FB2019_05, released Oct 15, 2019

Gene: Dmel\tomboy40

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General Information
Symbol
Dmel\tomboy40
Species
D. melanogaster
Name
tomboy40
Annotation Symbol
CG8330
Feature Type
protein_coding_gene
FlyBase ID
FBgn0033074
Gene Model Status
Current
Stock Availability
4 publicly available
Enzyme Name (EC)
Mitochondrial protein-transporting ATPase (7.4.2.3)
Chloroplast protein-transporting ATPase (7.4.2.4)
Gene Snapshot
Insufficient genetic data for FlyBase to solicit a summary. [Date last reviewed: 2016-06-30]
Other Summaries
Key Links
Genomic Location
Cytogenetic map
42A14-42A14
Sequence location
2R:6,225,634..6,226,884 [+]
Recombination map
2-55
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
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the Tom40 family. (A1Z6L1)
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
-
Predictions / Assertions
P-P-bond-hydrolysis-driven protein transmembrane transporter activity; protein transmembrane transporter activity
Catalytic Activity (EC)
Experimental Evidence
-
Predictions / Assertions
ATP + H(2)O + mitochondrial-protein(Side 1) = ADP + phosphate + mitochondrial-protein(Side 2) (7.4.2.3)
ATP + H(2)O + chloroplast-protein(Side 1) = ADP + phosphate + chloroplast-protein(Side 2) (7.4.2.4)
Summaries
Protein Function (UniProtKB)
Channel-forming protein essential for import of protein precursors into mitochondria.
(UniProt, A1Z6L1)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\tomboy40 or the JBrowse view of Dmel\tomboy40 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
Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
retrotransposed_protein_coding_gene
(dos Santos, 2014, Pan and Zhang, 2009, Bai et al., 2007, Langille and Clark, 2007, Dai et al., 2006)
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
tomboy40-RA
FBtr0085994
NM_136369
1251
340
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
tomboy40-PA
FBpp0085338
37.0
340
8.87
NP_610213
AAF57268
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
Subunit Structure (UniProtKB)
Forms part of the preprotein translocase of the outer mitochondrial membrane (TOM complex). Interacts with mitochondrial targeting sequences (By similarity).
(UniProt, A1Z6L1)
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\tomboy40 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 (7 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
P-P-bond-hydrolysis-driven protein transmembrane transporter activity
inferred from sequence or structural similarity with UniProtKB:O96008
(Sardiello et al., 2003.6.11)
protein transmembrane transporter activity
inferred from biological aspect of ancestor with PANTHER:PTN000085854
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
protein import into mitochondrial matrix
inferred from biological aspect of ancestor with PANTHER:PTN000085854
(assigned by GO_Central )
(Gaudet et al., 2011)
protein targeting to mitochondrion
inferred from sequence or structural similarity with UniProtKB:O96008
(Sardiello et al., 2003.6.11)
inferred from sequence or structural similarity with UniProtKB:Q75Q40
(assigned by UniProt )
(UniProt Curators, 2002-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
mitochondrial intermembrane space protein transporter complex
inferred from direct assay
(assigned by UniProt )
(Hwa et al., 2004)
mitochondrion
inferred from direct assay
(Hwa et al., 2004)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
mitochondrial outer membrane translocase complex
inferred from biological aspect of ancestor with PANTHER:PTN000085854
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with UniProtKB:O96008
(Sardiello et al., 2003.6.11)
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
spermatogenesis & adult stage | male
testis
(Hwa et al., 2004)
primary spermatocyte
(Hwa et al., 2004)
spermatid
(Hwa et al., 2004)
elongation stage spermatid
(Hwa et al., 2004)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
spermatogenesis & adult stage | male
germline cell
(Hwa et al., 2004)
Additional Descriptive Data
tomboy40 transcripts are expressed in primary spermatocytes, but not in male germ line stem cells or spermatogonia, in a pattern similar to that of tomboy20 expression.
(Hwa et al., 2004)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
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
mitochondrial intermembrane space protein transporter complex
inferred from direct assay
(assigned by UniProt )
(Hwa et al., 2004)
mitochondrion
inferred from direct assay
(Hwa et al., 2004)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\tomboy40 in GBrowse 2
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 0 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of tomboy40
Transgenic constructs containing regulatory region of tomboy40
Deletions and Duplications ( 0 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\TOMM40
14 of 15
Yes
No
Hsap\TOMM40L
11 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
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Tomm40
13 of 15
Yes
No
Mmus\Tomm40l
12 of 15
No
Yes
Rattus norvegicus (Norway rat) (2)
Rnor\Tomm40
13 of 13
Yes
Yes
Rnor\Tomm40l
12 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\tomm40
10 of 12
Yes
No
Xtro\tomm40l
4 of 12
No
No
Danio rerio (Zebrafish) (3)
Drer\tomm40
13 of 15
Yes
No
Drer\tomm40l
12 of 15
No
No
Drer\si:dkey-71l1.1
3 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\tomm-40
14 of 15
Yes
No
Arabidopsis thaliana (thale-cress) (2)
Atha\AT1G50400
9 of 9
Yes
Yes
Atha\TOM40
8 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\TOM40
14 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\tom40
11 of 12
Yes
No
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190AM0 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\tomboy40
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00006521
Drosophila simulans
Dsim\GD10402
Drosophila sechellia
Dsec\GM16540
Drosophila erecta
Dere\GG23200
Drosophila yakuba
Dyak\GE20769
Drosophila ananassae
Dana\GF11050
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091506QV )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17013775
Glossina morsitans
Tsetse fly
Gmor\GMOY009558
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_00165
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL007001
Anopheles darlingi
American malaria mosquito
Adar\ADAC009104
Anopheles gambiae
Malaria mosquito
Agam\AGAP007871
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ002542
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W09OP )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA013348
Danaus plexippus
Monarch butterfly
Dple\DPOGS203770-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL004227
Apis florea
Little honeybee
Aflo\2780916324
Apis florea
Little honeybee
Aflo\3680523204
Apis mellifera
Western honey bee
Amel\LOC408284
Apis mellifera
Western honey bee
Amel\GB44171
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP10079
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP10538
Bombus terrestris
Buff-tailed bumblebee
Bter\15213918
Bombus terrestris
Buff-tailed bumblebee
Bter\15204803
Linepithema humile
Argentine ant
Lhum\LH17125
Linepithema humile
Argentine ant
Lhum\LH16643
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:002bb8
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:00258f
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG007451
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG002150
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_03666
Tribolium castaneum
Red flour beetle
Tcas\TC003426
Pediculus humanus
Human body louse
Phum\PHUM366110
Rhodnius prolixus
Kissing bug
Rpro\RPRC009413
Cimex lectularius
Bed bug
Clec\CLEC006128
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI001526
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI069600
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI010046
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI005876
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_13011
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X096M )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR003443
Stegodyphus mimosarum
African social velvet spider
Smim\KFM61565.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur35g00170
Tetranychus urticae
Two-spotted spider mite
Turt\tetur12g04590
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_128731
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0MNA )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Tomm40
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000007630
Gallus gallus
Domestic chicken
Ggal\ENSGALG00000013827
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (2)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Tom40
9 of 10
CG4520
5 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 ( 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?
    TOMM40; translocase of outer mitochondrial membrane 40
    14 of 15
    608061
        TOMM40L; translocase of outer mitochondrial membrane 40 like
        11 of 15
            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
            Interactions Browser
            Summary of Genetic Interactions
            esyN Network Diagram
            Starting gene(s)
            Interaction type
            Interacting gene(s)
            Reference
            Starting gene(s)
            Interaction type
            Interacting gene(s)
            Reference
            External Data
            Subunit Structure (UniProtKB)
            Forms part of the preprotein translocase of the outer mitochondrial membrane (TOM complex). Interacts with mitochondrial targeting sequences (By similarity).
            (UniProt, A1Z6L1 )
            Linkouts
            DroID - A comprehensive database of gene and protein interactions.
            InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
            Pathways
            Gene Group - Pathway Membership (FlyBase)
            External Data
            Linkouts
            Genomic Location and Detailed Mapping Data
            Chromosome (arm)
            2R
            Recombination map
            2-55
            Cytogenetic map
            42A14-42A14
            Sequence location
            2R:6,225,634..6,226,884 [+]
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            42A14-42A14
            Limits computationally determined from genome sequence between P{lacW}l(2)k09848k09848&P{EP}EP407 and P{lacW}geminink14019&P{PZ}Adf101349
            Experimentally Determined Cytological Location
            Cytogenetic map
            Notes
            References
            Experimentally Determined Recombination Data
            Location
            2-55
            (FlyBase, 2016)
            2-55.8
            (Comeron et al., 2012)
            Left of (cM)
            Right of (cM)
            Notes
            Stocks and Reagents
            Stocks (4)
            Genomic Clones (16)
             

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

            cDNA Clones (12)
             

            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
            Other 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 identity of: tomboy40 CG8330
            (Hwa et al., 2004)
            Source for database merge of
            Additional comments
            The tomboy40 gene may have been derived from the Tom40 gene by retroposition.
            (Pan and Zhang, 2009, Bai et al., 2007, Langille and Clark, 2007, Dai et al., 2006)
            Other Comments
            tomboy40 is expressed only in the male germ line.
            (Hwa et al., 2004)
            Origin and Etymology
            Discoverer
            Etymology
            Identification
            External Crossreferences and Linkouts ( 22 )
            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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
            Other crossreferences
            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.
            Flygut - An atlas of the Drosophila adult midgut
            GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
            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
            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
            InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
            Synonyms and Secondary IDs (4)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            References (36)