alr-1 Homeobox ARX homolog alr-1 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: alr-1
Official Full Name: Homeobox ARX homolog alr-1
Primary source: WormBase:WBGene00044330
Locus tag: CELE_R08B4.2
See related: AllianceGenome:WB:WBGene00044330
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 transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including epidermis morphogenesis; positive regulation of transcription by RNA polymerase II; and sensory perception of touch. Located in nucleus. Is expressed in several structures, including anal region; hypodermal cell; neurons; socket cell; and somatic nervous system. Used to study non-syndromic X-linked intellectual disability and non-syndromic X-linked intellectual disability 1. Human ortholog(s) of this gene implicated in several diseases, including X-linked lissencephaly 2; X-linked recessive disease (multiple); corpus callosum agenesis-abnormal genitalia syndrome; gastrointestinal system cancer (multiple); and lung cancer (multiple). Orthologous to human ALX4 (ALX homeobox 4) and ARX (aristaless related homeobox). [provided by Alliance of Genome Resources, Jan 2025]
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Genomic context

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See alr-1 in Genome Data Viewer

Location:: chromosome: X

Exon count:: 6

Sequence:: Chromosome: X; NC_003284.9 (11121871..11125620, 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?

FLP neurons ectopically express the auxiliary transcription factor ALR-1 which ensures, but does not direct, differentiation to touch receptor neurons.
Title: Shared gene expression in distinct neurons expressing common selector genes.
Because ALR-1 and similar proteins (Drosophila Aristaless and human ARX) are needed for the expression of other transcription factors, we propose that proteins in this family may act to ensure differentiation more generally
Title: Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression.
role in the proper morphogenesis of the anterior hypodermis; may function cooperatively with the cell adhesion processes in maintaining the amphid sensory organs
Title: The Caenorhabditis elegans aristaless orthologue, alr-1, is required for maintaining the functional and structural integrity of the amphid sensory organs.

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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

R08B4.2 (e-PCR)
- UniSTS:322272

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 transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in amphid sensory organ development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epidermis morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron 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 cell shape	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 sensory perception of touch	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: Homeobox ARX homolog alr-1

NP_509860.1

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

11121871..11125620 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_077459.6 → NP_509860.1 Homeobox ARX homolog alr-1 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_509860.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q21836

Conserved Domains (1) summary

pfam00046
Location:121 → 174

Homeobox; Homeobox domain