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IRX3 iroquois homeobox 3 [ Homo sapiens (human) ]

Gene ID: 79191, updated on 2-Nov-2024

Summary

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Official Symbol
IRX3provided by HGNC
Official Full Name
iroquois homeobox 3provided by HGNC
Primary source
HGNC:HGNC:14360
See related
Ensembl:ENSG00000177508 MIM:612985; AllianceGenome:HGNC:14360
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-1; IRXB1
Summary
IRX3 is a member of the Iroquois homeobox gene family (see IRX1; MIM 606197) and plays a role in an early step of neural development (Bellefroid et al., 1998 [PubMed 9427753]). Members of this family appear to play multiple roles during pattern formation of vertebrate embryos (Lewis et al., 1999 [PubMed 10370142]).[supplied by OMIM, Aug 2009]
Expression
Biased expression in lung (RPKM 13.1), skin (RPKM 8.6) and 10 other tissues See more
Orthologs
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Genomic context

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See IRX3 in Genome Data Viewer
Location:
16q12.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (54283304..54286787, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (60081297..60084780, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (54317216..54320699, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene FTO alpha-ketoglutarate dependent dioxygenase Neighboring gene uncharacterized LOC105371271 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:54082723-54083657 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:54083658-54084591 Neighboring gene VISTA enhancer hs52 Neighboring gene Sharpr-MPRA regulatory region 5065 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:54228087-54228979 Neighboring gene Sharpr-MPRA regulatory region 10961 Neighboring gene long intergenic non-protein coding RNA 2169 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:54318795-54319714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:54319715-54320634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:54320768-54321268 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:54321269-54321769 Neighboring gene VISTA enhancer hs51 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:54325084-54325965 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:54364959-54365668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:54396413-54396916 Neighboring gene uncharacterized LOC105371272 Neighboring gene long intergenic non-protein coding RNA 2140 Neighboring gene NANOG hESC enhancer GRCh37_chr16:54459786-54460294 Neighboring gene NANOG hESC enhancer GRCh37_chr16:54464241-54464805 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:54523058-54523261 Neighboring gene VISTA enhancer hs43 Neighboring gene long intergenic non-protein coding RNA 2183

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 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. IRX3 plays an important role in the pathogenesis of metabolic-associated fatty liver disease by regulating hepatic lipid metabolism. Ma Y, et al. Front Endocrinol (Lausanne), 2022. PMID 35957832, Free PMC Article
  2. IRX3 is a genetic modifier for birth weight, adolescent obesity and transaminase metabolism. Liu C, et al. Pediatr Obes, 2018 Mar. PMID 28316138
  3. The proangiogenic effect of iroquois homeobox transcription factor Irx3 in human microvascular endothelial cells. Scarlett K, et al. J Biol Chem, 2015 Mar 6. PMID 25512384, Free PMC Article
  4. The partial inhibition of hypothalamic IRX3 exacerbates obesity. de Araujo TM, et al. EBioMedicine, 2019 Jan. PMID 30522931, Free PMC Article
  5. Hypothalamic IRX3: A New Player in the Development of Obesity. de Araújo TM, et al. Trends Endocrinol Metab, 2020 May. PMID 32035736

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Interaction analysis of FTO and IRX3 genes with obesity and related metabolic disorders in an admixed Latin American population: a possible risk increases of body weight excess.
    Title: Interaction analysis of FTO and IRX3 genes with obesity and related metabolic disorders in an admixed Latin American population: a possible risk increases of body weight excess.
  2. IRX3 plays an important role in the pathogenesis of metabolic-associated fatty liver disease by regulating hepatic lipid metabolism.
    Title: IRX3 plays an important role in the pathogenesis of metabolic-associated fatty liver disease by regulating hepatic lipid metabolism.
  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. IRX3 Overexpression Enhances Ucp1 Expression In Vivo.
    Title: IRX3 Overexpression Enhances Ucp1 Expression In Vivo.
  5. Clinical utility of irx3 in keratoconus.
    Title: Clinical utility of irx3 in keratoconus.
  6. Identification of Novel Genetic Variants Related to Trabecular Bone Score in Community-Dwelling Older Adults.
    Title: Identification of Novel Genetic Variants Related to Trabecular Bone Score in Community-Dwelling Older Adults.
  7. Hypothalamic IRX3: A New Player in the Development of Obesity.
    Title: Hypothalamic IRX3: A New Player in the Development of Obesity.
  8. Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
    Title: Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
  9. Primary preadipocytes from carriers of the obesity risk allele rs1421085, in which expression of IRX3 and IRX5 is increased, displayed excessive accumulation of triglycerides, reduced mitochondrial oxidative capacity, reduced white adipocyte browning, and reduced thermogenesis relative to primary preadipocytes from nonrisk allele carriers.
    Title: FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.
  10. Genome editing in primary preadipocytes to create the obesity risk allele of rs1421085 caused increased expression of IRX3 and IRX5 during early adipocyte differentiation by disrupting a binding site for the ARID5B repressor.
    Title: FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.
Submit: New GeneRIF Correction See all GeneRIFs (25)

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 scan for survival on dialysis in African-Americans with type 2 diabetes.
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)

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

  • FLJ99187

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
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 ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in His-Purkinje system cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in Purkinje myocyte development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in atrioventricular bundle cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cell development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in energy homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in mesoderm development IEA
Inferred from Electronic Annotation
more info
  
involved_in metanephros development IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of gap junction assembly ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in positive regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
acts_upstream_of regulation of cell communication by electrical coupling involved in cardiac conduction ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in specification of loop of Henle identity IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in axon IEA
Inferred from Electronic Annotation
more info
  
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
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-3
Names
homeodomain protein IRXB1
iroquois homeobox protein 3
iroquois-class homeodomain protein IRX-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_024336.3 → NP_077312.2  iroquois-class homeodomain protein IRX-3

    See identical proteins and their annotated locations for NP_077312.2

    Status: VALIDATED

    Source sequence(s)
    AC018553, AY335943, BC023667
    Consensus CDS
    CCDS10750.1
    UniProtKB/Swiss-Prot
    P78415, Q7Z4A4, Q7Z4A5, Q8IVC6
    Related
    ENSP00000331608.3, ENST00000329734.4
    Conserved Domains (2) summary
    smart00548
    Location:344 → 359
    IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function
    pfam05920
    Location:145 → 184
    Homeobox_KN; Homeobox KN domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    54283304..54286787 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005256139.4 → XP_005256196.1  iroquois-class homeodomain protein IRX-3 isoform X1

    Conserved Domains (2) summary
    smart00548
    Location:344 → 359
    IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function
    pfam05920
    Location:145 → 184
    Homeobox_KN; Homeobox KN domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    60081297..60084780 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054313909.1 → XP_054169884.1  iroquois-class homeodomain protein IRX-3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P78415.3 GenPept UniProtKB/Swiss-Prot:P78415

Gene LinkOut

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

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