Irx3 iroquois homeobox 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Irx3provided by RGD
Official Full Name: iroquois homeobox 3provided by RGD
Primary source: RGD:1307424
See related: Ensembl:ENSRNOG00000011533 AllianceGenome:RGD:1307424
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: Predicted to enable DNA-binding transcription activator activity; DNA-binding transcription repressor activity, RNA polymerase II-specific; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including His-Purkinje system development; energy homeostasis; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within kidney development; mesoderm development; and regulation of neuron differentiation. Predicted to be located in axon; cytoplasm; and nucleus. Orthologous to human IRX3 (iroquois homeobox 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 52.1), Lung (RPKM 46.3) and 5 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19p11

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (31384803..31388241)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (15211882..15215317)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (15838714..15842135, complement)

Chromosome 19 - NC_086037.1 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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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?

Study revealed that diet was an important factor modulating transcription of Fto and Irx3, but its effect is time-dependent. In contrast, the DNA methylation profiles of Fto and Irx3 were not altered by nutrition, which may indicate that the feeding type, when applied postnatally, did not affect DNA methylation of these genes.
Title: Nutrition modulates Fto and Irx3 gene transcript levels, but does not alter their DNA methylation profiles in rat white adipose tissues.

Submit: New GeneRIF Correction

General gene information

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Markers

RH139880 (e-PCR)
- UniSTS:221964

AI894186 (e-PCR)
- UniSTS:179780

Irx3 (e-PCR), detects polymorphism
- UniSTS:532300

Irx3 (e-PCR), detects polymorphism
- UniSTS:547250

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 repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in His-Purkinje system cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in Purkinje myocyte development	ISO Inferred from Sequence Orthology more info
involved_in atrioventricular bundle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in energy homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mesoderm development	ISO Inferred from Sequence Orthology more info
involved_in metanephros development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gap junction assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in proximal/distal pattern formation involved in nephron development	ISO Inferred from Sequence Orthology more info
acts_upstream_of regulation of cell communication by electrical coupling involved in cardiac conduction	ISO Inferred from Sequence Orthology more info
involved_in specification of loop of Henle identity	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in axon	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: iroquois-class homeodomain protein IRX-3

Names: Iroquois related homeobox 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_001395133.1 → NP_001382062.1 iroquois-class homeodomain protein IRX-3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000019

UniProtKB/TrEMBL

A6KD68

Conserved Domains (2) summary

smart00548
Location:345 → 362

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

pfam05920
Location:148 → 187

Homeobox_KN; Homeobox KN 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_086037.1 Reference GRCr8

Range

31384803..31388241

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006255192.5 → XP_006255254.1 iroquois-class homeodomain protein IRX-3 isoform X1

UniProtKB/TrEMBL

D3ZNE0

Related

ENSRNOP00000015583.5

Conserved Domains (2) summary

smart00548
Location:345 → 362

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

pfam05920
Location:148 → 187

Homeobox_KN; Homeobox KN domain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001107413.1: Suppressed sequence

Description

NM_001107413.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.