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Aliases for IRX1 Gene

Aliases for IRX1 Gene

  • Iroquois Homeobox 1 2 3 5
  • Iroquois Homeobox Protein 1 3 4
  • Homeodomain Protein IRXA1 3 4
  • IRXA1 3 4
  • Iroquois-Class Homeodomain Protein IRX-1 3
  • IRX-5 3

External Ids for IRX1 Gene

Previous GeneCards Identifiers for IRX1 Gene

  • GC05P003743
  • GC05P003629
  • GC05P003648
  • GC05P003649

Summaries for IRX1 Gene

Entrez Gene Summary for IRX1 Gene

  • This gene encodes a member of the Iroquois homeobox protein family. Homeobox genes in this family are involved in pattern formation in the embryo. The gene product has been identified as a tumor suppressor in gastric (PMID: 21602894, 20440264) and head and neck cancers (PMID: 18559491). A pseudogene of this gene is located on chromosome 13. [provided by RefSeq, Dec 2011]

GeneCards Summary for IRX1 Gene

IRX1 (Iroquois Homeobox 1) is a Protein Coding gene. Diseases associated with IRX1 include Pulmonary Immaturity. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is IRX3.

Gene Wiki entry for IRX1 Gene

Additional gene information for IRX1 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for IRX1 Gene

Genomics for IRX1 Gene

GeneHancer (GH) Regulatory Elements for IRX1 Gene

Promoters and enhancers for IRX1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J003594 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.8 760 5 CTCF POLR2A SUZ12 SIN3A CTBP2 REST EZH2 IRX1 ENSG00000259603
GH05J003309 Enhancer 0.8 FANTOM5 ENCODE 6.9 -284.9 -284937 3 SOX13 GATA3 NRF1 MNT FOS HES1 TCF7L2 IRX1 PIR62391 GC05M003135
GH05J003123 Enhancer 0.3 dbSUPER 5.9 -471.0 -471015 2.2 NANOG IRX1 GC05P003122 GC05P003139
GH05J004082 Enhancer 0.2 ENCODE 6.4 +487.6 487604 2.1 IRX1 ENSG00000249994 LINC02063
GH05J003600 Enhancer 0.6 ENCODE dbSUPER 0.7 +4.6 4568 0.7 CTBP2 EZH2 ENSG00000259603 IRX1 GC05P003602
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around IRX1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the IRX1 gene promoter:
  • MRF-2
  • Nkx6-1
  • FOXL1
  • GATA-2
  • Lhx3a
  • FOXC1
  • LHX3b
  • CUTL1

Genomic Locations for IRX1 Gene

Genomic Locations for IRX1 Gene
5,350 bases
Plus strand
5,350 bases
Plus strand

Genomic View for IRX1 Gene

Genes around IRX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IRX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IRX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IRX1 Gene

Proteins for IRX1 Gene

  • Protein details for IRX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Iroquois-class homeodomain protein IRX-1
    Protein Accession:
    Secondary Accessions:
    • Q7Z2F8
    • Q8N312

    Protein attributes for IRX1 Gene

    480 amino acids
    Molecular mass:
    49621 Da
    Quaternary structure:
    No Data Available

neXtProt entry for IRX1 Gene

Post-translational modifications for IRX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for IRX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for IRX1 Gene

Domains & Families for IRX1 Gene

Gene Families for IRX1 Gene

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

Suggested Antigen Peptide Sequences for IRX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the TALE/IRO homeobox family.
  • Belongs to the TALE/IRO homeobox family.
genes like me logo Genes that share domains with IRX1: view

Function for IRX1 Gene

Phenotypes From GWAS Catalog for IRX1 Gene

Gene Ontology (GO) - Molecular Function for IRX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IC --
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IDA 28473536
genes like me logo Genes that share ontologies with IRX1: view
genes like me logo Genes that share phenotypes with IRX1: view

Animal Models for IRX1 Gene

MGI Knock Outs for IRX1:
  • Irx1 Irx1<tm1.1(KOMP)Vlcg>

Animal Model Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for IRX1 Gene

Localization for IRX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for IRX1 Gene

Subcellular locations from

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 IRX1 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for IRX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with IRX1: view

Pathways & Interactions for IRX1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for IRX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 20440264
GO:0001656 metanephros development IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0072086 specification of loop of Henle identity IEA --
GO:0072272 proximal/distal pattern formation involved in metanephric nephron development IEA --
genes like me logo Genes that share ontologies with IRX1: view

No data available for Pathways by source and SIGNOR curated interactions for IRX1 Gene

Drugs & Compounds for IRX1 Gene

No Compound Related Data Available

Transcripts for IRX1 Gene

mRNA/cDNA for IRX1 Gene

(2) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(30) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for IRX1 Gene

Iroquois homeobox 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for IRX1 Gene

No ASD Table

Relevant External Links for IRX1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for IRX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for IRX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for IRX1 Gene

This gene is overexpressed in Minor Salivary Gland (x9.6), Breast - Mammary Tissue (x8.1), Kidney - Cortex (x6.4), and Skin - Sun Exposed (Lower leg) (x4.0).

Protein differential expression in normal tissues from HIPED for IRX1 Gene

This gene is overexpressed in Adipocyte (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for IRX1 Gene

Protein tissue co-expression partners for IRX1 Gene

NURSA nuclear receptor signaling pathways regulating expression of IRX1 Gene:


SOURCE GeneReport for Unigene cluster for IRX1 Gene:


Evidence on tissue expression from TISSUES for IRX1 Gene

  • Nervous system(4.3)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with IRX1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for IRX1 Gene

Orthologs for IRX1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for IRX1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia IRX1 34 33
  • 99.57 (n)
(Bos Taurus)
Mammalia IRX1 34 33
  • 88.02 (n)
(Canis familiaris)
Mammalia IRX1 34 33
  • 86.3 (n)
(Rattus norvegicus)
Mammalia Irx1 33
  • 85.97 (n)
(Mus musculus)
Mammalia Irx1 16 34 33
  • 85.9 (n)
(Monodelphis domestica)
Mammalia IRX1 34
  • 78 (a)
(Ornithorhynchus anatinus)
Mammalia IRX1 34
  • 75 (a)
(Gallus gallus)
Aves IRX1 34 33
  • 71.61 (n)
(Anolis carolinensis)
Reptilia IRX1 34
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia irx1 33
  • 67.82 (n)
Str.16884 33
African clawed frog
(Xenopus laevis)
Amphibia LOC397976 33
(Danio rerio)
Actinopterygii irx1a 34 33
  • 67.37 (n)
irx1b 34
  • 53 (a)
Dr.12613 33
Species where no ortholog for IRX1 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)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 IRX1 Gene

Gene Tree for IRX1 (if available)
Gene Tree for IRX1 (if available)
Evolutionary constrained regions (ECRs) for IRX1: view image

Paralogs for IRX1 Gene

Paralogs for IRX1 Gene

(3) SIMAP similar genes for IRX1 Gene using alignment to 1 proteins:

  • IRX1_HUMAN Pseudogenes for IRX1 Gene

genes like me logo Genes that share paralogs with IRX1: view

Variants for IRX1 Gene

Sequence variations from dbSNP and Humsavar for IRX1 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000111213 -- 3,595,256(+) C/A/G upstream_transcript_variant
rs1000717552 -- 3,599,935(+) G/T coding_sequence_variant, synonymous_variant
rs1000881736 -- 3,597,688(+) A/G intron_variant
rs1001331930 -- 3,597,452(+) C/T intron_variant
rs1002037820 -- 3,594,475(+) C/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for IRX1 Gene

Variant ID Type Subtype PubMed ID
dgv932n67 CNV gain 20364138
dgv9549n54 CNV loss 21841781
dgv9550n54 CNV loss 21841781
esv22909 CNV loss 19812545
esv2759317 CNV loss 17122850
nsv1029309 CNV gain 25217958
nsv10658 CNV gain 18304495
nsv1126709 CNV deletion 24896259
nsv428461 CNV loss 18775914
nsv461914 CNV loss 19166990
nsv516530 CNV loss 19592680
nsv596920 CNV loss 21841781
nsv596925 CNV loss 21841781
nsv596927 CNV gain 21841781
nsv822983 CNV gain 20364138
nsv822984 CNV gain 20364138

Variation tolerance for IRX1 Gene

Residual Variation Intolerance Score: 23.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.08; 38.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for IRX1 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for IRX1 Gene

Disorders for IRX1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for IRX1 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
pulmonary immaturity
  • primary atelectasis of newborn
- elite association - COSMIC cancer census association via MalaCards
Search IRX1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for IRX1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with IRX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for IRX1 Gene

Publications for IRX1 Gene

  1. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 44 58
  2. A genome-wide scan maps a novel high myopia locus to 5p15. (PMID: 18421076) Lam CY … Lam DS (Investigative ophthalmology & visual science 2008) 3 44 58
  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 58
  4. Impact of cytosine methylation on DNA binding specificities of human transcription factors. (PMID: 28473536) Yin Y … Taipale J (Science (New York, N.Y.) 2017) 3 58
  5. Exome sequencing reveals novel IRXI mutation in congenital heart disease. (PMID: 28358424) Guo C … Lu C (Molecular medicine reports 2017) 3 58

Products for IRX1 Gene

Sources for IRX1 Gene

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