FB2025_01 , released February 20, 2025
Gene: Dmel\Tom
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General Information
Symbol
Dmel\Tom
Species
D. melanogaster
Name
Twin of m4
Annotation Symbol
CG5185
Feature Type
FlyBase ID
FBgn0026320
Gene Model Status
Stock Availability
Gene Summary
Twin of m4 (Tom) is a member of the Bearded gene family that encodes a regulator of the Notch signaling pathway. [Date last reviewed: 2019-09-12] (FlyBase Gene Snapshot)
Also Known As

barbu

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
3-42
RefSeq locus
NT_037436 REGION:14969344..14970306
Sequence
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (7 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (0 terms)
Biological Process (5 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from direct assay
inferred from genetic interaction with FLYBASE:Su(H); FB:FBgn0004837
inferred from mutant phenotype
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR029686
inferred from electronic annotation with InterPro:IPR029686
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Twin of m4 (Tom) is a member of the Bearded gene family that encodes a regulator of the Notch signaling pathway. [Date last reviewed: 2019-09-12]
Pathway (FlyBase)
Negative Regulators of Notch Signaling Pathway -
The Notch receptor signaling pathway is activated by the binding of the transmembrane receptor Notch (N) to transmembrane ligands, Dl or Ser, presented on adjacent cells. This results in the proteolytic cleavage of N, releasing the intracellular domain (NICD). NICD translocates into the nucleus, interacting with Su(H) and mam to form a transcription complex, which up-regulates transcription of Notch-responsive genes. Negative regulators of the pathway down-regulate the signal from the sending cell or the response in the receiving cell. (Adapted from FBrf0225731 and FBrf0192604).
Gene Group (FlyBase)
BEARDED GENE FAMILY -
The Bearded gene family, named from homology with Brd, encode small proteins containing predicted basic amphipathic α-helical domains in their N-terminal regions. They are located in two genomic complexes - the Bearded Complex and the Enhancer of Split Complex. Some members have been implicated in Notch signaling. (Adapted from FBrf0123097).
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Tom 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 Q9V3S6)

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 5.46

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0075620
963
158
Additional Transcript Data and Comments
Reported size (kB)

1.3 (northern blot)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
FBpp0075373
18.4
158
9.95
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

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
Nucleotide / Polypeptide Records
 
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Tom 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).

-0.33

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

Tom is strongly expressed in neuroepithelial cells in the optic lobe and downregulated in neuroblasts.

Tom transcripts are detected in third instar larval eye discs in the morphogenetic furrow in stripes just anterior and posterior to the band of dpp expression in the furrow. They are detected in the pupal wing at 8h APF in large clusters of proximal campaniform sensilla.

Tom transcripts appear in 2-4hr embryos, peak in 4-8 and 8-12hr embryos and then decline. They are barely detectable after the first instar larval stage. Tom transcripts are detected in the anteriormost and central regions of early blastoderm embryos. In late blastoderm embryos, Tom is uniformly expressed except in the ventralmost regions where its expression is repressed by sna. From gastrulation until the end of germ band elongation, Tom is expressed throughout the mesoderm though by stage 11, expression occurs in a segmental pattern and is observed in tracheal pit precursors. Tom is also expressed in the ectoderm. During germband elongation and neuroblast segregation, Tom transcripts are excluded from one or two rows of ectodermal and mesectodermal cells in each segment. Later, Tom transcripts are transiently absent from segmental, bilaterally symmetric patches of cells. At the beginning of germ band retraction, Tom is more weakly expressed in the ventral region than in the dorsal region of the ectoderm. Expression rapidly decays during germ band retraction. After dorsal closure, Tom expression is observed only in lymph glands. In eye discs, Tom is expressed anterior and posterior to the morphogenetic furrow.

Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

The pattern of Tom protein distribution is the same as that observed for the mRNA.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Tom in JBrowse
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
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 7 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Tom
Transgenic constructs containing regulatory region of Tom
Aberrations (Deficiencies and Duplications) ( 6 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
external sensory organ precursor cell & dorsal mesothoracic disc, with Scer\GAL4sca-537.4
microchaeta & leg, with Scer\GAL4sca-537.4
scutum & microchaeta
scutum & microchaeta | ectopic, with Scer\GAL4pnr-MD237
wing sensillum & wing vein, with Scer\GAL469B
wing sensillum & wing vein, with Scer\GAL4Bx-MS1096
Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (0)
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (0)
Mus musculus (laboratory mouse) (0)
Xenopus tropicalis (Western clawed frog) (0)
Danio rerio (Zebrafish) (0)
Caenorhabditis elegans (Nematode, roundworm) (0)
Anopheles gambiae (African malaria mosquito) (1)
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:Tom. Refer to their site for version information.
Paralogs
Paralogs (via DIOPT v9.1)
Drosophila melanogaster (Fruit fly) (3)
4 of 13
3 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 ( 0 )
    Allele
    Disease
    Interaction
    References
    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?
    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:
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Other Interaction Browsers

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    RNA-RNA
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    esyN Network Key:
    Suppression
    Enhancement
    Other Interaction Browsers

    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.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyBase
    External Links
    External Data
    Linkouts
    SignaLink - A signaling pathway resource with multi-layered regulatory networks.
    Class of Gene
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3L
    Recombination map
    3-42
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    71A3-71A3
    Limits computationally determined from genome sequence between P{PZ}Mpcp00564 and P{PZ}l(3)rO220rO220
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    71A1-71A2
    71A-71A
    (determined by in situ hybridisation)
    Tom maps 2kb from Brd.
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (9)
    Genomic Clones (15)
     

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

    cDNA Clones (186)
     

    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)
    Other clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    Antibody Information
    Laboratory Generated Antibodies
    Commercially Available Antibodies
     
    Cell Line Information
    Publicly Available Cell Lines
     
      Other Stable Cell Lines
       
        Other Comments

        Overexpression of Tom inhibits the endocytosis of Dl in multiple tissues.

        ChEST reveals this is a target of Mef2.

        Overexpression of Tom antagonises the N pathway in multiple cell fate decisions during adult sensory organ development.

        Identification: as a protein that interacts with tin in a yeast two-hybrid screen.

        Tom can antagonise N signaling activity during lateral inhibition processes in the embryonic mesoderm, sensory organ specification in imaginal discs and cell type specification in developing ommatidia.

        Brd family over-expression phenotypes resemble N loss of function phenotypes.

        Overexpression of Tom results in both bristle tufting and balding phenotypes.

        Identification: Defined in yeast two hybrid system using tin as a bait.

        Relationship to Other Genes
        Source for database merge of

        Source for merge of: Tom anon- EST:fe1F6

        Additional comments
        Nomenclature History
        Source for database identify of

        Source for identity of: Tom anon- EST:fe1F6

        Source for identity of: Tom Bbu

        Nomenclature comments
        Etymology
        Synonyms and Secondary IDs (12)
        Reported As
        Secondary FlyBase IDs
        • FBgn0025249
        • FBgn0026264
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 38 )
        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.
        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
        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
        MIST (protein-protein) - An integrated Molecular Interaction Database
        SignaLink - A signaling pathway resource with multi-layered regulatory networks.
        References (89)