Irx6 Iroquois homeobox 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Irx6provided by MGI
Official Full Name: Iroquois homeobox 6provided by MGI
Primary source: MGI:MGI:1927642
See related: Ensembl:ENSMUSG00000031738 AllianceGenome:MGI:1927642
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and DNA-binding transcription repressor activity, RNA polymerase II-specific. Acts upstream of or within detection of visible light; regulation of DNA-templated transcription; and retina morphogenesis in camera-type eye. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; endocardial lining; genitourinary system; limb; and retina. Orthologous to human IRX6 (iroquois homeobox 6). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in limb E14.5 (RPKM 2.8), whole brain E14.5 (RPKM 0.9) and 3 other tissues See more
Orthologs: human all
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Genomic context

Location:: 8 C5; 8 44.99 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	8	NC_000074.7 (93400917..93407584)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	8	NC_000074.6 (92674289..92680956)

Chromosome 8 - NC_000074.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

In mouse embryos there was no significant upregulation of Haao expression in the developing male external genitalia. Irx6 was expressed in the ectodermal epithelium, demonstrating prominent dorsal ectodermal expression without expression in the ventral ectoderm adjacent to the urethral plate during the same period.
Title: Single Nucleotide Polymorphisms of HAAO and IRX6 Genes as Risk Factors for Hypospadias.
Regulation of retinal interneuron subtype identity by the Iroquois homeobox gene Irx6.
Title: Regulation of retinal interneuron subtype identity by the Iroquois homeobox gene Irx6.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Irx3 (e-PCR), detects polymorphism
- UniSTS:498475

Irx6 (e-PCR), detects polymorphism
- UniSTS:532302

D8Mit284 (e-PCR), detects polymorphism
- UniSTS:131496

PMC310936P5 (e-PCR)
- UniSTS:272822

NoName (e-PCR)
- UniSTS:495329

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
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 detection of visible light	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retina layer formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retinal bipolar neuron differentiation	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-6

Names: Iroquois related homeobox 6; homeodomain protein IRXB3; iroquois homeobox protein 6

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_001301137.1 → NP_001288066.1 iroquois-class homeodomain protein IRX-6 isoform 2

See identical proteins and their annotated locations for NP_001288066.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of the last exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.

Source sequence(s)

AK035140, AK053729, BU054800

Consensus CDS

CCDS80913.1

UniProtKB/Swiss-Prot

A1L3D2, E9Q2V2, Q9ER75

Related

ENSMUSP00000127446.2, ENSMUST00000167261.3

Conserved Domains (2) summary

COG5576
Location:142 → 232

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam05920
Location:161 → 200

Homeobox_KN; Homeobox KN domain
NM_022428.3 → NP_071873.2 iroquois-class homeodomain protein IRX-6 isoform 1

See identical proteins and their annotated locations for NP_071873.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK035140, AK053729

Consensus CDS

CCDS40428.1

UniProtKB/TrEMBL

Q8BFT1

Related

ENSMUSP00000034185.7, ENSMUST00000034185.13

Conserved Domains (2) summary

COG5576
Location:142 → 232

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam05920
Location:161 → 200

Homeobox_KN; Homeobox KN domain