBrf0221038).
    External Data
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-55
    Cytogenetic map
    Sequence location
    3R:14,577,217..14,608,079 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    88C6-88C9
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    88C-88C
    (determined by in situ hybridisation)
    88C-88E
    (determined by in situ hybridisation)
    30C-30D
    (determined by in situ hybridisation)
    In situ hybridisation using a stumps cDNA as a probe (the "gene C" or "anon- EST:CL47 " cDNA isolated in FBrf0090486) gave three signals, at 30C, 88C and 88E (only 30C was detected in FBrf0090486). Hybridisation to homozygous Df(3R)ry506-85C embryos using the same probe indicates that stumps maps to 88 as the stumps transcript is absent in these embryos.
    Maps by recombination and deficiency mapping to 88B--88E.
    Experimentally Determined Recombination Data
    Location
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (13)
    Genomic Clones (39)
    cDNA Clones (43)
     

    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
    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
      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: hbr dof
      Source for merge of: stumps hbr
      Source for merge of: stumps CG18485
      Additional comments
      Annotations CG18485, CG3375 merged as CG31317 in release 3 of the genome annotation.
      Other Comments
      ChEST reveals this is a target of Mef2.
      stumps function promotes FGF-directed cell migrations, either by potentiating the FGF signalling process or by coupling the signal to the cellular machinery required for directed cell movement.
      stumps participates in the signalling pathways of both FGF receptors (htl and btl), acting downstream of the FGF receptors but either upstream or in parallel to Ras85D.
      Mutations in stumps are associated with defects in the migration and later specification of mesodermal and tracheal cells.
      stumps is a component of the FGF receptor signaling pathway. It acts downstream of FGF receptors (htl and btl) and upstream of Ras to activate the MAPK kinase cascade in response to FGF signaling, but is not required for activation of the MAPK cascade via other receptor tyrosine kinases.
      Mutants exhibit mesodermal spreading (mesodermal cells migrate in an undirected fashion and fail to reach their normal dorsal positions) and cell fate specification loss of function phenotypes.
      Isolated from a subtractive cDNA library enriched in sequences expressed in the mesoderm.
      A stumps cDNA has been cloned and sequenced. stumps is expressed in the early mesoderm.
      Origin and Etymology
      Discoverer
      Etymology
      The gene was named "stumps" because no tracheal branches form in the mutant, except for an occasional short stump.
      Identification
      External Crossreferences and Linkouts ( 60 )
      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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
      Other crossreferences
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      InterPro - A database of protein families, domains and functional sites
      KEGG Genes - Molecular building blocks of life in the genomic space.
      modMine - A data warehouse for the modENCODE project
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      FLIGHT - Cell culture data for RNAi and other high-throughput technologies
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyMine - An integrated database for Drosophila genomics
      Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      MIST (genetic) - An integrated Molecular Interaction Database
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Synonyms and Secondary IDs (38)
      Reported As
      Symbol Synonym
      Dof/stumps/heartbroken
      anon-EST:CL47
      anon-estC
      heartbroken/dof
      l(3)S083710
      Secondary FlyBase IDs
      • FBgn0024898
      • FBgn0025779
      • FBgn0028088
      • FBgn0038245
      • FBgn0051317
      • FBgn0063634
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (174)