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IRX4 iroquois homeobox 4 [ Homo sapiens (human) ]

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

Summary

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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
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Genomic context

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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

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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. 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

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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

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Preferred Names
iroquois-class homeodomain protein IRX-4
Names
homeodomain protein IRXA3
iroquois homeobox protein 4

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_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

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