tra-1 Sex-determining transformer protein 1 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: tra-1
Official Full Name: Sex-determining transformer protein 1
Primary source: WormBase:WBGene00006604
Locus tag: CELE_Y47D3A.6
See related: AllianceGenome:WB:WBGene00006604
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including female somatic sex determination; negative regulation of transcription by RNA polymerase II; and positive regulation of neuron apoptotic process. Located in cytoplasm and nucleus. Is expressed in several structures, including germ line; gonad; intestine; nervous system; and somatic gonad precursor. Human ortholog(s) of this gene implicated in several diseases, including Culler-Jones syndrome; Pallister-Hall syndrome; anodontia; holoprosencephaly 9; and synostosis (multiple). Orthologous to human GLI1 (GLI family zinc finger 1); GLI2 (GLI family zinc finger 2); and GLI3 (GLI family zinc finger 3). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See tra-1 in Genome Data Viewer

Location:: chromosome: III

Exon count:: 18

Sequence:: Chromosome: III; NC_003281.10 (11170890..11195201, complement)

Chromosome III - NC_003281.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003281.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mutations in tra-1 and goa-1 decouple behavioural patterns from the number of X chromosomes. TRA-1 binds to a conserved binding site located in the goa-1 coding region, and downregulates goa-1 expression in hermaphrodites, particularly during embryogenesis when neuronal development largely occurs.
Title: Sex-specific regulation of neuronal functions in Caenorhabditis elegans: the sex-determining protein TRA-1 represses goa-1/Gα((i/o)).
WDR-5.1 associates with the fog-3 promoter and is required for TRA-1 to bind to fog-3 promoter.
Title: A role for WDR5 in TRA-1/Gli mediated transcriptional control of the sperm/oocyte switch in C. elegans.
TRA-1 promotes female development primarily by preventing the expression of genes involved in male development.
Title: TRA-1 ChIP-seq reveals regulators of sexual differentiation and multilevel feedback in nematode sex determination.
In the proximal germline, sperm-dependent physiological MPK-1 activation results in phosphorylation-based inactivation of NOS-3, FEM-CUL-2-mediated degradation of TRA-1 and the promotion of membrane organization during oogenesis.
Title: MPK-1 ERK controls membrane organization in C. elegans oogenesis via a sex-determination module.
The C. elegans p97/CDC-48-UFD-1-NPL-4 complex controls the sperm-oocyte switch by regulating CUL-2-mediated TRA-1A proteasome degradation.
Title: Caenorhabditis elegans p97 controls germline-specific sex determination by controlling the TRA-1 level in a CUL-2-dependent manner.
xol-1 is a transcriptional target of the terminal sex-determining factor tra-1.
Title: xol-1, the master sex-switch gene in C. elegans, is a transcriptional target of the terminal sex-determining factor TRA-1.
TRA-1 interacts with the class B synMuv genes, many of which are involved in chromatin-mediated transcriptional repression of cell proliferation
Title: TRA-1/GLI controls the expression of the Hox gene lin-39 during C. elegans vulval development.
3'UTR of the nematode homologue of GLI1, called tra-1, also contains a regulatory element through which translation is regulated by GLD-1.
Title: STAR proteins quaking-6 and GLD-1 regulate translation of the homologues GLI1 and tra-1 through a conserved RNA 3'UTR-based mechanism.
TRA-1A is negatively regulated by male-specific proteolysis that depends upon specific TRA-1A protein sequences and upon the activity of the fem genes.
Title: The C. elegans sex-determining GLI protein TRA-1A is regulated by sex-specific proteolysis.
TRA-1 is regulated by degradation mediated by a CUL-2-based ubiquitin ligase complex
Title: A CUL-2 ubiquitin ligase containing three FEM proteins degrades TRA-1 to regulate C. elegans sex determination.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Y47D3A.j (e-PCR)
- UniSTS:323935

Y47D3A.i (e-PCR)
- UniSTS:322923

Y47D3A.l (e-PCR)
- UniSTS:322924

Y47D3A.k (e-PCR)
- UniSTS:324347

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in female germ-line sex determination	TAS Traceable Author Statement more info	PubMed
involved_in female somatic sex determination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in female somatic sex determination	TAS Traceable Author Statement more info	PubMed
involved_in gonad development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in sex differentiation	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Sex-determining transformer protein 1

NP_001022880.2

Confirmed by transcript evidence

NP_001022881.2

Confirmed by transcript evidence

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

NC_003281.10 Reference assembly

Range

11170890..11195201 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001027709.4 → NP_001022880.2 Sex-determining transformer protein 1 [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/Swiss-Prot

P34708, Q95Q22, Q9U2C0

Conserved Domains (4) summary

COG5048
Location:177 → 358

COG5048; FOG: Zn-finger [General function prediction only]

COG5189
Location:272 → 362

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

sd00017
Location:246 → 270

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:292 → 319

zf-H2C2_2; Zinc-finger double domain
NM_001027710.6 → NP_001022881.2 Sex-determining transformer protein 1 [Caenorhabditis elegans]

Status: REVIEWED

Conserved Domains (1) summary

sd00017
Location:215 → 233

ZF_C2H2; C2H2 Zn finger [structural motif]