fox-1 Sex determination protein fox-1 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: fox-1
Official Full Name: Sex determination protein fox-1
Primary source: WormBase:WBGene00001484
Locus tag: CELE_T07D1.4
See related: AllianceGenome:WB:WBGene00001484
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 pre-mRNA intronic binding activity and single-stranded RNA binding activity. Involved in several processes, including mRNA alternative trans-splicing; primary sex determination; and regulation of gene expression. Located in nucleus. Is expressed in several structures, including body wall musculature; intestine; pharynx; tail; and vulval muscle. Human ortholog(s) of this gene implicated in congenital heart disease. Orthologous to several human genes including RBFOX1 (RNA binding fox-1 homolog 1) and RBFOX3 (RNA binding fox-1 homolog 3). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See fox-1 in Genome Data Viewer

Location:: chromosome: X

Exon count:: 8

Sequence:: Chromosome: X; NC_003284.9 (2445475..2455949, complement)

Chromosome X - NC_003284.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003284.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Dose-dependent action of the RNA binding protein FOX-1 to relay X-chromosome number and determine C. elegans sex.
Title: Dose-dependent action of the RNA binding protein FOX-1 to relay X-chromosome number and determine C. elegans sex.
Here we combine RNA-seq with in vitro binding assays to study how 4 different C. elegans SFs, ASD-1, FOX-1, MEC-8, and EXC-7, regulate splicing. The 4 SFs chosen all have well-characterised biology and well-studied loss-of-function genetic alleles, and all contain RRM domains
Title: The combinatorial control of alternative splicing in C. elegans.
SUP-12, coregulates the egl-15 alternative splicing.
Title: The Fox-1 family and SUP-12 coordinately regulate tissue-specific alternative splicing in vivo.

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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

T07D1.4 (e-PCR)
- UniSTS:310718

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables poly(A) binding	IDA Inferred from Direct Assay more info	PubMed
enables poly(G) binding	IDA Inferred from Direct Assay more info	PubMed
enables poly(U) RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables pre-mRNA intronic binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in dosage compensation by hypoactivation of X chromosome	IGI Inferred from Genetic Interaction more info	PubMed
involved_in dosage compensation by hypoactivation of X chromosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA alternative trans-splicing	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mating behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in primary sex determination	IGI Inferred from Genetic Interaction more info	PubMed
involved_in primary sex determination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of alternative mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of alternative mRNA splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in regulation of alternative mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sex differentiation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor 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 determination protein fox-1

NP_001317738.1

Confirmed by transcript evidence

NP_001317857.1

Confirmed by transcript evidence

NP_001317861.1

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_003284.9 Reference assembly

Range

2445475..2455949 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001330895.6 → NP_001317738.1 Sex determination protein fox-1 [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q10572
NM_001330894.3 → NP_001317857.1 Sex determination protein fox-1 [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/Swiss-Prot

A0A168HBS9, A0A168HBX9, Q10572, Q22304

Conserved Domains (2) summary

TIGR01628
Location:185 → 417

PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family

cd12407
Location:183 → 258

RRM_FOX1_like; RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins
NM_001330896.3 → NP_001317861.1 Sex determination protein fox-1 [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A168HBX9

Conserved Domains (2) summary

TIGR01628
Location:96 → 328

PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family

cd12407
Location:94 → 169

RRM_FOX1_like; RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins