Format

Send to:

Choose Destination

IRX5 iroquois homeobox 5 [ Homo sapiens (human) ]

Gene ID: 10265, updated on 2-Oct-2018

Summary

Official Symbol
IRX5provided by HGNC
Official Full Name
iroquois homeobox 5provided by HGNC
Primary source
HGNC:HGNC:14361
See related
Ensembl:ENSG00000176842 MIM:606195; Vega:OTTHUMG00000133201
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HMMS; IRXB2; IRX-2a
Summary
This gene encodes a member of the iroquois homeobox gene family, which are involved in several embryonic developmental processes. Knockout mice lacking this gene show that it is required for retinal cone bipolar cell differentiation, and that it negatively regulates potassium channel gene expression in the heart to ensure coordinated cardiac repolarization. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
Expression
Biased expression in lung (RPKM 4.8), skin (RPKM 3.3) and 10 other tissues See more
Orthologs

Genomic context

See IRX5 in Genome Data Viewer
Location:
16q12.2
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (54931199..54934485)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (54965111..54968397)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371275 Neighboring gene uncharacterized LOC105371276 Neighboring gene colorectal neoplasia differentially expressed Neighboring gene uncharacterized LOC105371277 Neighboring gene MT-ND5 pseudogene 34

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Hamamy syndrome
MedGen: C1970027 OMIM: 611174 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association analyses identify variants in developmental genes associated with hypospadias.
NHGRI GWA Catalog
Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
NHGRI GWA Catalog
Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
NHGRI GWA Catalog

Pathways from BioSystems

  • FTO Obesity Variant Mechanism, organism-specific biosystem (from WikiPathways)
    FTO Obesity Variant Mechanism, organism-specific biosystemMechanism underlying the association of FTO locus variants and obesity. The wild type T allele at rs1421085 in the FTO locus comprises a protein-DNA binding motif for ARID5B that represses the transc...
  • Preimplantation Embryo, organism-specific biosystem (from WikiPathways)
    Preimplantation Embryo, organism-specific biosystemThe source of this pathway is RNA-Seq data from single-cell pre-implantation embryos (Supplemental Table 1): http://www.nature.com/nsmb/journal/v20/n9/full/nsmb.2660.html Analysis options for runnin...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
vitamin D binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
embryonic cranial skeleton morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
gonad development IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuron maturation IEA
Inferred from Electronic Annotation
more info
 
regulation of heart rate IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
response to stimulus IEA
Inferred from Electronic Annotation
more info
 
retinal bipolar neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
iroquois-class homeodomain protein IRX-5
Names
homeodomain protein IRX-2A
homeodomain protein IRXB2

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_032773.1 RefSeqGene

    Range
    5001..8287
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001252197.1NP_001239126.1  iroquois-class homeodomain protein IRX-5 isoform 2

    See identical proteins and their annotated locations for NP_001239126.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate, in-frame acceptor splice site at the 3' terminal exon compared to variant 1. This results in an isoform (2) that is 1 aa shorter than isoform 1.
    Source sequence(s)
    AY335945
    Consensus CDS
    CCDS58462.1
    UniProtKB/Swiss-Prot
    P78411
    Related
    ENSP00000316250.5, OTTHUMP00000164260, ENST00000320990.9, OTTHUMT00000256912
    Conserved Domains (2) summary
    smart00548
    Location:326343
    IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function
    pfam05920
    Location:131170
    Homeobox_KN; Homeobox KN domain
  2. NM_005853.5NP_005844.4  iroquois-class homeodomain protein IRX-5 isoform 1

    See identical proteins and their annotated locations for NP_005844.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AY335945, BC074850
    Consensus CDS
    CCDS10751.1
    UniProtKB/Swiss-Prot
    P78411
    Related
    ENSP00000378132.4, OTTHUMP00000164259, ENST00000394636.8, OTTHUMT00000256911
    Conserved Domains (2) summary
    smart00548
    Location:327344
    IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function
    pfam05920
    Location:131170
    Homeobox_KN; Homeobox KN domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

    Range
    54931199..54934485
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522809.1XP_011521111.1  iroquois-class homeodomain protein IRX-5 isoform X1

    Conserved Domains (2) summary
    smart00548
    Location:257274
    IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function
    pfam05920
    Location:61100
    Homeobox_KN; Homeobox KN domain
Support Center