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IRX1 iroquois homeobox 1 [ Homo sapiens (human) ]

Gene ID: 79192, updated on 5-Mar-2024

Summary

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Official Symbol
IRX1provided by HGNC
Official Full Name
iroquois homeobox 1provided by HGNC
Primary source
HGNC:HGNC:14358
See related
Ensembl:ENSG00000170549 MIM:606197; AllianceGenome:HGNC:14358
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IRX-5; IRXA1
Summary
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]
Expression
Biased expression in kidney (RPKM 2.5), salivary gland (RPKM 1.1) and 4 other tissues See more
Orthologs
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Genomic context

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Location:
5p15.33
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (3595832..3601403)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (3514530..3520100)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (3595946..3601517)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1019 Neighboring gene long intergenic non-protein coding RNA 2162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3490824-3491324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3510857-3511356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3511427-3511928 Neighboring gene VISTA enhancer hs261 Neighboring gene long intergenic non-protein coding RNA 1017 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3518997-3519497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3520242-3520742 Neighboring gene Sharpr-MPRA regulatory region 3294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3598809-3599471 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:3599472-3600133 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3600797-3601457 Neighboring gene uncharacterized LOC107986399 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3627638-3628138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:3740365-3740866 Neighboring gene uncharacterized LOC105374625 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:3788141-3788778

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. IRX1 is a novel gene, overexpressed in high-grade IDH-mutant astrocytomas. Sugur HS, et al. Pathol Res Pract, 2023 May. PMID 37116364
  2. Prognostic value of Iroquois homeobox 1 methylation in non-small cell lung cancers. Lee JY, et al. Genes Genomics, 2020 May. PMID 32200543
  3. Investigating Role of IRX Family in Development of Female Adolescent Idiopathic Scoliosis: Which One Is Real Cause? Xia C, et al. World Neurosurg, 2019 Jul. PMID 30862593
  4. Identification of IRX1 as a Risk Locus for Rheumatoid Factor Positivity in Rheumatoid Arthritis in a Genome-Wide Association Study. Julià A, et al. Arthritis Rheumatol, 2016 Jun. PMID 26815016
  5. Helicobacter pylori induces promoter hypermethylation and downregulates gene expression of IRX1 transcription factor on human gastric mucosa. Guo XB, et al. J Gastroenterol Hepatol, 2011 Nov. PMID 21649733

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ADRA2A and IRX1 are putative risk genes for Raynaud's phenomenon.
    Title: ADRA2A and IRX1 are putative risk genes for Raynaud's phenomenon.
  2. IRX1 is a novel gene, overexpressed in high-grade IDH-mutant astrocytomas.
    Title: IRX1 is a novel gene, overexpressed in high-grade IDH-mutant astrocytomas.
  3. The Hematopoietic TALE-Code Shows Normal Activity of IRX1 in Myeloid Progenitors and Reveals Ectopic Expression of IRX3 and IRX5 in Acute Myeloid Leukemia.
    Title: The Hematopoietic TALE-Code Shows Normal Activity of IRX1 in Myeloid Progenitors and Reveals Ectopic Expression of IRX3 and IRX5 in Acute Myeloid Leukemia.
  4. HOXA9/IRX1 expression pattern defines two subgroups of infant MLL-AF4-driven acute lymphoblastic leukemia.
    Title: HOXA9/IRX1 expression pattern defines two subgroups of infant MLL-AF4-driven acute lymphoblastic leukemia.
  5. Downregulated microRNA-150 upregulates IRX1 to depress proliferation, migration, and invasion, but boost apoptosis of gastric cancer cells.
    Title: Downregulated microRNA-150 upregulates IRX1 to depress proliferation, migration, and invasion, but boost apoptosis of gastric cancer cells.
  6. Prognostic value of Iroquois homeobox 1 methylation in non-small cell lung cancers.
    Title: Prognostic value of Iroquois homeobox 1 methylation in non-small cell lung cancers.
  7. IRX1 hypermethylation promotes heart failure by inhibiting CXCL14 expression.
    Title: IRX1 hypermethylation promotes heart failure by inhibiting CXCL14 expression.
  8. The variant rs12517904 of the IRX1 gene is functionally associated with the development of adolescent idiopathic scoliosis in the Chinese population. For rs12517904, patients were found to have a significantly higher frequency of allele T than the controls. For rs117273909, neither the genotype nor the allele frequency was significantly different between the patients and controls.
    Title: Investigating Role of IRX Family in Development of Female Adolescent Idiopathic Scoliosis: Which One Is Real Cause?
  9. Through a combination of sequencing studies on eighteen North Carolina macular dystrophy families, two novel overlapping duplications at the MCDR3 locus, in a gene desert downstream of IRX1 and upstream of ADAMTS16, have been reported.
    Title: Duplication events downstream of IRX1 cause North Carolina macular dystrophy at the MCDR3 locus.
  10. Multiple evidences suggested that PRMT5 repressed transcription of tumor suppressor IRX1 via recruitment of DNMT3A on promoter.
    Title: Protein arginine methyltransferase 5-mediated epigenetic silencing of IRX1 contributes to tumorigenicity and metastasis of gastric cancer.
Submit: New GeneRIF Correction See all GeneRIFs (22)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of antibody response to smallpox vaccine.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
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
  
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in proximal/distal pattern formation involved in metanephric nephron development 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
  
involved_in response to organic cyclic compound IEA
Inferred from Electronic Annotation
more info
  
involved_in specification of loop of Henle identity IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
iroquois-class homeodomain protein IRX-1
Names
homeodomain protein IRXA1
iroquois homeobox protein 1

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)

  1. NM_024337.4 → NP_077313.3  iroquois-class homeodomain protein IRX-1

    See identical proteins and their annotated locations for NP_077313.3

    Status: VALIDATED

    Source sequence(s)
    AC016595, AY335938, BC029160
    Consensus CDS
    CCDS34132.1
    UniProtKB/Swiss-Prot
    P78414, Q7Z2F8, Q8N312
    Related
    ENSP00000305244.3, ENST00000302006.4
    Conserved Domains (3) summary
    smart00548
    Location:313 → 326
    IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function
    pfam05920
    Location:145 → 184
    Homeobox_KN; Homeobox KN domain
    cl01319
    Location:188 → 247
    HARE-HTH; HB1, ASXL, restriction endonuclease HTH domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    3595832..3601403
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    3514530..3520100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P78414.3 GenPept UniProtKB/Swiss-Prot:P78414

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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