Irx4 MGI Mouse Gene Detail - MGI:1355275

Symbol

Irx4
Name

Iroquois homeobox 4

Feature Type

protein coding gene
IDs

MGI:1355275
NCBI Gene: 50916
Alliance

genome feature page
Transcription Start Sites

4 TSS

Sequence Map

Chr13:73408598-73417727 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 13, 39.64 cM
Mapping Data

1 experiment

SNPs within 2kb

196 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1355275	protein coding gene	Chr13:73407708-73417741 (+)
129S1/SvImJ	ENSMUSG00200012920	protein coding gene	Chr13:67791166-67800497 (+)
A/J	ENSMUSG00195027819	protein coding gene	Chr13:68386878-68396167 (+)
AKR/J	ENSMUSG00220031273	protein coding gene	Chr13:66981263-66990549 (+)
BALB/cJ	ENSMUSG00180022524	protein coding gene	Chr13:68885270-68894556 (+)
C3H/HeJ	ENSMUSG00175007520	protein coding gene	Chr13:69166820-69176111 (+)
C57BL/6NJ	ENSMUSG00215005674	protein coding gene	Chr13:68951245-68960533 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0018699	protein coding gene	Chr13:67884131-67893445 (+)
CAST/EiJ	ENSTCUG00005011566	protein coding gene	Chr13:68475084-68484340 (+)
CBA/J	ENSMUSG00210008537	protein coding gene	Chr13:68486637-68495924 (+)
DBA/2J	ENSMUSG00185016709	protein coding gene	Chr13:72178160-72187452 (+)
FVB/NJ	ENSMUSG00205015935	protein coding gene	Chr13:67865530-67874821 (+)
JF1/MsJ	ENSUMUG00000021073	protein coding gene	Chr13:71945564-71954932 (+)
LP/J	ENSMUSG00230023035	protein coding gene	Chr13:82098774-82108139 (+)
NOD/ShiLtJ	ENSMUSG00190037162	protein coding gene	Chr13:68486493-68495867 (+)
NZO/HlLtJ	ENSMUSG00225027773	protein coding gene	Chr13:74596407-74605738 (+)
PWK/PhJ	ENSLUMG00010011707	protein coding gene	Chr13:67978171-67987460 (+)
SPRET/EiJ	ENSMSPG00010030062	protein coding gene	Chr13:68869340-68878512 (+)
WSB/EiJ	ENSIUOG00005018652	protein coding gene	Chr13:67742935-67752257 (+)

Human Ortholog

IRX4, iroquois homeobox 4

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

IRX4, iroquois homeobox 4
Synonyms

IRXA3
Links

HGNC:6129

NCBI Gene ID: 50805

UniProt: P78413
Chr Location

5p15.33; chr5:1877413-1887381 (-) GRCh38

MGI Vertebrate Homology

Irx4 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: IRX4
Gene Tree

Irx4

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Phenotype Summary

7 phenotypes from 1 allele in 1 genetic background
9 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

9
Chemically induced (other)

1
Endonuclease-mediated

5
Targeted

3
Genomic Mutations

1 involving Irx4
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

39 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygotes for a targeted null mutation exhibit abnormal ventricular gene expression followed by cardiomyopathy with hypertrophy and impaired contractile function.

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All GO Annotations

18
GO References

8

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

846
Tissues

150
cDNA Data

12
Literature Summary

57

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA IRX4

Xenbase irx4

ZFIN irx4a, irx4b

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All Sequences

42
RefSeq

12
UniProt

1
CCDS

CCDS26629.1

Ensembl

ENSMUSG00000021604 (Evidence)
NCBI Gene

50916

			Length	Strain/Species	Flank
genomic	ENSMUSG00000021604	Ensembl Gene Model \| MGI Sequence Detail	9130	C57BL/6J	± kb
transcript	ENSMUST00000176684	Ensembl \| MGI Sequence Detail	2384	Not Applicable
polypeptide	ENSMUSP00000134738	Ensembl \| MGI Sequence Detail	515	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000009110 iroquois-class homeodomain protein IRX-4

(term hierarchy)
InterPro Domains

IPR017970 Homeobox, conserved site

IPR001356 Homeodomain

IPR009057 Homeodomain-like superfamily

IPR003893 Iroquois-class homeodomain protein

IPR008422 KN homeodomain

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All nucleic 24

cDNA 13

Primer pair 5

Other 6

Antibodies 2

Microarray probesets 2

Summaries

All 88

Developmental Gene Expression 57

Gene Ontology 8

Phenotypes 9
Earliest

J:182573 Roderick TH, Producing and detecting paracentric chromosomal inversions in mice. Mutat Res. 1971 Jan;11(1):59-69
Latest

J:376814 Ranade SS, et al., Myocardial reprogramming by HMGN1 underlies heart defects in trisomy 21. Nature. 2025 Nov;647(8091):979-987

TSS for Irx4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr120310	Chr13:73408592-73408606 (+)	1 bp
Tssr120311	Chr13:73408629-73408665 (+)	49 bp
Tssr120312	Chr13:73408675-73408688 (+)	84 bp
Tssr120313	Chr13:73412721-73412722 (+)	4,124 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/01/2026 MGI 6.24