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General Information
Symbol
Dmel\trh
Species
D. melanogaster
Name
trachealess
Annotation Symbol
CG42865
Feature Type
FlyBase ID
FBgn0262139
Gene Model Status
Stock Availability
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)
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
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (18 terms)
Molecular Function (6 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from sequence or structural similarity with FLYBASE:sim; FB:FBgn0004666
inferred from sequence or structural similarity with HGNC:4910
inferred from biological aspect of ancestor with PANTHER:PTN001889196
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR011598, InterPro:IPR036638
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN001889196
(assigned by GO_Central )
Biological Process (11 terms)
Terms Based on Experimental Evidence (10 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
(assigned by CACAO )
inferred from mutant phenotype
(assigned by UniProt )
inferred from mutant phenotype
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000548738
(assigned by GO_Central )
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
located_in nucleus
inferred from sequence or structural similarity with UniProtKB:P05709
(assigned by UniProt )
inferred from sequence or structural similarity with FLYBASE:sim; FB:FBgn0004666
inferred from sequence or structural similarity with HGNC:4910
Protein Family (UniProt)
-
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:8557189, PubMed:8557198, PubMed:9374395, PubMed:10502111). It may induce a general fate of branched tubular structures of epithelial origin (PubMed:8557189, PubMed:8557198, PubMed:10502111). 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

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
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

Sequence Ontology: Class of Gene
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)

4.489 (compiled cDNA)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
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)

949 (aa); 150 (kD observed)

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)
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\trh 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
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
salivary gland body primordium

Comment: reported as salivary gland anlage

tracheal primordium

Comment: reported as tracheal system anlage

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.

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.

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

Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\trh in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
EMBL-EBI Single Cell Expression Atlas
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Images
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 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
abdominal lateral pentascolopidial chordotonal organ lch5 & growth cone
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (8)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
9 of 15
Yes
Yes
9 of 15
Yes
Yes
3 of 15
No
No
3 of 15
No
No
2 of 15
No
No
2 of 15
No
No
2  
2 of 15
No
No
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (7)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
9 of 15
Yes
Yes
9 of 15
Yes
Yes
3 of 15
No
No
3 of 15
No
No
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
Rattus norvegicus (Norway rat) (8)
8 of 13
Yes
Yes
2 of 13
No
No
2 of 13
No
No
2 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
Yes
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (5)
6 of 12
Yes
Yes
3 of 12
No
No
2 of 12
No
No
2 of 12
No
No
2 of 12
No
No
Danio rerio (Zebrafish) (12)
9 of 15
Yes
Yes
3 of 15
No
No
3 of 15
No
No
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
2 of 15
No
Yes
2 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
8 of 15
Yes
Yes
3 of 15
No
No
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG0919021O )
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
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091501P4 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W01PJ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0O1D )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G02J4 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (3)
4 of 10
3 of 10
2 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?
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
Summary of Genetic Interactions
esyN Network Diagram
esyN Network Key:
Suppression
Enhancement

Please look at the allele data for full details of the genetic interactions
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
External Data
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.
MIST (genetic) - An integrated Molecular Interaction Database
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
External Data
Linkouts
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}EP3104EP3104
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
61B3-61C3
Differs from the previously reported cytological location for trh (FBrf0041709).
Experimentally Determined Recombination Data
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (12)
Genomic Clones (19)
 
cDNA Clones (38)
 

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
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
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 database merge of

Source for merge of: CG13885 HDC07747

Source for merge of: trh CG13885

Additional comments

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

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.

Annotation CG13885 restored in release 4.3 of the genome annotation.

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

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.

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.

trh induces tracheal cell fates.

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.

The PAS domain of trh confers its target gene specificity.

The trh product is required for tubulogenesis.

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.

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

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.

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

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.

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

Origin and Etymology
Discoverer
Etymology
Identification
External Crossreferences and Linkouts ( 55 )
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
UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
Other crossreferences
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
EMBL-EBI Single Cell Expression Atlas
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
FlyMine - An integrated database for Drosophila genomics
GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
KEGG Genes - Molecular building blocks of life in the genomic space.
MARRVEL_MODEL
modMine - A data warehouse for the modENCODE project
Linkouts
DroID - A comprehensive database of gene and protein interactions.
DRSC - Results frm RNAi screens
Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
MIST (genetic) - An integrated Molecular Interaction Database
MIST (protein-protein) - An integrated Molecular Interaction Database
Synonyms and Secondary IDs (14)
Reported As
Symbol Synonym
HDC07747
Secondary FlyBase IDs
  • FBgn0010944
  • FBgn0026793
  • FBgn0082659
  • FBan0006883
  • FBgn0003749
  • FBgn0040689
  • FBgn0260471
Datasets (0)
Study focus (0)
Experimental Role
Project
Project Type
Title
References (265)