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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 and Griscelli Syndrome, Type 3. 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

Regulatory Elements for IRX1 Gene

Enhancers for IRX1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05H003309 0.9 FANTOM5 ENCODE 6.9 -284.9 -284937 3 SOX13 GATA3 NRF1 MNT FOS HES1 TCF7L2 IRX1 PIR62391 GC05M003135
GH05H004082 0.2 ENCODE 6.4 +487.6 487604 2.1 IRX1 ENSG00000249994 LINC02063
GH05H003123 0.2 dbSUPER 5.9 -471.0 -471015 2.2 IRX1 GC05P003122 GC05P003139
GH05H003594 0.8 ENCODE dbSUPER 0.7 +0.8 761 5 POLR2A SUZ12 CTBP2 REST EZH2 ENSG00000259603 IRX1
GH05H003599 0.7 ENCODE dbSUPER 0.7 +3.8 3808 0.2 RING1 CTCF EZH2 ENSG00000259603 IRX1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around IRX1 on UCSC Golden Path with GeneCards custom track

Promoters for IRX1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000177663 -254 401 POLR2A EZH2

Genomic Locations for IRX1 Gene

Genomic Locations for IRX1 Gene
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:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific 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 tm1.1(KOMP)Vlcg

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 (3)
  • Nucleoplasm (3)
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 from RNA polymerase II promoter 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, PaxDb, 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 33 34
  • 99.57 (n)
(Bos Taurus)
Mammalia IRX1 33 34
  • 88.02 (n)
(Canis familiaris)
Mammalia IRX1 33 34
  • 86.3 (n)
(Rattus norvegicus)
Mammalia Irx1 33
  • 85.97 (n)
(Mus musculus)
Mammalia Irx1 33 16 34
  • 85.9 (n)
(Monodelphis domestica)
Mammalia IRX1 34
  • 78 (a)
(Ornithorhynchus anatinus)
Mammalia IRX1 34
  • 75 (a)
(Gallus gallus)
Aves IRX1 33 34
  • 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 33 34
  • 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)

Paralogs for IRX1 Gene

Paralogs for IRX1 Gene

(3) SIMAP similar genes for IRX1 Gene using alignment to 1 proteins: 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 Sequence Context AA Info Type
rs1000111213 -- 3,595,256(+) GAGGC(A/C/G)GGTCA upstream-variant-2KB
rs1000717552 -- 3,599,935(+) GGTGC(G/T)CCCAA reference, synonymous-codon
rs1000881736 -- 3,597,688(+) TAATT(A/G)GAAAA intron-variant
rs1001331930 -- 3,597,452(+) AACGC(C/T)CCTCA intron-variant
rs1002037820 -- 3,594,475(+) GCCGC(A/C)TTCAT upstream-variant-2KB

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

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

Relevant External Links for IRX1 Gene

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

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

Disorders for IRX1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
pulmonary immaturity
  • primary atelectasis of newborn
griscelli syndrome, type 3
  • griscelli syndrome type 3
- elite association - COSMIC cancer census association via MalaCards
Search IRX1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for IRX1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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 45 60
  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 45 60
  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 60
  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 60
  5. Identification of IRX1 as a Risk Locus for Rheumatoid Factor Positivity in Rheumatoid Arthritis in a Genome-Wide Association Study. (PMID: 26815016) Julià A … Marsal S (Arthritis & rheumatology (Hoboken, N.J.) 2016) 3 60

Products for IRX1 Gene

Sources for IRX1 Gene

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