IRX4 iroquois homeobox 4 [Homo sapiens (human)] - Gene

Summary

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 located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in prostate (RPKM 2.5), skin (RPKM 2.0) and 3 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5p15.33

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (1877413..1887179, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (1794071..1803829, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (1877527..1887293, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Dynamics and recognition of homeodomain containing protein-DNA complex of IRX4.
Title: Dynamics and recognition of homeodomain containing protein-DNA complex of IRX4.
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.
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.
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.
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.
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.
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Irx3 (e-PCR), detects polymorphism
- UniSTS:498475

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
located_in 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)

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
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

ENSP00000421772.2, ENST00000511126.2

Conserved Domains (1) summary

pfam05920
Location:186 → 225

Homeobox_KN; Homeobox KN domain
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
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

Conserved Domains (1) summary

pfam05920
Location:186 → 225

Homeobox_KN; Homeobox KN domain
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