irx3.L iroquois homeobox 3 L homeolog [Xenopus laevis (African clawed frog)] - Gene

Summary

Official Symbol: irx3.L
Official Full Name: iroquois homeobox 3 L homeolog
Primary source: Xenbase:XB-GENE-480490
Locus tag: XELAEV_18022387mg
See related: EnsemblRapid:ENSXLAG00005007493 AllianceGenome:Xenbase:XB-GENE-480490
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Xenopus laevis
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus
Also known as: iro3; irx3; irx3b; xiro3; xiro-3
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. Acts upstream of or within several processes, including kidney development; regulation of neuron differentiation; and regulation of transcription by RNA polymerase II. Predicted to be located in axon; cytoplasm; and nucleus. Is expressed in anatomical system; mesenchyme; pharyngeal arch; and primary germ layer. Orthologous to human IRX3 (iroquois homeobox 3). [provided by Alliance of Genome Resources, Dec 2024]
Annotation information: Annotation category: partial on reference assembly
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Genomic context

Location:: chromosome: 4L

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
101	current	Xenopus_laevis_v10.1 (GCF_017654675.1)	4L	NC_054377.1 (33774565..33778405, complement)
100	previous assembly	Xenopus_laevis_v2 (GCF_001663975.1)	4L	NC_030730.1 (31932687..31936527, complement)

Chromosome 4L - NC_054377.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

barH-like homeobox-2 gene barhl2 acts downstream of orthodentricle-2 and together with iroquois-3 in establishment of the caudal forebrain signaling center induced by Sonic Hedgehog
Title: The conserved barH-like homeobox-2 gene barhl2 acts downstream of orthodentricle-2 and together with iroquois-3 in establishment of the caudal forebrain signaling center induced by Sonic Hedgehog.
Irx3 is transcriptionally induced by the Wnt/beta-catenin signaling pathway during anteroposterior patterning of the neural axis.
Title: Direct control of Hoxd1 and Irx3 expression by Wnt/beta-catenin signaling during anteroposterior patterning of the neural axis in Xenopus.
Irx3 is the first gene known to be necessary and sufficient to specify nephron segment fate in vivo.
Title: The prepattern transcription factor Irx3 directs nephron segment identity.

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General gene information

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Gene Ontology Provided by Xenbase

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within brain development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dorsal/ventral pattern formation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dorsal/ventral pattern formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within kidney development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within maintenance of kidney identity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mesoderm development	ISA Inferred from Sequence Alignment more info	PubMed
acts_upstream_of_or_within metanephros development	ISA Inferred from Sequence Alignment more info	PubMed
acts_upstream_of_or_within negative regulation of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of neuron differentiation	ISA Inferred from Sequence Alignment more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neural plate development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of neuron differentiation	ISA Inferred from Sequence Alignment more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within pronephros development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within proximal/distal pattern formation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within proximal/distal pattern formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within proximal/distal pattern formation involved in nephron development	ISA Inferred from Sequence Alignment more info	PubMed
acts_upstream_of_or_within proximal/distal pattern formation involved in pronephric nephron development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within specification of loop of Henle identity	ISA Inferred from Sequence Alignment more info	PubMed
acts_upstream_of_or_within specification of pronephric tubule identity	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in axon	ISA Inferred from Sequence Alignment more info	PubMed
located_in cytoplasm	ISA Inferred from Sequence Alignment more info	PubMed
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISA Inferred from Sequence Alignment more info	PubMed
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: iroquois-class homeodomain protein irx-3

Names: homeobox transcription factor iroquois 3; iroquois type homeobox

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001090735.1 → NP_001084204.1 iroquois-class homeodomain protein irx-3

See identical proteins and their annotated locations for NP_001084204.1

Status: PROVISIONAL

Source sequence(s)

AF027175

UniProtKB/Swiss-Prot

O42261, Q32NJ5

UniProtKB/TrEMBL

A0A974HN56

Related

ENSXLAP00005021290.1, ENSXLAT00005021972.1

Conserved Domains (2) summary

smart00548
Location:304 → 321

IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function

pfam05920
Location:126 → 165

Homeobox_KN; Homeobox KN domain

RefSeqs of Annotated Genomes: Xenopus laevis Annotation Release 101 details...

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

Reference Xenopus_laevis_v10.1 Primary Assembly

Genomic

NC_054377.1 Reference Xenopus_laevis_v10.1 Primary Assembly

Range

33774565..33778405 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)