irx1a iroquois homeobox 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: irx1aprovided by ZNC
Official Full Name: iroquois homeobox 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040707-1
See related: Ensembl:ENSDARG00000101831 AllianceGenome:ZFIN:ZDB-GENE-040707-1
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: irx1; ziro1; ziro1a; zgc:109702; zgc:136490
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 central nervous system neuron differentiation; embryonic morphogenesis; and eye development. Predicted to be active in nucleus. Is expressed in several structures, including liver; nervous system; neural plate; pericardial region; and pleuroperitoneal region. Human ortholog(s) of this gene implicated in congenital heart disease. Orthologous to human IRX1 (iroquois homeobox 1). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs: all
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Genomic context

Location:: chromosome: 16

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	16	NC_007127.7 (813574..817781)
105	previous assembly	GRCz10 (GCF_000002035.5)	16	NC_007127.6 (737662..741827)

Chromosome 16 - NC_007127.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Observations suggest that Irx2 functions downstream of irx1a to control shh expression in the retina. Study proposed a novel transcriptional cascade of ath5-irx1a-irx2a in the regulation of hedgehog waves during vertebrate retinal development.
Title: A cascade of irx1a and irx2a controls shh expression during retinogenesis.
Data revealed that expression of DNA binding inhibitor 3, early B cell factor 2, Ebf3, Iroquois related homeobox 1, Kruppel-like factor 7 , mab-21-like 1 , fatty acid binding protein 7 and stathmin-like 4,were enriched in the diencephalon of zebrafish.
Title: Expression of ventral diencephalon-enriched genes in zebrafish.
irx1a is not required for the initial specification but it is required for the complete differentiation of 5HT neurons
Title: Zebrafish homologue irx1a is required for the differentiation of serotonergic neurons.
Our results reveal a role for Iroquois genes in controlling hedgehog expression during vertebrate retinogenesis.
Title: The homeobox gene irx1a is required for the propagation of the neurogenic waves in the zebrafish retina.

Submit: New GeneRIF Correction

General gene information

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Markers

z25714 (e-PCR), detects polymorphism
- UniSTS:238876

Z9535 (e-PCR)
- UniSTS:47052

Gene Ontology Provided by ZFIN

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 DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation 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 cell development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within central nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within central nervous system neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic pectoral fin morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within eye photoreceptor cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IDA Inferred from Direct Assay more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cell cycle	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retina development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retina morphogenesis in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: iroquois-class homeodomain protein IRX-1a

Names: iroquois homeobox protein 1, a

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_207184.2 → NP_997067.2 iroquois-class homeodomain protein IRX-1a isoform 1

Status: VALIDATED

Source sequence(s)

CABZ01062628

UniProtKB/TrEMBL

Q90XQ7

Related

ENSDARP00000137879.1, ENSDART00000162474.2
NM_207185.2 → NP_997068.2 iroquois-class homeodomain protein IRX-1a isoform 2

Status: VALIDATED

Source sequence(s)

CABZ01062628

UniProtKB/TrEMBL

Q8JH33

Related

ENSDARP00000137032.1, ENSDART00000161774.2