FlyBase Gene Report: Dmel\tomboy40

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

Gene Snapshot

Contributions welcome

Other Summaries

Alliance
Auto summary
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

42A14-42A14

Sequence location

2R:6,225,634..6,226,884 [+]

Recombination map

2-55

RefSeq locus

NT_033778 REGION:6225634..6226884

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Help me choose

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (6 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables 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

involved_in protein import into mitochondrial matrix

inferred from biological aspect of ancestor with PANTHER:PTN000085854

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in protein targeting to mitochondrion

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

part_of mitochondrial intermembrane space protein transporter complex

inferred from direct assay

(assigned by UniProt )

(Hwa et al., 2004)

located_in mitochondrion

inferred from direct assay

(Hwa et al., 2004)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of mitochondrial outer membrane translocase complex

inferred from biological aspect of ancestor with PANTHER:PTN000085854

(assigned by GO_Central )

(Gaudet et al., 2011)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the Tom40 family. (A1Z6L1)

Protein Signatures (InterPro)

Summaries

Protein Function (UniProtKB)

Channel-forming protein essential for import of protein precursors into mitochondria.

(UniProt, A1Z6L1)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see 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

Nucleotide / Polypeptide Records

UniProt

A1Z6L1

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.

tomboy40_1

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

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

• membrane

(Aradska et al., 2015)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

part_of mitochondrial intermembrane space protein transporter complex

inferred from direct assay

(assigned by UniProt )

(Hwa et al., 2004)

located_in 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

View exonic expression by developmental stage for Dmel\tomboy40

View exonic expression by tissue for Dmel\tomboy40

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

FBgn0033074

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG8330-RA

Flygut - An atlas of the Drosophila adult midgut

FBgn0033074

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

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal, with Dcr-2^UAS.cDa, Scer\GAL4^e22c, Scer\GAL4^sqh.PW

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

tomboy40^GD13779

viable, with Scer\GAL4^pnr-MD237

tomboy40^GD13779

viable, with Scer\GAL4^tin.CΔ4

tomboy40^GD13779

Other Phenotypes

Allele

flight defective, with Scer\GAL4^Mef2.PR

tomboy40^GD13779

visible, with Scer\GAL4^pnr-MD237

tomboy40^GD13779

Phenotype manifest in

Allele

trichogen cell, with Scer\GAL4^pnr-MD237

tomboy40^GD13779

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (3)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\TOMM40

14 of 15

Yes

Hsap\TOMM40L

11 of 15

Yes

Hsap\MIR5187

2 of 15

Yes

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (2)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Tomm40

14 of 15

Yes

Mmus\Tomm40l

11 of 15

Yes

Rattus norvegicus (Norway rat) (2)

Rnor\Tomm40

13 of 13

Yes

Rnor\Tomm40l

12 of 13

Yes

Xenopus tropicalis (Western clawed frog) (2)

Xtro\tomm40

12 of 12

Yes

Xtro\tomm40l

6 of 12

Danio rerio (Zebrafish) (3)

Drer\tomm40

13 of 15

Yes

Drer\tomm40l

12 of 15

Drer\si:dkey-71l1.1

3 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (1)

Cele\tomm-40

14 of 15

Yes

Arabidopsis thaliana (thale-cress) (2)

Atha\AT1G50400

9 of 9

Yes

Atha\TOM40

8 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\TOM40

13 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\tom40

10 of 12

Yes

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190AM0 )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

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 v8.0)

Drosophila melanogaster (Fruit fly) (2)

Gene Symbol

Score

Source

Alignment

9 of 10

6 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

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.

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.

FBgn0033074

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

35553

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

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)k09848^k09848&P{EP}EP407 and P{lacW}geminin^k14019&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)

Bloomington

29573

y¹ v¹; P{TRiP.JF03252}attP2

82094

y¹ v¹; P{TKO.GS04921}attP40

VDRC

v105557

P{KK104751}VIE-260B

v42439

w¹¹¹⁸; P{GD13779}v42439

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 sequenced

BDGP DGC clones

AT01036

Other clones

FI16501

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.

FBgn0033074

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0033074

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

35553

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 ( 23 )

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.

35553

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.

AAF57268

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

A1Z6L1

Other crossreferences

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0033074

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

tomboy40_1

Flygut - An atlas of the Drosophila adult midgut

FBgn0033074

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

35553

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

Dmel_CG8330

modMine - A data warehouse for the modENCODE project

FBgn0033074

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0033074

DRSC - Results frm RNAi screens

FBgn0033074

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0033074

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG8330-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0033074

FlyMine - An integrated database for Drosophila genomics

FBgn0033074

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

35553

Synonyms and Secondary IDs (4)

Reported As

Symbol Synonym

CG8330

(Lu et al., 2016, Hosono et al., 2015, Tsubouchi et al., 2012, Singh et al., 2011, Bai et al., 2009, Keleman et al., 2009.8.5, Pan and Zhang, 2009, Pan and Zhang, 2009, Perkins et al., 2009, Dai et al., 2006, Hwa et al., 2004)

Tomboy40

(Chen et al., 2020, Bai et al., 2007, Bai et al., 2007)

tomboy40

(Trinh et al., 2019, Transgenic RNAi Project members, 2017-, Lu et al., 2016, dos Santos, 2014, Tsubouchi et al., 2012, Bai et al., 2009, Bai et al., 2007, Langille and Clark, 2007, Langille and Clark, 2007)

Name Synonyms

dtomboy40

(Hwa et al., 2004)

tomboy40

(Tsubouchi et al., 2012, Bai et al., 2007)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (38)

The following external sites may use different assemblies or annotations than FlyBase.

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