trh trachealess [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: trhprovided by FlyBase
Official Full Name: trachealessprovided by FlyBase
Primary source: FLYBASE:FBgn0262139
Locus tag: Dmel_CG42865
See related: AllianceGenome:FB:FBgn0262139
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Drosophila melanogaster
Lineage: Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as: 3.1; bHLHe13; BP1081; CG13885; CG42865; CG6883; Dmel\CG42865; DMU42699; HDC07747; l(3)10512; Trh; TRH
Old locus tag: CG13885; Dmel_CG13885; Dmel_CG6883
Summary: Enables DNA-binding transcription factor activity; protein heterodimerization activity; and sequence-specific DNA binding activity. Contributes to DNA-binding transcription activator activity, RNA polymerase II-specific. Involved in several processes, including epithelial tube morphogenesis; open tracheal system development; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including central nervous system; epithelial tube; ganglia; organism subdivision; and tracheal primordium. Orthologous to human NPAS1 (neuronal PAS domain protein 1) and NPAS3 (neuronal PAS domain protein 3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: 61C1-61C1; 3-0.5 cM

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	3L	NT_037436.4 (366524..392633, complement)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	3L	NT_037436.3 (366524..392633, complement)

Chromosome 3L - NT_037436.4 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

an upstream regulatory region of cv is directly responsive to the basic, helix-loop-helix-PAS domain factors Trachealess (Trh) and Tango (Tgo), that function to specify tracheal fate.
Title: Crossveinless is a direct transcriptional target of Trachealess and Tango in Drosophila tracheal precursor cells.
The authors propose that the coupling of trachealess expression with the invaginated epithelial sheet structure ensures that only invaginated cells canalize robustly into the tracheal fate.
Title: Two-step regulation of trachealess ensures tight coupling of cell fate with morphogenesis in the Drosophila trachea.
In the mutant for Trh smaller synaptic boutons form clusters named satellite boutons appear at larval neuromuscular junctions, which is induced by the reduction of internal oxygen levels due to defective tracheal branches. Sima is critical in mediating hypoxia-induced satellite bouton formation. Sima upregulates the level of the Wg signal in glia, leading to reorganized microtubule structures within presynaptic sites.
Title: Glial response to hypoxia in mutants of NPAS1/3 homolog Trachealess through Wg signaling to modulate synaptic bouton organization.
expression of every tracheal gene we tested was dependent on Trh, suggesting a major role for Trh in activation and maintenance of tracheal gene expression
Title: Trachealess (Trh) regulates all tracheal genes during Drosophila embryogenesis.
Study shows that jing is a direct downstream target of Trh/Tgo and that Vvl and Pnt are also involved in jing tracheal activation.
Title: The Drosophila jing gene is a downstream target in the Trachealess/Tango tracheal pathway.
three genes, dead ringer (dri), Serrate (Ser), and trh itself, are expressed in the embryonic salivary duct independently of trh
Title: Specification of cell fates within the salivary gland primordium.
trachealess and tango, both encoding bHLH-PAS proteins that are required for the formation of the embryonic tracheal system, are essential for forming two adjacent distal segments of the leg
Title: Fate determination of Drosophila leg distal regions by trachealess and tango through repression and stimulation, respectively, of Bar homeobox gene expression in the future pretarsus and tarsus.
competitive interactions between basic helix-loop-helix-PAS proteins (Dysfusion, Trachealess, and possibly Similar) may be important for the proper development of the trachea
Title: The Drosophila dysfusion basic helix-loop-helix (bHLH)-PAS gene controls tracheal fusion and levels of the trachealess bHLH-PAS protein.
Activity of crossveinless-c, a gene coding for a RhoGAP and whose specific transcriptional activation in the tracheal cells is triggered by both the trachealess patterning gene and the EGF Receptor (EGFR) signaling pathway.
Title: The RhoGAP crossveinless-c links trachealess and EGFR signaling to cell shape remodeling in Drosophila tracheal invagination.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by FlyBase

Function	Evidence Code	Pubs
contributes_to DNA-binding transcription activator activity, RNA polymerase II-specific	IPI Inferred from Physical Interaction more info	PubMed
contributes_to DNA-binding transcription factor activity	IPI Inferred from Physical Interaction more info	PubMed
enables DNA-binding transcription factor activity	IPI Inferred from Physical Interaction more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in Malpighian tubule morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in appendage development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epithelial cell fate determination, open tracheal system	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epithelial tube formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in open tracheal system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in salivary gland development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in salivary gland morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spiracle morphogenesis, open tracheal system	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tracheal pit formation in open tracheal system	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info	PubMed

General protein information

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Preferred Names: trachealess

Names: CG42865-PA; CG42865-PB; CG42865-PC; CG42865-PD; CG42865-PE; CG42865-PF; CG42865-PG; trh-PA; trh-PB; trh-PC; trh-PD; trh-PE; trh-PF; trh-PG

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NT_037436.4 Reference assembly

Range

366524..392633 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001274280.1 → NP_001261209.1 trachealess, isoform F [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001261209.1

Status: REVIEWED

UniProtKB/TrEMBL

F9W343, M9PE27

Conserved Domains (5) summary

smart00091
Location:213 → 273

PAS; PAS domain

cd00083
Location:122 → 174

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

cd00130
Location:434 → 536

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam00989
Location:217 → 273

PAS; PAS fold

pfam08447
Location:446 → 533

PAS_3; PAS fold
NM_001103991.2 → NP_001097461.2 trachealess, isoform C [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001097461.2

Status: REVIEWED

UniProtKB/TrEMBL

F9W343

Conserved Domains (5) summary

smart00091
Location:213 → 273

PAS; PAS domain

cd00083
Location:122 → 174

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

cd00130
Location:411 → 513

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam00989
Location:217 → 273

PAS; PAS fold

pfam08447
Location:423 → 510

PAS_3; PAS fold
NM_001274281.1 → NP_001261210.1 trachealess, isoform G [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001261210.1

Status: REVIEWED

UniProtKB/TrEMBL

F9W343, M9PDQ7

Conserved Domains (5) summary

smart00091
Location:176 → 236

PAS; PAS domain

cd00083
Location:85 → 137

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

cd00130
Location:368 → 470

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam00989
Location:180 → 236

PAS; PAS fold

pfam08447
Location:380 → 467

PAS_3; PAS fold
NM_001274279.1 → NP_001261208.1 trachealess, isoform E [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001261208.1

Status: REVIEWED

UniProtKB/TrEMBL

F9W343, M9PDI8

Conserved Domains (5) summary

smart00091
Location:176 → 236

PAS; PAS domain

cd00083
Location:85 → 137

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

cd00130
Location:397 → 499

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam00989
Location:180 → 236

PAS; PAS fold

pfam08447
Location:409 → 496

PAS_3; PAS fold
NM_001043110.2 → NP_001036575.1 trachealess, isoform B [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001036575.1

Status: REVIEWED

UniProtKB/TrEMBL

F9W343, H9TV77

Conserved Domains (5) summary

smart00091
Location:176 → 236

PAS; PAS domain

cd00083
Location:85 → 137

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

cd00130
Location:374 → 476

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam00989
Location:180 → 236

PAS; PAS fold

pfam08447
Location:386 → 473

PAS_3; PAS fold
NM_079148.3 → NP_523872.2 trachealess, isoform A [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_523872.2

Status: REVIEWED

UniProtKB/TrEMBL

F9W343

Related

FBpp0293063

Conserved Domains (5) summary

smart00091
Location:176 → 236

PAS; PAS domain

cd00083
Location:85 → 137

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

cd00130
Location:403 → 505

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam00989
Location:180 → 236

PAS; PAS fold

pfam08447
Location:415 → 502

PAS_3; PAS fold
NM_001274278.1 → NP_001261207.1 trachealess, isoform D [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001261207.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A8JNH0, A8WHG8, Q0E8K2, Q24119, Q24165, Q8SX13, Q9W0Q7

UniProtKB/TrEMBL

F9W343, M9PBG9

Conserved Domains (5) summary

smart00091
Location:176 → 236

PAS; PAS domain

cd00083
Location:85 → 137

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

cd00130
Location:403 → 505

PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...

pfam00989
Location:180 → 236

PAS; PAS fold

pfam08447
Location:415 → 502

PAS_3; PAS fold