pitx2 paired-like homeodomain 2 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: pitx2provided by ZNC
Official Full Name: paired-like homeodomain 2provided by ZNC
Primary source: ZFIN:ZDB-GENE-990714-27
See related: Ensembl:ENSDARG00000036194 AllianceGenome:ZFIN:ZDB-GENE-990714-27
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: pitx2a; pitx2c; zgc:110508
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 camera-type eye development; left/right pattern formation; and nervous system development. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Is expressed in several structures, including brain; dental epithelium; digestive system; head; and mesoderm. Used to study Axenfeld-Rieger syndrome. Human ortholog(s) of this gene implicated in Arts syndrome; Axenfeld-Rieger syndrome; Axenfeld-Rieger syndrome type 1; anterior segment dysgenesis 4; and ring dermoid of cornea. Orthologous to human PITX2 (paired like homeodomain 2). [provided by Alliance of Genome Resources, Jul 2025]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 14

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2025_04	current	GRCz12tu (GCF_049306965.1)	14	NC_133189.1 (40836464..40847539)
RS_2024_08	previous assembly	GRCz11 (GCF_000002035.6)	14	NC_007125.7 (36220499..36229825)

Chromosome 14 - NC_133189.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Disruption of foxc1 genes in zebrafish results in dosage-dependent phenotypes overlapping Axenfeld-Rieger syndrome.
Title: Disruption of foxc1 genes in zebrafish results in dosage-dependent phenotypes overlapping Axenfeld-Rieger syndrome.
Pitx2c controls cardiac rhythmicity in zebrafish larvae.
Title: Early sarcomere and metabolic defects in a zebrafish pitx2c cardiac arrhythmia model.
Pitx2c orchestrates embryonic axis extension via mesendodermal cell migration.
Title: Pitx2c orchestrates embryonic axis extension via mesendodermal cell migration.
These data further support the link between PITX2 and the WNT pathway and suggest a new role in regulation of collagen gene expression during development.
Title: PITX2 deficiency and associated human disease: insights from the zebrafish model.
Late zygotic oep mutants have strongly reduced or absent pitx2 expression in the lateral plate mesoderm (LPM), but this expression can be rescued to strong levels by restoring oep in midline structures only.
Title: Antagonistic interactions in the zebrafish midline prior to the emergence of asymmetric gene expression are important for left-right patterning.
asymmetric expression of fatty acid elongase 6 gene is controlled by left right Nodal signaling and is independent of Pitx2 function in zebrafish
Title: Mutations in zebrafish pitx2 model congenital malformations in Axenfeld-Rieger syndrome but do not disrupt left-right placement of visceral organs.
This study found PITX2 to be decreased in patients with sustained Atrial Fibrillation, suggesting a PITX2 loss of function mechanism in Atrial Fibrillation.
Title: Association Between rs2200733 Polymorphism on Chromosome 4q25 and Atrial Fibrillation in a Greek Population.
Antagonism between Nodal and Pitx2c activities sets an upper limit on parapineal cell numbers. Restricting parapineal cell number is crucial for the correct elaboration of epithalamic asymmetry.
Title: Pitx2c ensures habenular asymmetry by restricting parapineal cell number.
Pitx2, implicated in left-right asymmetry, possessed appropriate 'atypical' Pegasus binding sites in its promoter.
Title: Pegasus, the 'atypical' Ikaros family member, influences left-right asymmetry and regulates pitx2 expression.
Data indicate that retinoic acid (RA) induces the expression patterns of genes normally expressed in the posterior tooth-forming region, such as pitx2 and dlx2b.
Title: Retinoic acid expands the evolutionarily reduced dentition of zebrafish.

Submit: New GeneRIF Correction See all GeneRIFs (13)

General gene information

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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	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 anatomical structure morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in animal organ morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in camera-type eye development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within camera-type eye morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within closure of optic fissure	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cornea development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of digestive tract left/right asymmetry	IDA Inferred from Direct Assay more info
acts_upstream_of_or_within determination of left/right asymmetry in diencephalon	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in diencephalon development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic camera-type eye morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic heart tube left/right pattern formation	IDA Inferred from Direct Assay more info
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epithalamus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within face morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within habenula development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within iris morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mesendoderm development	IDA Inferred from Direct Assay more info
acts_upstream_of_or_within odontogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within prechordal plate formation	IGI Inferred from Genetic Interaction 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 convergent extension involved in gastrulation	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
acts_upstream_of_or_within regulation of vascular permeability	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within retinoic acid receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
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: pituitary homeobox 2

Names: homeobox protein PITX2; paired-like homeodomain transcription factor 2; paired-like homeodomain transcription factor 2a; pitx2b

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.