FlyBase Gene Report: Dmel\trh

FB2026_01 , released March 12, 2026

FB2026_01 , released March 12, 2026

Gene: Dmel\trh

General Information

Symbol

Dmel\trh

Species

D. melanogaster

Name

trachealess

Annotation Symbol

CG42865

Feature Type

protein_coding_gene

FlyBase ID

FBgn0262139

Gene Model Status

Stock Availability

77 publicly available

Gene Summary

trachealess (trh) encodes a bHLH-PAS nuclear transcription factor required for the formation of the tube of the salivary duct, trachea and filzkorper. It is also required for expression of all tracheal genes. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Red Book
Interactive Fly

Also Known As

l(3)10512

Key Links

Genomic Location

Cytogenetic map

Sequence location

3L:366,524..392,633 [-]

Recombination map

3-0.5

RefSeq locus

NT_037436 REGION:366524..392633

Sequence

Get Decorated FASTA

Genomic Maps

Other Genome Views

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

Function

Gene Ontology (GO) Annotations (20 terms)

Molecular Function (7 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

contributes_to DNA-binding transcription activator activity, RNA polymerase II-specific

inferred from physical interaction with FLYBASE:tgo; FB:FBgn0264075

(Sonnenfeld et al., 1997)

contributes_to DNA-binding transcription factor activity

inferred from physical interaction with FLYBASE:tgo; FB:FBgn0264075

(Morozova et al., 2010)

enables DNA-binding transcription factor activity

inferred from physical interaction with FLYBASE:tgo; FB:FBgn0264075

(Jiang and Crews, 2007)

enables protein heterodimerization activity

inferred from physical interaction with FLYBASE:tgo; FB:FBgn0264075

(Sonnenfeld et al., 1997)

enables sequence-specific DNA binding

inferred from direct assay

(Jiang and Crews, 2007)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables DNA-binding transcription factor activity, RNA polymerase II-specific

inferred from biological aspect of ancestor with PANTHER:PTN001889196

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with FLYBASE:sim; FB:FBgn0004666

(Isaac and Andrew, 1996)

inferred from sequence or structural similarity with UniProtKB:Q16665

(Isaac and Andrew, 1996)

enables protein dimerization activity

inferred from electronic annotation with InterPro:IPR011598, InterPro:IPR036638

(InterPro Project Members, 2004-)

enables RNA polymerase II transcription regulatory region sequence-specific DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN001889196

(GO Reference Genome Project, 2011-)

Biological Process (12 terms)

Terms Based on Experimental Evidence (10 terms)

CV Term

Evidence

References

involved_in appendage development

inferred from mutant phenotype

(Tajiri et al., 2007)

involved_in epithelial cell fate determination, open tracheal system

inferred from mutant phenotype

(Jin et al., 2001)

involved_in epithelial tube formation

inferred from mutant phenotype

(Isaac and Andrew, 1996)

involved_in Malpighian tubule morphogenesis

inferred from mutant phenotype

(Jack and Myette, 1999)

involved_in open tracheal system development

inferred from mutant phenotype

(Chung et al., 2011)

inferred from mutant phenotype

(Wilk et al., 1996)

involved_in positive regulation of transcription by RNA polymerase II

inferred from mutant phenotype

(Morozova et al., 2010)

involved_in salivary gland development

inferred from mutant phenotype

(Wilk et al., 1996)

involved_in salivary gland morphogenesis

inferred from mutant phenotype

(Haberman et al., 2003)

involved_in spiracle morphogenesis, open tracheal system

inferred from mutant phenotype

(Hu and Castelli-Gair, 1999)

involved_in tracheal pit formation in open tracheal system

inferred from mutant phenotype

(Brodu and Casanova, 2006)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in regulation of DNA-templated transcription

inferred from electronic annotation with InterPro:IPR013767

(InterPro Project Members, 2004-)

involved_in regulation of transcription by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN000548738

(GO Reference Genome Project, 2011-)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Araújo and Casanova, 2011)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN008588220

(GO Reference Genome Project, 2011-)

located_in nucleus

inferred from sequence or structural similarity with UniProtKB:P05709

(Wilk et al., 1996)

inferred from sequence or structural similarity with FLYBASE:sim; FB:FBgn0004666

(Isaac and Andrew, 1996)

inferred from sequence or structural similarity with UniProtKB:Q16665

(Isaac and Andrew, 1996)

Gene Group (FlyBase)

BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS

Protein Family (UniProt)

-

Protein Signatures (InterPro)

Summaries

Gene Snapshot

trachealess (trh) encodes a bHLH-PAS nuclear transcription factor required for the formation of the tube of the salivary duct, trachea and filzkorper. It is also required for expression of all tracheal genes. [Date last reviewed: 2019-03-14]

Gene Group (FlyBase)

BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS -: Basic helix-loop-helix (bHLH) transcription factors are sequence-specific DNA-binding proteins that regulate transcription. They are characterized by a 60 amino acid region comprising a basic DNA binding domain followed by a HLH motif formed from two amphipathic α-helices connected by a loop. bHLH transcription factors form homo- and hetero-dimeric complexes, which bind to a E box consensus sequence. (Adapted from PMID:15186484).

Protein Function (UniProtKB)

Transcription factor, master regulator of tracheal cell fates in the embryo, necessary for the development of the salivary gland duct, Malpighian tubules and the posterior spiracles (PubMed:10502111, PubMed:8557189, PubMed:8557198, PubMed:9374395). It may induce a general fate of branched tubular structures of epithelial origin (PubMed:10502111, PubMed:8557189, PubMed:8557198). Functions with tgo to regulate expression of btl (PubMed:9374395).

(UniProt, Q24119)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

trh: trachealess

Embryonic lethal. Tracheae are absent and filzkorper not elongated.

Summary (Interactive Fly)

bHLH-PAS nuclear transcription factor required for the formation of the tube of the salivary duct, trachea and filzkorper - required for expression of all tracheal genes - mutants exhibit a defect in the ability of the tracheal precursors to organize tubes, the same defect seen in salivary glands

Interactive Fly

Gene Model and Products

Number of Transcripts

7

Number of Unique Polypeptides

7

Please see the JBrowse view of Dmel\trh 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 Q24119)

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 5.44

Stop-codon suppression (UAG) postulated; FBrf0216884.

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

Gene model reviewed during 5.46

Gene model reviewed during 5.56

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

FBtr0304120

4588

958

FBtr0304121

4501

929

FBtr0304122

4517

966

FBtr0330146

4588

1022

FBtr0330147

4570

952

FBtr0333901

4586

989

FBtr0333902

4483

923

Additional Transcript Data and Comments

Reported size (kB)

4.565 (compiled cDNA)

(Isaac and Andrew, 1996)

4.489 (compiled cDNA)

(Wilk et al., 1996)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

FBpp0293063

102.2

958

7.09

FBpp0293064

99.3

929

7.02

FBpp0293065

103.6

966

7.15

FBpp0303179

109.2

1022

7.14

FBpp0303180

101.6

952

7.17

FBpp0306032

105.9

989

7.26

FBpp0306033

98.7

923

7.10

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

924 (aa)

(Isaac and Andrew, 1996)

949 (aa); 150 (kD observed)

(Wilk et al., 1996)

Comments

External Data

Subunit Structure (UniProtKB)

Efficient DNA binding requires dimerization with another bHLH protein. Heterodimer with tgo.

(UniProt, Q24119)

Post Translational Modification

Ser-673 phosphorylation by PKB/Akt1 is required for nuclear targeting and transcriptional activity.

(UniProt, Q24119)

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\trh using the Feature Mapper tool.

External Data

Crossreferences

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

trh_1
trh_2

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).

-1.06

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

(Wilk et al., 1996)

tracheal primordium

(Haberman et al., 2003, Wilk et al., 1996)

larval tracheal system

(Wilk et al., 1996)

salivary gland body primordium

(Wilk et al., 1996)

presumptive embryonic salivary gland

(Haberman et al., 2003)

embryonic stage 8 -- 17

embryonic/larval tracheal section

(Isaac and Andrew, 1996)

embryonic/larval salivary gland

(Isaac and Andrew, 1996)

embryonic/larval salivary gland duct

(Isaac and Andrew, 1996)

embryonic stage 9 -- 10

salivary gland body primordium

Comment: reported as salivary gland anlage

(Fisher et al., 2012)

tracheal primordium

Comment: reported as tracheal system anlage

(Fisher et al., 2012)

embryonic stage 10

tracheal primordium

(Sotillos et al., 2010, Hombria et al., 2005)

salivary gland body primordium

(Sotillos et al., 2010)

embryonic stage 10 -- 11

tracheal primordium

(Karsten et al., 2006, Affolter and Shilo, 2000)

salivary gland body primordium

(Karsten et al., 2006)

embryonic stage 11

embryonic labial segment

(Brown et al., 2001)

(Brown et al., 2001)

embryonic/larval tracheal section

(Chung et al., 2011)

presumptive embryonic salivary gland

(Chung et al., 2011)

embryonic stage 11 -- 12

salivary gland body primordium

Comment: reported as salivary gland primordium

(Fisher et al., 2012)

tracheal primordium

(Fisher et al., 2012)

embryonic stage 11 -- 17

(Isaac and Andrew, 1996)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic salivary gland duct

(Fisher et al., 2012)

larval nervous system

(Fisher et al., 2012)

embryonic/larval salivary gland common duct

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

embryonic stage 13 -- 17

central nervous system | restricted

(Isaac and Andrew, 1996)

embryonic stage 14

tracheal section

(Hombria et al., 2005)

larval central nervous system

(Chung et al., 2011)

(Tajiri et al., 2007)

tarsal segment 5

(Tajiri et al., 2007)

Additional Descriptive Data

In situ hybridization with probes specific to the three isoforms of trh show that all display similar expression patterns in the embryo. Expression is observed in the tube-forming cells of the salivary duct, trachea, and filzkorper, and in a subset of cells in the central nervous system.

(Chung et al., 2011)

trh transcripts are detected in the entire salivary gland primordia by embryonic stage 9 but disappear from the secretory cells during stage 12. Expression in tracheal cells begins in stage 8 and continues throughout embryogenesis. trh is expressed in the cells that connect the trachea to the posterior spiracles (which will form the filzkorper) starting in stage 11. It is also expressed in a subset of CNS cells.

(Isaac and Andrew, 1996)

trh transcripts are expressed initially in the trahceal placodes, tracheal pits, and in salivary placodes. Later, they are expressed in migrating tracheal cells.

(Wilk et al., 1996)

Marker for

(Brown et al., 2001)

tracheal primordium

(Hombria et al., 2005)

tracheal section

(Hombria et al., 2005)

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

larval tracheal system

(Wilk et al., 1996)

tracheal section

• nucleus

(Dorfman et al., 2002)

embryonic stage 10

salivary gland duct anlage & salivary gland body primordium

(Andrew et al., 2000)

embryonic stage 11

tracheal primordium

(Jin et al., 2001)

embryonic stage 11 -- 14

salivary gland duct primordium

(Andrew et al., 2000)

embryonic stage 12 -- 13

tracheal primordium

(Adryan et al., 2000)

embryonic stage 14

embryonic/larval posterior spiracle

(Wilk et al., 1996)

embryonic stage 14 -- 17

larval tracheal system

(Adryan et al., 2000)

embryonic stage 15

embryonic/larval salivary gland duct

(Wilk et al., 1996)

embryonic salivary gland duct

(Andrew et al., 2000)

third instar larval stage

(Tajiri et al., 2007)

leg disc | restricted

(Tajiri et al., 2007)

Additional Descriptive Data

Protein is detected in 10 ectodermal placodes along each dorsal-lateral side of the embryo.

(Jin et al., 2001)

trh protein is detected in the nuclei of all tracheal cells. Staining is also observed in the salivary gland ducts and cells that will give rise to the posterior spiracles. Weak staining is seen in salivary glands.

(Wilk et al., 1996)

Marker for

larval tracheocyte

(Franch-Marro and Casanova, 2000)

Subcellular Localization

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Araújo and Casanova, 2011)

Expression Deduced from Reporters

Reporter: P{ET-L}trh-1-eve-1

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

embryonic/larval tracheal section

(Perrimon et al., 1991)

embryonic stage & larval stage

larval tracheal system

(Wilk et al., 1996)

embryonic stage 10

(Wilk et al., 1996)

embryonic stage 10 -- 17

larval tracheal system

(Samakovlis et al., 1996)

presumptive embryonic/larval tracheal system

(Wilk et al., 2000)

embryonic stage 11 -- 14

tracheal primordium

(Wolf and Schuh, 2000)

tracheal dorsal trunk anterior branch primordium

(Wolf and Schuh, 2000)

tracheal dorsal trunk posterior branch primordium

(Wolf and Schuh, 2000)

tracheal fusion cell

(Wolf and Schuh, 2000)

embryonic stage 11 -- 17

larval tracheal system

(Perrimon et al., 1991)

embryonic stage 13

embryonic/larval tracheal section

(Kamimura et al., 2001)

embryonic stage 15

embryonic/larval salivary gland duct

(Wilk et al., 1996)

third instar larval stage

leg disc | restricted

(Tajiri et al., 2007)

Reporter: P{GMR14D03-GAL4}

Stage

Tissue/Position (including subcellular localization)

Reference

adult tracheal section

(Guo et al., 2013)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\trh in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\trh

View exonic expression by tissue for Dmel\trh

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0262139

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

38065/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0262139

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0262139

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG42865

Images

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 41 )

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 trh

Transgenic constructs containing regulatory region of trh

Aberrations (Deficiencies and Duplications) ( 15 )

Inferred from experimentation ( 15 )

Gene not disrupted in

(Isaac and Andrew, 1996)

(Spradling et al., 1999, Isaac and Andrew, 1996)

(Isaac and Andrew, 1996)

(Spradling et al., 1999, Isaac and Andrew, 1996)

(BDGP Project Members, 1994-1999)

Inferred from location ( 5 )

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

lethal | pupal stage, with Scer\GAL4^pnr-MD237

trh^GD12826

lethal | recessive

lethal - all die during embryonic stage | recessive

partially lethal - majority die | pupal stage, with Scer\GAL4^pnr-MD237

trh^GD12826

partially lethal - majority die | recessive

trh¹⁰⁵¹²

Other Phenotypes

Allele

abnormal neuroanatomy | embryonic stage

trh¹⁰⁵¹²

some die during embryonic stage | recessive

visible, with Scer\GAL4^pnr-MD237

trh^GD12826

visible | male limited, with Scer\GAL4^Bx-MS1096

trh^{UAS.ORF.GW.Tag:HA}

Phenotype manifest in

Allele

abdominal lateral pentascolopidial chordotonal organ lch5 & growth cone

trh¹⁰⁵¹²

chaeta | increased number, with Scer\GAL4^pnr-MD237

trh^GD12826

embryonic/first instar larval cuticle

trh¹⁰⁵¹²

embryonic/larval dorsal tracheal branch, with Scer\GAL4^hs.2sev

trh^{DN.UAS.Tag:T7}

embryonic/larval hindgut | embryonic stage

trh¹

embryonic/larval salivary gland | embryonic stage

embryonic/larval salivary gland duct | embryonic stage

trh^ET

embryonic/larval tracheal dorsal trunk, with Scer\GAL4^hs.2sev

trh^{DN.UAS.Tag:T7}

embryonic/larval tracheal section

embryonic/larval tracheal section | embryonic stage

trh⁸

embryonic epidermis, with Scer\GAL4^69B

trh^UAS.cWa

embryonic epidermis, with Scer\GAL4^ptc-559.1

trh^UAS.cWa

embryonic salivary gland duct

larval muscle system

trh³

larval tracheocyte

trh¹

Malpighian tubule

presumptive embryonic/larval tracheal system

trh¹

pulvillus | somatic clone

trh¹⁰⁵¹²

tarsal segment 4 | somatic clone - Minute background

trh¹⁰⁵¹²

tarsal segment 5 | somatic clone - Minute background

trh¹⁰⁵¹²

tracheal branch primordium

tracheal branch primordium, with Scer\GAL4^hs.2sev

trh^{DN.UAS.Tag:T7}

tracheal pit, with Scer\GAL4^hs.2sev

tracheal pit | ectopic, with Scer\GAL4^salm-459.2

trh^UAS.cWa

tracheal primordium

trh¹

tracheal primordium | ectopic, with Scer\GAL4^arm.PS

tracheal section

unguis | somatic clone

trh¹⁰⁵¹²

unguis | somatic clone - Minute background

trh¹⁰⁵¹²

trh¹

wing | male limited, with Scer\GAL4^Bx-MS1096

trh^{UAS.ORF.GW.Tag:HA}

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (28)

11 of 14

Yes

Yes

10 of 14

No

Yes

6 of 14

No

No

6 of 14

No

No

1

4 of 14

No

No

4 of 14

No

No

1

4 of 14

No

No

1 of 14

No

No

1

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1

1 of 14

No

No

1

1 of 14

No

No

1 of 14

No

No

1

1 of 14

No

No

2

1 of 14

No

No

1

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1

1 of 14

No

No

3

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (17)

11 of 14

Yes

Yes

6 of 14

No

No

5 of 14

No

No

5 of 14

No

No

4 of 14

No

No

4 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

Yes

1 of 14

No

No

Mus musculus (laboratory mouse) (17)

10 of 14

Yes

Yes

10 of 14

Yes

Yes

6 of 14

No

No

6 of 14

No

No

4 of 14

No

No

4 of 14

No

No

4 of 14

No

No

1 of 14

No

No

2

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

Xenopus tropicalis (Western clawed frog) (14)

7 of 13

Yes

Yes

4 of 13

No

No

2 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

1 of 13

No

No

Danio rerio (Zebrafish) (25)

10 of 14

Yes

Yes

10 of 14

Yes

Yes

6 of 14

No

No

6 of 14

No

No

5 of 14

No

No

5 of 14

No

No

5 of 14

No

No

5 of 14

No

No

4 of 14

No

Yes

4 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

Caenorhabditis elegans (Nematode, roundworm) (5)

10 of 14

Yes

Yes

5 of 14

No

No

1 of 14

No

No

1 of 14

No

No

1 of 14

No

No

Anopheles gambiae (African malaria mosquito) (15)

Agam\AgaP_AGAP000056

10 of 12

Yes

Yes

Agam\AgaP_AGAP000773

5 of 12

No

No

Agam\AgaP_AGAP010058

4 of 12

No

No

Agam\AgaP_AGAP002942

3 of 12

No

No

Agam\AgaP_AGAP001856

1 of 12

No

No

Agam\AgaP_AGAP003844

1 of 12

No

No

Agam\AgaP_AGAP003965

1 of 12

No

No

Agam\AgaP_AGAP005655

1 of 12

No

No

Agam\AgaP_AGAP005711

1 of 12

No

No

Agam\AgaP_AGAP006022

1 of 12

No

No

Agam\AgaP_AGAP007450

1 of 12

No

No

Agam\AgaP_AGAP009664

1 of 12

No

No

Agam\AgaP_AGAP009748

1 of 12

No

No

Agam\AgaP_AGAP010259

1 of 12

No

No

Agam\AgaP_AGAP012873

1 of 12

No

No

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:trh. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (12)

9 of 13

7 of 13

3 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

cancer, tracheal model of angiogenesis

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?

NPAS1; neuronal PAS domain protein 1

11 of 14

NPAS3; neuronal PAS domain protein 3

10 of 14

SIM1; SIM bHLH transcription factor 1

6 of 14

SIM2; SIM bHLH transcription factor 2

6 of 14

EPAS1; endothelial PAS domain protein 1

4 of 14

ERYTHROCYTOSIS, FAMILIAL, 4; ECYT4

familial erythrocytosis 4

HIF1A; hypoxia inducible factor 1 subunit alpha

4 of 14

HYPOXIA-INDUCIBLE FACTOR 1, ALPHA SUBUNIT; HIF1A

HIF3A; hypoxia inducible factor 3 subunit alpha

4 of 14

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

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

two hybrid array

(Shokri et al., 2019)

(Ma et al., 2000)

two hybrid array

(Shokri et al., 2019)

anti tag coimmunoprecipitation, anti tag western blot

(Mortimer and Moberg, 2007)

two hybrid array

(Shokri et al., 2019)

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, anti tag western blot, two hybrid, two hybrid array

(Shokri et al., 2019, Sonnenfeld et al., 2010, Sonnenfeld et al., 1997)

pull down, autoradiography

(Zelzer and Shilo, 2000)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

(Jin et al., 2001)

enhanceable

(Sedaghat et al., 2002)

enhanceable

(Sedaghat et al., 2002)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

(Mortimer and Moberg, 2007)

External Data

Subunit Structure (UniProtKB)

Efficient DNA binding requires dimerization with another bHLH protein. Heterodimer with tgo.

(UniProt, Q24119 )

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0262139

MIST (genetic) - An integrated Molecular Interaction Database

38065

MIST (protein-protein) - An integrated Molecular Interaction Database

38065

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

gene_with_stop_codon_read_through

(Jungreis et al., 2011)

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

3L

Recombination map

3-0.5

Cytogenetic map

Sequence location

3L:366,524..392,633 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

61C1-61C1

Limits computationally determined from genome sequence between P{PZ}trh¹⁰⁵¹² and P{EP}EP3104^EP3104

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Differs from the previously reported cytological location for trh (FBrf0041709).

(Isaac and Andrew, 1996)

61B3-61C3

(Shilo, 1995.8.8)

61C1-61C2

(Andrew, 1995.12.8, BDGP Project Members, 1994-1999)

61C1-61C2

(determined by in situ hybridisation)

(Spradling et al., 1999, Isaac and Andrew, 1996, Perrimon et al., 1996, Issac and Andrew, 1995)

61C-61C

(Gibson et al., 1999)

Experimentally Determined Recombination Data

Location

3-0.5

(FlyBase, 2016)

3-0.1

(Comeron et al., 2012)

3-1

(Tearle and Nusslein-Volhard, 1987)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (77)

Genomic Clones (19)

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

cDNA Clones (36)

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

RH17284

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.

FBgn0262139

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0262139

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Rosa et al., 2018, Hsouna et al., 2010, Wilk et al., 1996)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

dsRNA has been made from templates generated with primers directed against this gene. RNAi of trh results in reduction of the dendritic field size of ddaE and ddaD neurons. There is a minor reduction in both primary branch outgrowth and the number of lateral branches and a more marked reduction in the overall length of lateral branches. Consequently, the most distal regions of the dendritic field are not innervated. RNAi also causes defects in muscle, defects in dendrite morphogenesis but does not cause obvious defects in da dendrite development.

(Parrish et al., 2006)

Annotation CG13885 restored in release 4.3 of the genome annotation.

(FlyBase Genome Annotators, 2005)

Annotation CG13885 was eliminated in release 3 of the genome annotation, October 2002.

(FlyBase Genome Annotators, 2002-2003)

Nuclear localisation of the tgo protein is dependent on the presence of either sim or trh protein, and nuclear entry of sim or trh protein requires interaction with tgo protein.

(Ward et al., 1998)

btl expression in the developing trachea is regulated by direct interactions between trh/tgo heterodimers and three central midline elements located in the btl minimum enhancer.

(Ohshiro and Saigo, 1997)

trh induces tracheal cell fates.

(Shilo et al., 1997)

sim and trh activate transcription by forming dimers with the tgo protein. Gene dosage studies reveal in vivo interactions between sim and tgo, and trh and tgo. The interacting proteins in vivo control CNS midline and tracheal transcription and development.

(Sonnenfeld et al., 1997)

The PAS domain of trh confers its target gene specificity.

(Zelzer et al., 1997)

The trh product is required for tubulogenesis.

(Isaac and Andrew, 1996)

The distinction between pregland and preduct cells is made by the combination of two spatially separated negative regulatory steps: the Egfr signaling pathway represses fkh in the preduct cells and fkh represses duct specific genes in the pregland cells. trh is a duct-specific gene activator and is one of the targets of fkh repression.

(Kuo et al., 1996)

The autosomal "FLP-DFS" technique (using the P{ovoD1-18} P{FRT(w^hs)} P{hsFLP} chromosomes) has been used to study the zygotic lethal mutation.

(Perrimon et al., 1996)

trh encodes a bHLH-PAS protein that is an inducer of tracheal cell fates. Expression is first induced by exogenous cues and is subsequently autoregulated. The role of trh in the formation of several tubular tissues in the embryo suggests it may induce a general fate of branched tubular structures of epithelial origin.

(Wilk et al., 1996)

trh is required for both salivary gland and tracheal development, and may be a direct downstream target of Scr.

(Issac and Andrew, 1995)

trh and the spi group of genes probably act in two separate pathways that are both necessary for proper salivary duct development. In the absence of trh pre-duct cells are not specified.

(Jones et al., 1995)

trh mutants display no tracheae and the filzkorper are not elongated.

(Jurgens et al., 1984)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG13885 HDC07747

(FlyBase Genome Annotators, 2005)

Source for merge of: trh CG13885

(FlyBase Genome Annotators, 2010)

Additional comments

Annotations CG6883 and CG13885 merged as CG42865 in release 5.30 of the genome annotation.

(FlyBase Genome Annotators, 2010)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (14)

Reported As

Symbol Synonym

3.1

(Gibson et al., 1999)

BP1081

(Yandell et al., 2005)

CG13885

(Sotillos et al., 2010, Keleman et al., 2009.8.5)

CG42865

(FlyBase Genome Annotators, 2010, Ni et al., 2010.12.1)

CG6883

(Keleman et al., 2009.8.5, Perkins et al., 2009, Stevens et al., 2008, Stevens et al., 2008)

DMU42699

(Colson and Goldstein, 1999)

HDC07747

TRH

(Brodu and Casanova, 2006, Nagao and Yanagida, 2002, Haberman et al., 2001, Henderson and Andrew, 2000, Colson and Goldstein, 1999)

bHLHe13

(Stevens et al., 2008)

l(3)10512

(Perrimon et al., 1996)

trachealess

(Hombría and Sotillos, 2013, Edwards et al., 2006)

trh

(Peng et al., 2024, Collins et al., 2023, Corthals et al., 2023, Fisher et al., 2023, Guzman et al., 2021, Anllo et al., 2019, Chen et al., 2019, Kondo and Hayashi, 2019, Lovato et al., 2019, Shokri et al., 2019, Zhou et al., 2019, Bischof et al., 2018, Ogura et al., 2018, Calleja et al., 2016, Peng et al., 2016, Sánchez-Higueras and Hombría, 2016, Matsuda et al., 2015, Matsuda et al., 2015, Schertel et al., 2015, Ashwal-Fluss et al., 2014, Kondo et al., 2014, Sánchez-Higueras et al., 2014, Tsikala et al., 2014, Hombría and Sotillos, 2013, Ismat et al., 2013, Mortimer and Moberg, 2013, Spokony and White, 2013.7.5, Japanese National Institute of Genetics, 2012.5.21, Zhou et al., 2012, Bellen et al., 2011, Chung et al., 2011, Jungreis et al., 2011, Letizia et al., 2011, Tolhuis et al., 2011, Baer et al., 2010, Biehs et al., 2010, Brodu et al., 2010, Hsouna et al., 2010, Kerman and Andrew, 2010, Morozova et al., 2010, Sonnenfeld et al., 2010, Sotillos et al., 2010, Christensen et al., 2009.5.6, Chung et al., 2009, Cook et al., 2009.11.25, Mortimer and Moberg, 2009, Hauenschild et al., 2008, Shindo et al., 2008, Weaver and Krasnow, 2008, Araujo et al., 2007, Choi et al., 2007, Christensen et al., 2007.10.29, Harris and Beckendorf, 2007, Inoue and Hayashi, 2007, Jiang and Crews, 2007, Krattinger et al., 2007, Nishimura et al., 2007, Parrish et al., 2007, Tajiri et al., 2007, Arbouzova et al., 2006, Franch-Marro et al., 2006, Gresens and Cook, 2006.12.5, Jung et al., 2006, Kamimura et al., 2006, Karsten et al., 2006, Ng et al., 2006, Hombria et al., 2005, Rawlings et al., 2004, Jiang and Crews, 2003, Myat et al., 2000)

Name Synonyms

Trachealess

(Reid and O'Brochta, 2016, Chandran et al., 2014, Chung et al., 2011, Morozova et al., 2010, Sonnenfeld et al., 2010, Chung et al., 2009, Massarwa et al., 2009, Centanin et al., 2008, Chung et al., 2008, Hsouna and Hsu, 2008, Choi et al., 2007, Mortimer and Moberg, 2007, Mortimer and Moberg, 2007, Cela and Llimargas, 2006, Jiang and Crews, 2006)

Secondary FlyBase IDs

FBgn0010944
FBgn0026793
FBgn0082659
FBan0006883
FBgn0003749
FBgn0040689
FBgn0260471

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 58 )

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.

38065

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.

Q24119

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q24119

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.

Q24119

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0262139

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

38065/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0262139

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0262139

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

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

dme:Dmel_CG42865

MARRVEL_MODEL - MARRVEL (model organism gene)

38065

Linkouts

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

FBgn0262139

DroID - A comprehensive database of gene and protein interactions.

FBgn0262139

DRSC - Results frm RNAi screens

FBgn0262139

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

trh_1
trh_2

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0262139

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG42865

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC001448

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

MIST (genetic) - An integrated Molecular Interaction Database

38065

MIST (protein-protein) - An integrated Molecular Interaction Database

38065

References (281)