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spaw southpaw [ Danio rerio (zebrafish) ]

Gene ID: 338101, updated on 2-Nov-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, Nov 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 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. 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
  2. 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
  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. The retinitis pigmentosa protein RP2 interacts with polycystin 2 and regulates cilia-mediated vertebrate development. Hurd T, et al. Hum Mol Genet, 2010 Nov 15. PMID 20729296, Free PMC Article
  5. Selective asymmetry in a conserved forebrain to midbrain projection. Kuan YS, et al. J Exp Zool B Mol Dev Evol, 2007 Sep 15. PMID 17592620

See all (215) 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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