U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    IRX4 iroquois homeobox 4 [ Homo sapiens (human) ]

    Gene ID: 50805, updated on 5-Mar-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    IRX4provided by HGNC
    Official Full Name
    iroquois homeobox 4provided by HGNC
    Primary source
    HGNC:HGNC:6129
    See related
    Ensembl:ENSG00000113430 MIM:606199; AllianceGenome:HGNC:6129
    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
    IRXA3
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in cell development; neuron differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within heart development. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in prostate (RPKM 2.5), skin (RPKM 2.0) and 3 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    5p15.33
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (1877413..1887179, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (1794071..1803829, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (1877527..1887293, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 3 subunit A Neighboring gene uncharacterized LOC124901164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1865987-1866486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1875699-1876211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1876212-1876724 Neighboring gene uncharacterized LOC101929081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1883903-1884755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1885305-1885838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1889419-1890219 Neighboring gene IRX4 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1919083-1919896 Neighboring gene keratin-associated protein 5-5-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1930660-1931240 Neighboring gene uncharacterized LOC105374618 Neighboring gene meiotic recombination hotspot 5A Neighboring gene NANOG hESC enhancer GRCh37_chr5:1944459-1944980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1945776-1946394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1948847-1949348 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:1950332-1951531 Neighboring gene Sharpr-MPRA regulatory region 501

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Identification and Characterization of Alternatively Spliced Transcript Isoforms of IRX4 in Prostate Cancer. Fernando A, et al. Genes (Basel), 2021 Apr 21. PMID 33919200, Free PMC Article
    2. Epigenetic inactivation of IRX4 is responsible for acceleration of cell growth in human pancreatic cancer. Chakma K, et al. Cancer Sci, 2020 Dec. PMID 32894817, Free PMC Article
    3. Variants at IRX4 as prostate cancer expression quantitative trait loci. Xu X, et al. Eur J Hum Genet, 2014 Apr. PMID 24022300, Free PMC Article
    4. Two novel mutations of the IRX4 gene in patients with congenital heart disease. Cheng Z, et al. Hum Genet, 2011 Nov. PMID 21544582
    5. Genetic analysis of the Irx4 gene in hypertrophic cardiomyopathy. Bayrak F, et al. Turk Kardiyol Dern Ars, 2008 Mar. PMID 18497553

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Dynamics and recognition of homeodomain containing protein-DNA complex of IRX4.
      Title: Dynamics and recognition of homeodomain containing protein-DNA complex of IRX4.
    2. Identification and Characterization of Alternatively Spliced Transcript Isoforms of IRX4 in Prostate Cancer.
      Title: Identification and Characterization of Alternatively Spliced Transcript Isoforms of IRX4 in Prostate Cancer.
    3. Epigenetic inactivation of IRX4 is responsible for acceleration of cell growth in human pancreatic cancer.
      Title: Epigenetic inactivation of IRX4 is responsible for acceleration of cell growth in human pancreatic cancer.
    4. We independently validated IRX4 as a potential prostate cancer risk gene through cis-expression quantitative trait loci analysis of prostate cancer risk variants.
      Title: Variants at IRX4 as prostate cancer expression quantitative trait loci.
    5. the prostate cancer (PC)-susceptibility locus represented by rs12653946 at 5p15 is likely to regulate IRX4 expression in prostate which could suppress PC growth by interacting with the VDR pathway, conferring to PC susceptibility
      Title: IRX4 at 5p15 suppresses prostate cancer growth through the interaction with vitamin D receptor, conferring prostate cancer susceptibility.
    6. IRX4 had a potential causative impact on the development of congenital heart disease, particularly ventricular septal defect.
      Title: Two novel mutations of the IRX4 gene in patients with congenital heart disease.
    7. Among migraineurs with aura rs7698623 in MEPE (OR = 6.37; 95% CI 3.15-12.90; p = 2.7x10(-7)) and rs4975709 in IRX4 (OR = 5.06; 95% CI 2.66-9.62; p = 7.7x10(-7)) appeared to be associated with ischemic stroke.
      Title: Genetic determinants of cardiovascular events among women with migraine: a genome-wide association study.
    8. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    9. Polymorphism A381>G of the Irx4 gene may have a modifier effect on septal thickness, resulting in increased corrected QT dispersion and higher outflow gradients.
      Title: Genetic analysis of the Irx4 gene in hypertrophic cardiomyopathy.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    Submit: New GeneRIF Correction

    Phenotypes

    Go to the top of the page Help

    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
    Genetic determinants of cardiovascular events among women with migraine: a genome-wide association study.
    EBI GWAS Catalog

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC131996

    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 RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in establishment of animal organ orientation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heart development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    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

    Go to the top of the page Help
    Preferred Names
    iroquois-class homeodomain protein IRX-4
    Names
    homeodomain protein IRXA3
    iroquois homeobox protein 4

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001278632.1 → NP_001265561.1  iroquois-class homeodomain protein IRX-4 isoform b

      See identical proteins and their annotated locations for NP_001265561.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR and lacks an alternate internal exon compared to variant 4. It encodes isoform b which is shorter than isoform a.
      Source sequence(s)
      AB690778, AC025183, AI566193
      Consensus CDS
      CCDS3867.1
      UniProtKB/Swiss-Prot
      B2RMW5, D3DTC5, H1AFL0, H1AFL1, P78413, Q2NL64, Q9UHR2
      Related
      ENSP00000424235.1, ENST00000513692.5
      Conserved Domains (1) summary
      pfam05920
      Location:160 → 199
      Homeobox_KN; Homeobox KN domain

    2. NM_001278633.1 → NP_001265562.1  iroquois-class homeodomain protein IRX-4 isoform a

      See identical proteins and their annotated locations for NP_001265562.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 4. Both variants 2 and 4 encode the same protein.
      Source sequence(s)
      AB690779, AC025183, AI566193
      Consensus CDS
      CCDS75225.1
      UniProtKB/Swiss-Prot
      P78413
      Related
      ENSP00000481396.1, ENST00000622814.4
      Conserved Domains (1) summary
      pfam05920
      Location:186 → 225
      Homeobox_KN; Homeobox KN domain

    3. NM_001278634.2 → NP_001265563.1  iroquois-class homeodomain protein IRX-4 isoform b

      See identical proteins and their annotated locations for NP_001265563.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate internal exon compared to variant 4. It encodes isoform b, which is shorter than isoform a.
      Source sequence(s)
      AB690780, AC025183, AI566193
      Consensus CDS
      CCDS3867.1
      UniProtKB/Swiss-Prot
      B2RMW5, D3DTC5, H1AFL0, H1AFL1, P78413, Q2NL64, Q9UHR2
      Related
      ENSP00000423161.1, ENST00000505790.5
      Conserved Domains (1) summary
      pfam05920
      Location:160 → 199
      Homeobox_KN; Homeobox KN domain

    4. NM_001278635.2 → NP_001265564.1  iroquois-class homeodomain protein IRX-4 isoform a

      See identical proteins and their annotated locations for NP_001265564.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) represents the longest transcript. Both variants 2 and 4 encode the same protein.
      Source sequence(s)
      AB690781, AC025183, AI566193
      Consensus CDS
      CCDS75225.1
      UniProtKB/Swiss-Prot
      P78413
      Related
      ENSP00000482393.1, ENST00000613726.4
      Conserved Domains (1) summary
      pfam05920
      Location:186 → 225
      Homeobox_KN; Homeobox KN domain

    5. NM_016358.3 → NP_057442.1  iroquois-class homeodomain protein IRX-4 isoform b

      See identical proteins and their annotated locations for NP_057442.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate internal exon compared to variant 4. It encodes isoform b which is shorter than isoform a.
      Source sequence(s)
      AC025183, AF124733, AI566193, BC110912, BC136505
      Consensus CDS
      CCDS3867.1
      UniProtKB/Swiss-Prot
      B2RMW5, D3DTC5, H1AFL0, H1AFL1, P78413, Q2NL64, Q9UHR2
      Related
      ENSP00000231357.2, ENST00000231357.7
      Conserved Domains (1) summary
      pfam05920
      Location:160 → 199
      Homeobox_KN; Homeobox KN 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
      1877413..1887179 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      1794071..1803829 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P78413.2 GenPept UniProtKB/Swiss-Prot:P78413

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous