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    nkx2.4a NK2 homeobox 4a [ Danio rerio (zebrafish) ]

    Gene ID: 562300, updated on 17-Aug-2024

    Summary

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    Official Symbol
    nkx2.4aprovided by ZNC
    Official Full Name
    NK2 homeobox 4aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-6336
    See related
    Ensembl:ENSDARG00000075107 AllianceGenome:ZFIN:ZDB-GENE-030131-6336
    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
    fi48a12; wu:fi48a12; zgc:171531
    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. Acts upstream of or within hypothalamus development. Predicted to be active in nucleus. Is expressed in caudal tuberculum; diencephalon; forebrain; hypothalamus; and intermediate hypothalamus. Orthologous to human NKX2-4 (NK2 homeobox 4). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    all
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    Genomic context

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    See nkx2.4a in Genome Data Viewer
    Location:
    chromosome: 17
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 17 NC_007128.7 (42095247..42097267, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 17 NC_007128.6 (42106373..42108393, complement)

    Chromosome 17 - NC_007128.7Genomic Context describing neighboring genes Neighboring gene Ral GTPase activating protein catalytic subunit alpha 2 Neighboring gene si:dkeyp-57d12.1 Neighboring gene kizuna centrosomal protein Neighboring gene uncharacterized LOC103909072 Neighboring gene uncharacterized LOC108179796

    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 fish with no sex: gonadal and adrenal functions partition between zebrafish NR5A1 co-orthologs. Yan YL, et al. Genetics, 2021 Feb 9. PMID 33724412, Free PMC Article
    2. nkx2.1 and nkx2.4 genes function partially redundant during development of the zebrafish hypothalamus, preoptic region, and pallidum. Manoli M, et al. Front Neuroanat, 2014. PMID 25520628, Free PMC Article
    3. Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming. Murphy PJ, et al. Cell, 2018 Feb 22. PMID 29456083
    4. Bsx Is Essential for Differentiation of Multiple Neuromodulatory Cell Populations in the Secondary Prosencephalon. Schredelseker T, et al. Front Neurosci, 2020. PMID 32581684, Free PMC Article
    5. Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos. Armant O, et al. Dev Biol, 2013 Aug 15. PMID 23684812, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC193671, MGC193672, MGC193815, MGC193826

    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 differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within hypothalamus development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription 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
    		  
    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
    NK2 homeobox 4a
    Names
    NK2 homeobox 4 a

    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_001111166.1 → NP_001104636.1  NK2 homeobox 4a isoform 1

      See identical proteins and their annotated locations for NP_001104636.1

      Status: PROVISIONAL

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      BC153953
      UniProtKB/TrEMBL
      A8KB41
      Related
      ENSDARP00000104286.1, ENSDART00000110871.4
      Conserved Domains (1) summary
      pfam00046
      Location:163 → 216
      Homeobox; Homeobox domain

    2. NM_001160384.1 → NP_001153856.1  NK2 homeobox 4a isoform 2

      See identical proteins and their annotated locations for NP_001153856.1

      Status: PROVISIONAL

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region compared to variant 1. This results in a shorter protein (isoform b) compared to isoform 1.
      Source sequence(s)
      BC162246
      UniProtKB/TrEMBL
      B3DG22, B3DG27, X1WE81
      Related
      ENSDARP00000128532.1, ENSDART00000155484.2
      Conserved Domains (1) summary
      pfam00046
      Location:154 → 207
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007128.7 Reference GRCz11 Primary Assembly

      Range
      42095247..42097267 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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