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    spat-3 E3 ubiquitin-protein ligase RING2 homolog spat-3 [ Caenorhabditis elegans ]

    Gene ID: 259704, updated on 9-Dec-2024

    Summary

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    Official Symbol
    spat-3
    Official Full Name
    E3 ubiquitin-protein ligase RING2 homolog spat-3
    Primary source
    WormBase:WBGene00020496
    Locus tag
    CELE_T13H2.5
    See related
    AllianceGenome:WB:WBGene00020496
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Caenorhabditis elegans (strain: Bristol N2)
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
    Summary
    Enables histone ubiquitin ligase activity. Involved in several processes, including negative regulation of gene expression, epigenetic; negative regulation of vulval development; and nematode male tail tip morphogenesis. Predicted to be part of PcG protein complex and ubiquitin ligase complex. Is expressed in several structures, including nervous system. Used to study developmental disorder of mental health. Human ortholog(s) of this gene implicated in Luo-Schoch-Yamamoto syndrome. Orthologous to human RING1 (ring finger protein 1) and RNF2 (ring finger protein 2). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See spat-3 in Genome Data Viewer
    Location:
    chromosome: X
    Exon count:
    19
    Sequence:
    Chromosome: X; NC_003284.9 (4596011..4605928, complement)

    Chromosome X - NC_003284.9Genomic Context describing neighboring genes Neighboring gene Endoplasmic reticulum junction formation protein lunapark;Endoplasmic reticulum junction formation protein lunapark-1 Neighboring gene FMRF-Like Peptide Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene Prion-like-(Q/N-rich)-domain-bearing protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003284.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. De novo mutation in RING1 with epigenetic effects on neurodevelopment. Pierce SB, et al. Proc Natl Acad Sci U S A, 2018 Feb 13. PMID 29386386, Free PMC Article
    2. MIG-32 and SPAT-3A are PRC1 homologs that control neuronal migration in Caenorhabditis elegans. Karakuzu O, et al. Development, 2009 Mar. PMID 19211678, Free PMC Article
    3. PRC1 chromatin factors strengthen the consistency of neuronal cell fate specification and maintenance in C. elegans. Bordet G, et al. PLoS Genet, 2022 May. PMID 35604893, Free PMC Article
    4. Transdifferentiation. Sequential histone-modifying activities determine the robustness of transdifferentiation. Zuryn S, et al. Science, 2014 Aug 15. PMID 25124442
    5. A genomewide screen for suppressors of par-2 uncovers potential regulators of PAR protein-dependent cell polarity in Caenorhabditis elegans. Labbé JC, et al. Genetics, 2006 Sep. PMID 16816419, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 WormBase

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone ubiquitin ligase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of gene expression, epigenetic IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in negative regulation of vulval development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in nematode male tail tip morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in reproductive process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of PcG protein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of ubiquitin ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of ubiquitin ligase complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase RING2 homolog spat-3
    NP_001024904.2
    • Confirmed by transcript evidence
    NP_001024905.1
    • Confirmed by transcript evidence

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003284.9 Reference assembly

      Range
      4596011..4605928 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001029733.6 → NP_001024904.2  E3 ubiquitin-protein ligase RING2 homolog spat-3 [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001024904.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      H2KYH3, Q22463
      Conserved Domains (5) summary
      cd16544
      Location:158 → 203
      RING-HC_RNF138; RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins
      pfam08226
      Location:2150 → 2199
      DUF1720; Domain of unknown function (DUF1720)
      pfam09770
      Location:1724 → 1845
      PAT1; Topoisomerase II-associated protein PAT1
      pfam15782
      Location:1301 → 1430
      GREB1; Gene regulated by oestrogen in breast cancer
      NF012181
      Location:290 → 583
      MSCRAMM_SdrD; MSCRAMM family adhesin SdrD

    2. NM_001029734.5 → NP_001024905.1  E3 ubiquitin-protein ligase RING2 homolog spat-3 [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_001024905.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      Q22463
    Nucleotide Protein
    Heading Accession and Version

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