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    Irx3 iroquois homeobox 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 307721, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Irx3provided by RGD
    Official Full Name
    iroquois homeobox 3provided by RGD
    Primary source
    RGD:1307424
    See related
    EnsemblRapid:ENSRNOG00000011533 AllianceGenome:RGD:1307424
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; DNA-binding transcription repressor activity, RNA polymerase II-specific; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including His-Purkinje system development; kidney development; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within mesoderm development; negative regulation of neuron differentiation; and positive regulation of neuron differentiation. Predicted to be located in axon; cytoplasm; and nucleus. Orthologous to human IRX3 (iroquois homeobox 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 52.1), Lung (RPKM 46.3) and 5 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    19p11
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (31384803..31388241)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (15211882..15215317)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (15838714..15842135, complement)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102555119 Neighboring gene uncharacterized LOC134483614 Neighboring gene uncharacterized LOC102556484 Neighboring gene FTO, alpha-ketoglutarate dependent dioxygenase Neighboring gene Rpgrip1-like

    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 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. Nutrition modulates Fto and Irx3 gene transcript levels, but does not alter their DNA methylation profiles in rat white adipose tissues. Nowacka-Woszuk J, et al. Gene, 2017 Apr 30. PMID 28179100
    2. 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
    3. Biological activities encoded by the murine mesenchymal stem cell transcriptome provide a basis for their developmental potential and broad therapeutic efficacy. Phinney DG, et al. Stem Cells, 2006 Jan. PMID 16100003
    4. A homeodomain protein code specifies progenitor cell identity and neuronal fate in the ventral neural tube. Briscoe J, et al. Cell, 2000 May 12. PMID 10830170
    5. Obesity-associated variants within FTO form long-range functional connections with IRX3. Smemo S, et al. Nature, 2014 Mar 20. PMID 24646999, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 His-Purkinje system cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in Purkinje myocyte development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in atrioventricular bundle cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in energy homeostasis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within mesoderm development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in metanephros development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of gap junction assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in proximal/distal pattern formation involved in nephron development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of regulation of cell communication by electrical coupling involved in cardiac conduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in specification of loop of Henle identity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in axon ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    iroquois-class homeodomain protein IRX-3
    Names
    Iroquois related homeobox 3

    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_001395133.1 → NP_001382062.1  iroquois-class homeodomain protein IRX-3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      A6KD68
      Conserved Domains (2) summary
      smart00548
      Location:345 → 362
      IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function
      pfam05920
      Location:148 → 187
      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
      31384803..31388241
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006255192.5 → XP_006255254.1  iroquois-class homeodomain protein IRX-3 isoform X1

      UniProtKB/TrEMBL
      D3ZNE0
      Related
      ENSRNOP00000015583.5, ENSRNOT00000015583.7
      Conserved Domains (2) summary
      smart00548
      Location:345 → 362
      IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function
      pfam05920
      Location:148 → 187
      Homeobox_KN; Homeobox KN domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001107413.1: Suppressed sequence

      Description
      NM_001107413.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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