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    rtcb-1 RNA-splicing ligase RtcB homolog [ Caenorhabditis elegans ]

    Gene ID: 184556, updated on 2-Nov-2024

    Summary

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    Official Symbol
    rtcb-1
    Official Full Name
    RNA-splicing ligase RtcB homolog
    Primary source
    WormBase:WBGene00008877
    Locus tag
    CELE_F16A11.2
    See related
    AllianceGenome:WB:WBGene00008877
    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 RNA ligase (ATP) activity. Involved in IRE1-mediated unfolded protein response. Acts upstream of or within with a positive effect on germ cell development and vulval development. Located in cytoplasm and nucleus. Is expressed in body wall musculature; pharynx; and vulval muscle. Used to study Parkinson's disease. Orthologous to human RTCB (RNA 2',3'-cyclic phosphate and 5'-OH ligase). [provided by Alliance of Genome Resources, Nov 2024]
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    Genomic context

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    See rtcb-1 in Genome Data Viewer
    Location:
    chromosome: I
    Exon count:
    5
    Sequence:
    Chromosome: I; NC_003279.8 (9390833..9393095, complement)

    Chromosome I - NC_003279.8Genomic Context describing neighboring genes Neighboring gene Serine/threonine-protein phosphatase 4 regulatory subunit 1 Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene RING finger and SPRY domain-containing protein 1 Neighboring gene pseudo

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003279.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. RTCB-1 mediates neuroprotection via XBP-1 mRNA splicing in the unfolded protein response pathway. Ray A, et al. J Neurosci, 2014 Nov 26. PMID 25429148, Free PMC Article
    2. The RtcB RNA ligase is an essential component of the metazoan unfolded protein response. Kosmaczewski SG, et al. EMBO Rep, 2014 Dec. PMID 25366321, Free PMC Article
    3. A Functional Non-coding RNA Is Produced from xbp-1 mRNA. Liu X, et al. Neuron, 2020 Sep 9. PMID 32640191, Free PMC Article
    4. RNA ligation in neurons by RtcB inhibits axon regeneration. Kosmaczewski SG, et al. Proc Natl Acad Sci U S A, 2015 Jul 7. PMID 26100902, Free PMC Article
    5. Coordinate Regulation of Ribosome and tRNA Biogenesis Controls Hypoxic Injury and Translation. Itani OA, et al. Curr Biol, 2021 Jan 11. PMID 33157031, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by WormBase

    Function Evidence Code Pubs
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA ligase (ATP) activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables RNA ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ligase activity, forming phosphoric ester bonds IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in IRE1-mediated unfolded protein response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within_positive_effect germ cell development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tRNA splicing, via endonucleolytic cleavage and ligation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA splicing, via endonucleolytic cleavage and ligation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within_positive_effect vulval development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in nuclear envelope ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of tRNA-splicing ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of tRNA-splicing ligase complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of tRNA-splicing ligase complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    RNA-splicing ligase RtcB homolog
    NP_492498.1
    • 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_003279.8 Reference assembly

      Range
      9390833..9393095 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_060097.6 → NP_492498.1  RNA-splicing ligase RtcB homolog [Caenorhabditis elegans]

      See identical proteins and their annotated locations for NP_492498.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      P90838
      Conserved Domains (2) summary
      COG1690
      Location:28 → 505
      RtcB; RNA-splicing ligase RtcB, repairs tRNA damage [Translation, ribosomal structure and biogenesis]
      pfam01139
      Location:65 → 505
      RtcB; tRNA-splicing ligase RtcB

    RNA

    1. NR_136370.1 RNA Sequence

      Status: REVIEWED

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P90838.2

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