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    spaw southpaw [ Danio rerio (zebrafish) ]

    Gene ID: 338101, updated on 9-Dec-2024

    Summary

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    Official Symbol
    spawprovided by ZNC
    Official Full Name
    southpawprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030219-1
    See related
    Ensembl:ENSDARG00000014309 AllianceGenome:ZFIN:ZDB-GENE-030219-1
    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
    Summary
    Predicted to enable cytokine activity. Acts upstream of or within left/right pattern formation. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Is expressed in anterior neural rod; cardiovascular system; diencephalon; mesoderm; and tail bud. Used to study anxiety disorder. Human ortholog(s) of this gene implicated in visceral heterotaxy. Orthologous to human NODAL (nodal growth differentiation factor). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
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    Genomic context

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    See spaw in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 5 NC_007116.7 (68878133..68885056)
    105 previous assembly GRCz10 (GCF_000002035.5) 5 NC_007116.6 (68107466..68114389)

    Chromosome 5 - NC_007116.7Genomic Context describing neighboring genes Neighboring gene ubiquitin specific peptidase 39 Neighboring gene surfactant protein Bb Neighboring gene ankyrin 1, erythrocytic a Neighboring gene microRNA mir-2188 Neighboring gene solute carrier family 25 member 45

    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
    • 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 southpaw joins the roster: the role of the zebrafish nodal-related gene southpaw in cardiac LR asymmetry. Ahmad N, et al. Trends Cardiovasc Med, 2004 Feb. PMID 15030788
    2. Early, H+-V-ATPase-dependent proton flux is necessary for consistent left-right patterning of non-mammalian vertebrates. Adams DS, et al. Development, 2006 May. PMID 16554361, Free PMC Article
    3. Regional cell shape changes control form and function of Kupffer's vesicle in the zebrafish embryo. Wang G, et al. Dev Biol, 2012 Oct 1. PMID 22841644, Free PMC Article
    4. Functional characterization of tektin-1 in motile cilia and evidence for TEKT1 as a new candidate gene for motile ciliopathies. Ryan R, et al. Hum Mol Genet, 2018 Jan 15. PMID 29121203
    5. The actin nucleator Cordon-bleu is required for development of motile cilia in zebrafish. Ravanelli AM, et al. Dev Biol, 2011 Feb 1. PMID 21129373, Free PMC Article

    See all (216) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Zebrafish Klf8 regulates left-right asymmetric patterning by modulating both Kupffer's vesicle morphogenesis and spaw expression in the left lateral plate mesoderm (LPM).
      Title: Klf8 regulates left-right asymmetric patterning through modulation of Kupffer's vesicle morphogenesis and spaw expression.
    2. In a unique mutant defective for the Nodal-related southpaw gene, preferential dextral looping in the heart is maintained, whereas gut and brain asymmetries are randomized.
      Title: A Nodal-independent and tissue-intrinsic mechanism controls heart-looping chirality.
    3. investigate whether loss of Brachyury/Notail or Tbx16/Spadetail disrupts the balance of Nodal ligands (Southpaw) and antagonists (Charon) around Kupffers Vesicle
      Title: Nodal activity around Kupffer's vesicle depends on the T-box transcription factors Notail and Spadetail and on Notch signaling.
    4. Antagonistic interactions between Charon and Southpaw play an important role in L/R patterning in zebrafish
      Title: The Cerberus/Dan-family protein Charon is a negative regulator of Nodal signaling during left-right patterning in zebrafish.
    5. required for organizing at least the initial phase of diencephalic left-right (LR) asymmetry; experiments suggest that heart and brain LR patterning may be coordinated by southpaw signaling [review]
      Title: A southpaw joins the roster: the role of the zebrafish nodal-related gene southpaw in cardiac LR asymmetry.
    6. In zebrafish, it appears that pkd2 is not responsible for the activation of spaw transcription, but is required for a mechanism to restrict spaw expression to the left half of the embryo.
      Title: Zebrafish curly up encodes a Pkd2 ortholog that restricts left-side-specific expression of southpaw.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables cytokine activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables growth factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within determination of digestive tract left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within determination of heart left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within determination of left/right asymmetry in diencephalon IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within determination of left/right asymmetry in lateral mesoderm IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within determination of left/right asymmetry in lateral mesoderm IMP
    Inferred from Mutant Phenotype
    more info
    		  
    acts_upstream_of_or_within determination of left/right symmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within determination of liver left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within determination of pancreatic left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryonic heart tube development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryonic heart tube left/right pattern formation IMP
    Inferred from Mutant Phenotype
    more info
    		  
    acts_upstream_of_or_within establishment of left/right asymmetry IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within establishment of left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within heart jogging IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within heart looping IMP
    Inferred from Mutant Phenotype
    more info
    		  
    acts_upstream_of_or_within lateral mesoderm development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    southpaw
    Names
    ndr3
    unm s457
    unm t30973
    unm_s457
    unm_t30973

    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_180967.2 → NP_851298.1  southpaw precursor

      See identical proteins and their annotated locations for NP_851298.1

      Status: PROVISIONAL

      Source sequence(s)
      AY240027
      UniProtKB/TrEMBL
      Q7ZZT5
      Related
      ENSDARP00000113959.1, ENSDART00000139933.2
      Conserved Domains (2) summary
      pfam00688
      Location:50 → 188
      TGFb_propeptide; TGF-beta propeptide
      cd13759
      Location:302 → 404
      TGF_beta_NODAL; transforming growth factor beta (TGF-beta) like domain found in Nodal (NODAL)-related proteins

    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_007116.7 Reference GRCz11 Primary Assembly

      Range
      68878133..68885056
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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