IRX1 iroquois homeobox 1 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

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_000005.10 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
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?

ADRA2A and IRX1 are putative risk genes for Raynaud's phenomenon.
Title: ADRA2A and IRX1 are putative risk genes for Raynaud's phenomenon.
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.
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.
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.
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.
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.
IRX1 hypermethylation promotes heart failure by inhibiting CXCL14 expression.
Title: IRX1 hypermethylation promotes heart failure by inhibiting CXCL14 expression.
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?
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.
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 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

RH98982 (e-PCR)
- UniSTS:86059

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

SHGC-56703 (e-PCR)
- UniSTS:52856

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)

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