daf-19 RFX-like transcription factor daf-19 [Caenorhabditis elegans] - Gene

Summary

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Gene symbol: daf-19
Gene description: RFX-like transcription factor daf-19
Primary source: WormBase:WBGene00000914
Locus tag: CELE_F33H1.1
See related: AllianceGenome:WB:WBGene00000914
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: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in defense response to Gram-negative bacterium; positive regulation of transcription by RNA polymerase II; and regulation of non-motile cilium assembly. Acts upstream of or within serotonin biosynthetic process. Located in nucleus. Is expressed in several structures, including body wall musculature; hypodermis; intestine; neurons; and somatic nervous system. Orthologous to human RFX1 (regulatory factor X1); RFX2 (regulatory factor X2); and RFX3 (regulatory factor X3). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See daf-19 in Genome Data Viewer

Location:: chromosome: II

Exon count:: 13

Sequence:: Chromosome: II; NC_003280.10 (10157520..10169346, complement)

Chromosome II - NC_003280.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003280.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The C. elegans regulatory factor X (RFX) DAF-19M module: A shift from general ciliogenesis to cell-specific ciliary and behavioral specialization.
Title: The C. elegans regulatory factor X (RFX) DAF-19M module: A shift from general ciliogenesis to cell-specific ciliary and behavioral specialization.
Aberrant splicing of daf-19c to upstream cryptic sites results in in-frame and functional products.
Title: A splice acceptor mutation in C. elegans daf-19/Rfx disrupts functional specialization of male-specific ciliated neurons but does not affect ciliogenesis.
Our results suggest that pathogenic cues trigger a common core-signaling pathway via tissue-specific mechanisms and demonstrate a novel role for RFX factors in neuronal and innate immune responses to infection
Title: RFX transcription factor DAF-19 regulates 5-HT and innate immune responses to pathogenic bacteria in Caenorhabditis elegans.
Data suggest that an enhancer element appears to co-regulate ciliary genes in a DAF-19 dependent manner.
Title: The in vivo dissection of direct RFX-target gene promoters in C. elegans reveals a novel cis-regulatory element, the C-box.
Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.
Title: Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.
the RFX TF DAF-19 regulates ciliogenesis via X-box containing ciliogenic genes and controls ciliary specialization by regulating non-X-box containing sensory genes
Title: Functional specialization of sensory cilia by an RFX transcription factor isoform.
Data show that mutations in daf-19 result in the complete absence of all sensory cilia and thus of external sensory input.
Title: Worms with a single functional sensory cilium generate proper neuron-specific behavioral output.
Results describe and functionally characterize three different isoforms of DAF-19.
Title: Distinct isoforms of the RFX transcription factor DAF-19 regulate ciliogenesis and maintenance of synaptic activity.
Data show that the sensory function of HOB neuron requires the combined action of the EGL-46 and DAF-19 regulatory pathways.
Title: Distinct roles of transcription factors EGL-46 and DAF-19 in specifying the functionality of a polycystin-expressing sensory neuron necessary for C. elegans male vulva location behavior.

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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

F33H1.1 (e-PCR)
- UniSTS:321430

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	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

Process	Evidence Code	Pubs
involved_in defense response to Gram-negative bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in male mating behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	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 gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within serotonin biosynthetic process	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	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: RFX-like transcription factor daf-19

NP_001022139.1

Confirmed by transcript evidence

NP_001022140.1

Confirmed by transcript evidence

NP_001254236.1

Confirmed by transcript evidence

NP_001254237.1

Confirmed by transcript evidence

NP_001293485.1

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_003280.10 Reference assembly

Range

10157520..10169346 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001267307.5 → NP_001254236.1 RFX-like transcription factor daf-19 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001254236.1

Status: REVIEWED

UniProtKB/TrEMBL

C0P280

Conserved Domains (1) summary

pfam02257
Location:113 → 190

RFX_DNA_binding; RFX DNA-binding domain
NM_001026969.4 → NP_001022140.1 RFX-like transcription factor daf-19 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022140.1

Status: REVIEWED

UniProtKB/Swiss-Prot

C0P280, G5EBW8, Q09555, Q9NHC9, S6EZR7

Conserved Domains (1) summary

pfam02257
Location:257 → 332

RFX_DNA_binding; RFX DNA-binding domain
NM_001026968.5 → NP_001022139.1 RFX-like transcription factor daf-19 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022139.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q09555

Conserved Domains (1) summary

pfam02257
Location:232 → 307

RFX_DNA_binding; RFX DNA-binding domain
NM_001306556.3 → NP_001293485.1 RFX-like transcription factor daf-19 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001293485.1

Status: REVIEWED

UniProtKB/TrEMBL

S6EZR7

Conserved Domains (1) summary

pfam02257
Location:91 → 165

RFX_DNA_binding; RFX DNA-binding domain
NM_001267308.3 → NP_001254237.1 RFX-like transcription factor daf-19 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001254237.1

Status: REVIEWED

UniProtKB/TrEMBL

G5EBW8

Conserved Domains (1) summary

pfam02257
Location:75 → 149

RFX_DNA_binding; RFX DNA-binding domain