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    Irx5 iroquois homeobox 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 498918, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Irx5provided by RGD
    Official Full Name
    iroquois homeobox 5provided by RGD
    Primary source
    RGD:1565518
    See related
    EnsemblRapid:ENSRNOG00000011180 AllianceGenome:RGD:1565518
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables DNA-binding transcription factor binding activity and identical protein binding activity. Involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human IRX5 (iroquois homeobox 5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Heart (RPKM 40.9), Kidney (RPKM 35.7) and 5 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Irx5 in Genome Data Viewer
    Location:
    19p11
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (30812033..30816885, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (14639052..14643911, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (16415813..16421088)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134483503 Neighboring gene uncharacterized LOC120098515 Neighboring gene colorectal neoplasia differentially expressed Neighboring gene FUN14 domain-containing protein 2 pseudogene Neighboring gene transfer RNA serine (anticodon AGA) 11

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Iroquois homeobox transcription factor (Irx5) promotes G1/S-phase transition in vascular smooth muscle cells by CDK2-dependent activation. Liu D, et al. Am J Physiol Cell Physiol, 2016 Aug 1. PMID 27170637, Free PMC Article
    2. Aetiology-specific patterns in end-stage heart failure patients identified by functional annotation and classification of microarray data. Beisvag V, et al. Eur J Heart Fail, 2006 Jun. PMID 16753336
    3. Regional variation in mRNA transcript abundance within the ventricular wall. Rosati B, et al. J Mol Cell Cardiol, 2006 Feb. PMID 16412459
    4. Mutations in IRX5 impair craniofacial development and germ cell migration via SDF1. Bonnard C, et al. Nat Genet, 2012 May 13. PMID 22581230
    5. Interaction between transcription factors Iroquois proteins 4 and 5 controls cardiac potassium channel Kv4.2 gene transcription. He W, et al. Cardiovasc Res, 2009 Jan 1. PMID 18815185, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Irx5 plays an important role in VSMC G1/S-phase cell cycle checkpoint control.
      Title: Iroquois homeobox transcription factor (Irx5) promotes G1/S-phase transition in vascular smooth muscle cells by CDK2-dependent activation.
    2. Interaction between transcription factors Iroquois proteins 4 and 5 controls cardiac potassium channel Kv4.2 gene transcription across the left ventricular wall of rodent hearts.
      Title: Interaction between transcription factors Iroquois proteins 4 and 5 controls cardiac potassium channel Kv4.2 gene transcription.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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 binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cell development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in embryonic cranial skeleton morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in gonad development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within neuron maturation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of heart rate ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within retinal bipolar neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    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-5
    Names
    iroquois homeobox protein 5

    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_001030044.1 → NP_001025215.1  iroquois-class homeodomain protein IRX-5

      See identical proteins and their annotated locations for NP_001025215.1

      Status: PROVISIONAL

      Source sequence(s)
      DQ109812
      UniProtKB/TrEMBL
      A0A0G2K2M1, A6KD61, Q45V74
      Related
      ENSRNOP00000072299.2, ENSRNOT00000089975.3
      Conserved Domains (2) summary
      smart00548
      Location:328 → 345
      IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function
      pfam05920
      Location:130 → 169
      Homeobox_KN; Homeobox KN domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086037.1 Reference GRCr8

      Range
      30812033..30816885 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006255197.5 → XP_006255259.1  iroquois-class homeodomain protein IRX-5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K2M1, A6KD61
      Conserved Domains (2) summary
      smart00548
      Location:254 → 271
      IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function
      pfam05920
      Location:56 → 95
      Homeobox_KN; Homeobox KN domain
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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