FB2024_03 , released June 25, 2024
Gene: Dmel\tomb
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General Information
Symbol
Dmel\tomb
Species
D. melanogaster
Name
tombola
Annotation Symbol
CG14016
Feature Type
protein_coding_gene
FlyBase ID
FBgn0031715
Gene Model Status
Current
Stock Availability
7 publicly available
Gene Summary
tombola (tomb) encodes a tesmin/TSO1-family protein involved in the transcriptional activation of the male germline. [Date last reviewed: 2019-09-19] (FlyBase Gene Snapshot)
All Summaries
Key Links
Genomic Location
Cytogenetic map
25E5-25E5
Sequence location
Recombination map
2-17
RefSeq locus
NT_033779 REGION:5535861..5536758
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 (7 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables protein binding
inferred from physical interaction with FLYBASE:aly; FB:FBgn0004372
(Jiang et al., 2007)
inferred from physical interaction with FLYBASE:comr; FB:FBgn0034667
(Jiang et al., 2007)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
acts_upstream_of_positive_effect male meiosis I
inferred from mutant phenotype
(Jiang et al., 2007)
involved_in positive regulation of transcription by RNA polymerase II
inferred from mutant phenotype
(Jiang et al., 2007)
involved_in spermatogenesis
inferred from mutant phenotype
(Jiang et al., 2007)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in regulation of DNA-templated transcription
inferred from biological aspect of ancestor with PANTHER:PTN000278298
(GO Reference Genome Project, 2011-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
part_of chromatin
inferred from direct assay
(Jiang et al., 2007)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000278298
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
tombola (tomb) encodes a tesmin/TSO1-family protein involved in the transcriptional activation of the male germline. [Date last reviewed: 2019-09-19]
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\tomb 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 Q9VMQ3)

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 5.41

Gene model reviewed during 5.52

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
tomb-RA
FBtr0079127
NM_135092
836
243
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
tomb-PA
FBpp0078758
26.2
243
9.60
Q9VMQ3
NP_608936
AAF52259
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
 
UniProt
Mapped Features

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

4.26

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
spermatogenesis & adult stage | male
primary spermatocyte
(Jiang et al., 2007)
RT-PCR
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage | male
testis
(Jiang et al., 2007)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage | male & spermatogenesis
primary spermatocyte
(Jiang et al., 2007)
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage | male
testis
(Beall et al., 2007)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of chromatin
inferred from direct assay
(Jiang et al., 2007)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\tomb 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
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 3 )
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 tomb
Transgenic constructs containing regulatory region of tomb
Aberrations (Deficiencies and Duplications) ( 2 )
Inferred from experimentation ( 2 )
Gene disrupted in
Df(2L)Exel6012
(Ryder, 2004.4.26)
Df(2L)Exel7023
(Ryder, 2004.4.26)
Inferred from location ( 0 )
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
viable
Sterility
Allele
female fertile (with Df(2L)cl-h1)
female fertile (with Df(2L)cl-h3)
male sterile
male sterile (with Df(2L)cl-h1)
male sterile (with Df(2L)cl-h3)
Other Phenotypes
Allele
abnormal meiotic cell cycle | male
Phenotype manifest in
Allele
nuclear chromosome & primary spermatocyte
testis
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) (2)
Hsap\LIN54
2 of 14
Yes
No
Hsap\TESMIN
2 of 14
Yes
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) (2)
Rnor\Lin54
2 of 14
Yes
No
Rnor\Tesmin
2 of 14
Yes
No
Mus musculus (laboratory mouse) (2)
Mmus\Tesmin
2 of 14
Yes
No
Mmus\Lin54
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (1)
Xtro\lin54
1 of 13
Yes
No
Danio rerio (Zebrafish) (2)
Drer\lin54
2 of 14
Yes
No
Drer\tesmin
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\lin-54
1 of 14
Yes
No
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP010380
2 of 12
Yes
No
Arabidopsis thaliana (thale-cress) (8)
Atha\AT3G16160
3 of 13
Yes
No
Atha\AT2G20110
2 of 13
No
No
Atha\AT4G29000
2 of 13
No
No
Atha\AT5G25790
2 of 13
No
No
Atha\AT3G04850
1 of 13
No
No
Atha\SOL1
1 of 13
No
No
Atha\TCX2
1 of 13
No
Yes
Atha\TSO1
1 of 13
No
No
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:tomb. 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)
mip120
2 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 ( 1 )
    Allele
    Disease
    Interaction
    References
    tombHMS01557
    ameliorates  amyotrophic lateral sclerosis type 10
    modeled by Hsap\TARDBPM.UAS.Tag:FLAG
    (Azpurua et al., 2021)
    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
    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
    tomb - aly
    two hybrid, anti tag coimmunoprecipitation, anti tag western blot, western blot
    (Jiang et al., 2007)
    tomb - comr
    two hybrid
    (Jiang et al., 2007)
    tomb - mip40
    anti bait coimmunoprecipitation, Identification by mass spectrometry
    (Beall et al., 2007)
    Summary of Genetic Interactions
    esyN Network Diagram
    Other 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.
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2L
    Recombination map
    2-17
    Cytogenetic map
    25E5-25E5
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    25E5-25E5
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    2-17

    (FlyBase, 2016)

    2-18.5

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (7)
    Genomic Clones (16)
     

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

    cDNA Clones (1)
     

    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
           
          Commercially Available Antibodies
           
          Cell Line Information
          Publicly Available Cell Lines
           
            Other Stable Cell Lines
             
              Other Comments

              tomb is required for localisation of aly and comr proteins, but not topi protein, to chromatin during spermatogenesis.

              (Jiang et al., 2007)

              Mutant testes have an "aly"-class meiotic arrest phenotype.

              (Jiang et al., 2007)

              Identification: yeast two hybrid assy for proteins interacting with the aly gene product.

              (White-Cooper et al., 2005)
              Relationship to Other Genes
              Source for database merge of
              Additional comments
              Nomenclature History
              Source for database identify of

              Source for identity of: tomb CG14016

              (White-Cooper, 2005.9.6)
              Nomenclature comments
              Etymology

              The gene is named "tombola" based on the testis phenotype of mutants; mutant testes resemble a tube full of balls, as in the lottery game.

              (Jiang et al., 2007)
              Synonyms and Secondary IDs (4)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              Study result (0)
              Result
              Result Type
              Title
              External Crossreferences and Linkouts ( 24 )
              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 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
              Flygut - An atlas of the Drosophila adult midgut
              References (33)