IRX3 is a member of the Iroquois homeobox gene family (see IRX1; MIM 606197) and plays a role in an early step of neural development (Bellefroid et al., 1998 [PubMed 9427753]). Members of this family appear to play multiple roles during pattern formation of vertebrate embryos (Lewis et al., 1999 [PubMed 10370142]).[supplied by OMIM, Aug 2009] See more...

Aliases for IRX3 Gene

Aliases for IRX3 Gene

  • Iroquois Homeobox 3 2 3 5
  • Iroquois-Class Homeodomain Protein IRX-3 3 4
  • Iroquois Homeobox Protein 3 3 4
  • Homeodomain Protein IRXB1 3 4
  • IRXB1 3 4
  • Iroquois-Class Homeodomain Protein IRX-1 3
  • IRX-1 3

External Ids for IRX3 Gene

Previous GeneCards Identifiers for IRX3 Gene

  • GC16M044731
  • GC16M054372
  • GC16M054055
  • GC16M054095
  • GC16M052874
  • GC16M040203

Summaries for IRX3 Gene

Entrez Gene Summary for IRX3 Gene

  • IRX3 is a member of the Iroquois homeobox gene family (see IRX1; MIM 606197) and plays a role in an early step of neural development (Bellefroid et al., 1998 [PubMed 9427753]). Members of this family appear to play multiple roles during pattern formation of vertebrate embryos (Lewis et al., 1999 [PubMed 10370142]).[supplied by OMIM, Aug 2009]

GeneCards Summary for IRX3 Gene

IRX3 (Iroquois Homeobox 3) is a Protein Coding gene. Diseases associated with IRX3 include Transient Refractive Change and Cycloplegia. Among its related pathways are FTO Obesity Variant Mechanism. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is IRX1.

UniProtKB/Swiss-Prot Summary for IRX3 Gene

  • Transcription factor involved in SHH-dependent neural patterning. Together with NKX2-2 and NKX6-1 acts to restrict the generation of motor neurons to the appropriate region of the neural tube. Belongs to the class I proteins of neuronal progenitor factors, which are repressed by SHH signals. Involved in the transcriptional repression of MNX1 in non-motor neuron cells. Acts as a regulator of energy metabolism.

Gene Wiki entry for IRX3 Gene

Additional gene information for IRX3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for IRX3 Gene

Genomics for IRX3 Gene

GeneHancer (GH) Regulatory Elements for IRX3 Gene

Promoters and enhancers for IRX3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J054281 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +1.8 1755 6.2 ZNF217 CTCF POLR2G NCOR1 PHF8 ZNF639 ZIC2 POLR2A ZBTB10 ZBTB26 ENSG00000283689 IRX3 RBL2 RPGRIP1L ENSG00000261056 LINC02169 lnc-IRX3-7
GH16J054926 Promoter/Enhancer 1.9 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.4 -645.4 -645444 14.2 HNRNPK ZNF217 NRF1 USF1 SP1 RBAK PHF8 JUND TEAD4 SIX5 IRX5 IRX3 CRNDE ENSG00000259711 ENSG00000259725
GH16J054175 Enhancer 1.3 FANTOM5 ENCODE CraniofacialAtlas 10.6 +111.2 111167 3.2 EP300 FOXK2 POLR2G NCOR1 KDM6A TCF7 FOXA1 GABPA RFX1 ZBTB25 RBL2 ENSG00000261056 IRX3 lnc-IRX3-5 lnc-IRX3-11
GH16J054446 Enhancer 1 Ensembl ENCODE 9.9 -160.5 -160545 3.2 JUND REST ZNF623 TRIM28 TARDBP HES1 CTBP1 JUN NCOR1 NEUROD1 IRX3 HSALNG0111585 HSALNG0111582
GH16J054242 Enhancer 0.8 Ensembl ENCODE 11.3 +44.6 44643 0.8 ZNF217 USF1 SIX5 ZIC2 REST USF2 NFYB RAD51 HCFC1 GATA3 IRX3 LINC02169 ENSG00000259759
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around IRX3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for IRX3

Top Transcription factor binding sites by QIAGEN in the IRX3 gene promoter:
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AP-2gamma
  • C/EBPbeta
  • E47
  • ER-alpha
  • FOXD1
  • Olf-1
  • Pax-5

Genomic Locations for IRX3 Gene

Genomic Locations for IRX3 Gene
chr16:54,283,300-54,286,856
(GRCh38/hg38)
Size:
3,557 bases
Orientation:
Minus strand
chr16:54,317,212-54,320,675
(GRCh37/hg19)
Size:
3,464 bases
Orientation:
Minus strand

Genomic View for IRX3 Gene

Genes around IRX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IRX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IRX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IRX3 Gene

Proteins for IRX3 Gene

  • Protein details for IRX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P78415-IRX3_HUMAN
    Recommended name:
    Iroquois-class homeodomain protein IRX-3
    Protein Accession:
    P78415
    Secondary Accessions:
    • Q7Z4A4
    • Q7Z4A5
    • Q8IVC6

    Protein attributes for IRX3 Gene

    Size:
    501 amino acids
    Molecular mass:
    52119 Da
    Quaternary structure:
    No Data Available

neXtProt entry for IRX3 Gene

Post-translational modifications for IRX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for IRX3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for IRX3 Gene

Domains & Families for IRX3 Gene

Gene Families for IRX3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for IRX3 Gene

Blocks:
  • Iroquois-class homeodomain protein
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for IRX3 Gene

GenScript: Design optimal peptide antigens:
  • Iroquois homeobox protein 3 (IRX3_HUMAN)
  • IRX3 protein (Q8N4G7_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P78415

UniProtKB/Swiss-Prot:

IRX3_HUMAN :
  • Belongs to the TALE/IRO homeobox family.
Family:
  • Belongs to the TALE/IRO homeobox family.
genes like me logo Genes that share domains with IRX3: view

Function for IRX3 Gene

Molecular function for IRX3 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor involved in SHH-dependent neural patterning. Together with NKX2-2 and NKX6-1 acts to restrict the generation of motor neurons to the appropriate region of the neural tube. Belongs to the class I proteins of neuronal progenitor factors, which are repressed by SHH signals. Involved in the transcriptional repression of MNX1 in non-motor neuron cells. Acts as a regulator of energy metabolism.

Phenotypes From GWAS Catalog for IRX3 Gene

Gene Ontology (GO) - Molecular Function for IRX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS 19274049
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with IRX3: view
genes like me logo Genes that share phenotypes with IRX3: view

Animal Models for IRX3 Gene

MGI Knock Outs for IRX3:

Animal Model Products

miRNA for IRX3 Gene

miRTarBase miRNAs that target IRX3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for IRX3 Gene

Localization for IRX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for IRX3 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for IRX3 gene
Compartment Confidence
nucleus 5
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 1
endoplasmic reticulum 1
cytosol 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for IRX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0030424 axon IEA --
genes like me logo Genes that share ontologies with IRX3: view

Pathways & Interactions for IRX3 Gene

PathCards logo

SuperPathways for IRX3 Gene

SuperPathway Contained pathways
1 FTO Obesity Variant Mechanism
genes like me logo Genes that share pathways with IRX3: view

Pathways by source for IRX3 Gene

1 BioSystems pathway for IRX3 Gene

Gene Ontology (GO) - Biological Process for IRX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001656 metanephros development IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IEA --
GO:0007498 mesoderm development IEA --
genes like me logo Genes that share ontologies with IRX3: view

No data available for SIGNOR curated interactions for IRX3 Gene

Drugs & Compounds for IRX3 Gene

No Compound Related Data Available

Transcripts for IRX3 Gene

mRNA/cDNA for IRX3 Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for IRX3 Gene

No ASD Table

Relevant External Links for IRX3 Gene

GeneLoc Exon Structure for
IRX3

Expression for IRX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for IRX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for IRX3 Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x7.8), Skin - Sun Exposed (Lower leg) (x5.6), Heart - Left Ventricle (x4.1), and Minor Salivary Gland (x4.1).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for IRX3

SOURCE GeneReport for Unigene cluster for IRX3 Gene:

Hs.499205

Evidence on tissue expression from TISSUES for IRX3 Gene

  • Muscle(4.4)
  • Heart(2.5)
genes like me logo Genes that share expression patterns with IRX3: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for IRX3 Gene

Orthologs for IRX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for IRX3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia IRX3 31 30
  • 99.4 (n)
OneToOne
dog
(Canis familiaris)
Mammalia IRX3 31 30
  • 89.75 (n)
OneToOne
cow
(Bos Taurus)
Mammalia IRX3 31 30
  • 88.44 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Irx3 17 31 30
  • 85.96 (n)
oppossum
(Monodelphis domestica)
Mammalia IRX3 31
  • 84 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.2093 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.4522 30
zebrafish
(Danio rerio)
Actinopterygii irx3a 31
  • 58 (a)
OneToOne
iro3 30
fruit fly
(Drosophila melanogaster)
Insecta mirr 32
  • 60 (a)
caup 32
  • 47 (a)
ara 32
  • 43 (a)
Species where no ortholog for IRX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for IRX3 Gene

ENSEMBL:
Gene Tree for IRX3 (if available)
TreeFam:
Gene Tree for IRX3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for IRX3: view image

Paralogs for IRX3 Gene

Paralogs for IRX3 Gene

(2) SIMAP similar genes for IRX3 Gene using alignment to 3 proteins:

  • IRX3_HUMAN
  • J3QR11_HUMAN
  • Q8N4G7_HUMAN
genes like me logo Genes that share paralogs with IRX3: view

Variants for IRX3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for IRX3 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
704001 Benign: not provided 54,285,422(-) G/T SYNONYMOUS_VARIANT
704543 Benign: not provided 54,285,470(-) C/T SYNONYMOUS_VARIANT
718710 Likely Benign: not provided 54,284,546(-) C/T SYNONYMOUS_VARIANT
744457 Likely Benign: not provided 54,284,681(-) C/T SYNONYMOUS_VARIANT
rs1126960 - p.Gln479His

Additional dbSNP identifiers (rs#s) for IRX3 Gene

Structural Variations from Database of Genomic Variants (DGV) for IRX3 Gene

Variant ID Type Subtype PubMed ID
esv2664461 CNV deletion 23128226
nsv827655 CNV gain 20364138
nsv833235 CNV gain 17160897
nsv833236 CNV loss 17160897
nsv952678 CNV deletion 24416366

Variation tolerance for IRX3 Gene

Residual Variation Intolerance Score: 53.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.99; 79.98% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for IRX3 Gene

Human Gene Mutation Database (HGMD)
IRX3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
IRX3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for IRX3 Gene

Disorders for IRX3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for IRX3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
transient refractive change
cycloplegia
  • ciliary muscle paresis
- elite association - COSMIC cancer census association via MalaCards
Search IRX3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for IRX3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with IRX3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for IRX3 Gene

Publications for IRX3 Gene

  1. Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes. (PMID: 21546767) Murea M … Freedman BI (American journal of nephrology 2011) 3 41 54
  2. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 41 54
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  4. The partial inhibition of hypothalamic IRX3 exacerbates obesity. (PMID: 30522931) de Araujo TM … Velloso LA (EBioMedicine 2019) 3 54
  5. ΔNp63α Suppresses TGFB2 Expression and RHOA Activity to Drive Cell Proliferation in Squamous Cell Carcinomas. (PMID: 30232004) Abraham CG … Espinosa JM (Cell reports 2018) 3 54

Products for IRX3 Gene

Sources for IRX3 Gene