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    irx5a iroquois homeobox 5a [ Danio rerio (zebrafish) ]

    Gene ID: 573346, updated on 2-Nov-2024

    Summary

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    Official Symbol
    irx5aprovided by ZNC
    Official Full Name
    iroquois homeobox 5aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-010716-2
    See related
    Ensembl:ENSDARG00000034043 AllianceGenome:ZFIN:ZDB-GENE-010716-2
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    iro5
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in visual perception. Acts upstream of or within embryonic skeletal joint development and regulation of chondrocyte differentiation. Predicted to be active in nucleus. Is expressed in several structures, including brain; head; hindbrain neural plate; mesoderm; and midbrain neural keel. Orthologous to human IRX5 (iroquois homeobox 5). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See irx5a in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (35706770..35710263, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (35435293..35438786, complement)

    Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101885114 Neighboring gene matrix metallopeptidase 2 Neighboring gene uncharacterized LOC110439935 Neighboring gene iroquois homeobox 6a Neighboring gene uncharacterized LOC103911398 Neighboring gene uncharacterized LOC137496182

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. de la Calle-Mustienes E, et al. Genome Res, 2005 Aug. PMID 16024824, Free PMC Article
    2. Expression of two novel zebrafish iroquois homologues (ziro1 and ziro5) during early development of axial structures and central nervous system. Wang X, et al. Mech Dev, 2001 Jul. PMID 11429297
    3. A duplication on chromosome 16q12 affecting the IRXB gene cluster is associated with autosomal dominant cone dystrophy with early tritanopic color vision defect. Kohl S, et al. Hum Mol Genet, 2021 Jun 17. PMID 33891002, Free PMC Article
    4. Gill developmental program in the teleost mandibular arch. Thiruppathy M, et al. Elife, 2022 Jun 28. PMID 35762575, Free PMC Article
    5. A cascade of irx1a and irx2a controls shh expression during retinogenesis. Choy SW, et al. Dev Dyn, 2010 Dec. PMID 21046643

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Clone Names

    • MGC92554

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within embryonic skeletal joint development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of chondrocyte differentiation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in visual perception IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    Iroquois homeobox protein 5a
    Names
    iroquois homeobox protein 5
    iroquois homeobox protein 5a
    iroquois-class homeodomain protein IRX-5a

    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_001045227.1 → NP_001038692.1  Iroquois homeobox protein 5a

      See identical proteins and their annotated locations for NP_001038692.1

      Status: PROVISIONAL

      Source sequence(s)
      BX005202
      UniProtKB/Swiss-Prot
      Q1LXU5, Q1LYH4
      Related
      ENSDARP00000043856.4, ENSDART00000043857.5
      Conserved Domains (2) summary
      smart00548
      Location:307 → 324
      IRO; Motif in Iroquois-class homeodomain proteins (only). Unknown function
      pfam05920
      Location:129 → 168
      Homeobox_KN; Homeobox KN domain

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007118.7 Reference GRCz11 Primary Assembly

      Range
      35706770..35710263 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q1LXU5.1 GenPept UniProtKB/Swiss-Prot:Q1LXU5

    Gene LinkOut

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