Pitx3 paired-like homeodomain 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pitx3provided by RGD
Official Full Name: paired-like homeodomain 3provided by RGD
Primary source: RGD:3332
See related: Ensembl:ENSRNOG00000019194 AllianceGenome:RGD:3332
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables DNA-binding transcription factor activity. Involved in several processes, including cellular response to glial cell derived neurotrophic factor; positive regulation of cell proliferation in midbrain; and response to alkaloid. Located in chromatin; cytoplasm; and nucleus. Human ortholog(s) of this gene implicated in anterior segment dysgenesis; anterior segment dysgenesis 1; cataract; cataract 11 multiple types; and cataract 9 multiple types. Orthologous to human PITX3 (paired like homeodomain 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Restricted expression toward (RPKM 20.1) See more
Orthologs: human mouse all
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Genomic context

Location:: 1q54

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (254942550..254955325, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (245001106..245013881, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (265886766..265899947, complement)

Chromosome 1 - NC_086019.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

a significant reduction in expression of the dopaminergic regulation factors Nurr1 and Pitx3 could not effectively regulate TH in the VTA during chronic morphine dependence, which affects the survival of dopaminergic neurons and ultimately leads to neuronal pathology.
Title: Dysregulation of Dopaminergic Regulatory Factors TH, Nurr1, and Pitx3 in the Ventral Tegmental Area Associated with Neuronal Injury Induced by Chronic Morphine Dependence.
Thus, this study demonstrates for the first time a transcription regulatory role for FoxP1 on the Pitx3 gene in mammalian stem cells.
Title: FoxP1 promotes midbrain identity in embryonic stem cell-derived dopamine neurons by regulating Pitx3.
results show that the expression of both Nurr1 and Pitx3 increased in prenatally stressed adult offspring in the ventral tegmental area, whereas no changes were observed in the substantia nigra area
Title: Immunocytochemical expression of dopamine-related transcription factors Pitx3 and Nurr1 in prenatally stressed adult rats.
Pitx3-transfection in astrocytes can up-regulate brain-derived neurotrophic factor and glial cell line-derived neurotrophic factor expression and produce protective benefit to dopamine neurons
Title: Pitx3-transfected astrocytes secrete brain-derived neurotrophic factor and glial cell line-derived neurotrophic factor and protect dopamine neurons in mesencephalon cultures.
higher Pitx3 expression levels in ventral tegmental area than in substantia nigra neurons may contribute to the different vulnerability of these dopaminergic nuclei to neurodegeneration
Title: Differential expression of the homeobox gene Pitx3 in midbrain dopaminergic neurons.

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General gene information

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Markers

Pitx3 (e-PCR), detects polymorphism
- UniSTS:226063

RH142219 (e-PCR)
- UniSTS:231469

Pitx3 (e-PCR), detects polymorphism
- UniSTS:144186

UniSTS:144187 (e-PCR)
- UniSTS:144187

Pitx3 (e-PCR), detects polymorphism
- UniSTS:144187

UniSTS:256827 (e-PCR)
- UniSTS:256827

Pitx3 (e-PCR), detects polymorphism
- UniSTS:256827

AF005772 (e-PCR)
- UniSTS:160847

D1Bda64 (e-PCR)
- UniSTS:239817

Pitx3 (e-PCR), detects polymorphism
- UniSTS:547287

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
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
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in anatomical structure morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to glial cell derived neurotrophic factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in dopaminergic neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in dopaminergic neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in lens development in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in lens development in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info
involved_in lens fiber cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in lens morphogenesis in camera-type eye	ISO Inferred from Sequence Orthology more info
involved_in lens morphogenesis in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within locomotory behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within midbrain development	ISO Inferred from Sequence Orthology more info
involved_in midbrain development	ISO Inferred from Sequence Orthology more info
involved_in midbrain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of gliogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of neurogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within neuron development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell proliferation in midbrain	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of neuron apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to cocaine	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to immobilization stress	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to methamphetamine hydrochloride	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: pituitary homeobox 3

Names: homeobox protein PITX3; homeobox protein PTX3; paired-like homeodomain transcription factor 3

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_019247.2 → NP_062120.1 pituitary homeobox 3

See identical proteins and their annotated locations for NP_062120.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

P81062

UniProtKB/TrEMBL

A6JHL3

Related

ENSRNOP00000026013.2, ENSRNOT00000026013.4

Conserved Domains (3) summary

PTZ00395
Location:142 → 236

PTZ00395; Sec24-related protein; Provisional

pfam00046
Location:66 → 119

Homeobox; Homeobox domain

pfam03826
Location:258 → 275

OAR; OAR domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

254942550..254955325 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006231478.4 → XP_006231540.1 pituitary homeobox 3 isoform X1

See identical proteins and their annotated locations for XP_006231540.1

UniProtKB/Swiss-Prot

P81062

UniProtKB/TrEMBL

A6JHL3

Conserved Domains (3) summary

PTZ00395
Location:142 → 236

PTZ00395; Sec24-related protein; Provisional

pfam00046
Location:66 → 119

Homeobox; Homeobox domain

pfam03826
Location:258 → 275

OAR; OAR domain