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    rtcb RNA 2',3'-cyclic phosphate and 5'-OH ligase [ Danio rerio (zebrafish) ]

    Gene ID: 406376, updated on 2-Nov-2024

    Summary

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    Official Symbol
    rtcbprovided by ZNC
    Official Full Name
    RNA 2',3'-cyclic phosphate and 5'-OH ligaseprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-2096
    See related
    Ensembl:ENSDARG00000101047 AllianceGenome:ZFIN:ZDB-GENE-040426-2096
    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
    zgc:76871
    Summary
    Predicted to enable RNA ligase (GTP) activity. Predicted to be involved in tRNA splicing, via endonucleolytic cleavage and ligation. Predicted to act upstream of or within tRNA processing. Predicted to be located in cytoplasm. Predicted to be part of tRNA-splicing ligase complex. Predicted to be active in nucleus. Orthologous to human RTCB (RNA 2',3'-cyclic phosphate and 5'-OH ligase). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See rtcb in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 4 NC_007115.7 (676710..685412, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 4 NC_007115.6 (663262..671964, complement)

    Chromosome 4 - NC_007115.7Genomic Context describing neighboring genes Neighboring gene parathyroid hormone-like hormone a Neighboring gene exportin, tRNA (nuclear export receptor for tRNAs) Neighboring gene uncharacterized LOC137487247 Neighboring gene F-box protein 7

    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. CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration. Schaffer AE, et al. Cell, 2014 Apr 24. PMID 24766810, Free PMC Article
    2. Contrasted innate responses to two viruses in zebrafish: insights into the ancestral repertoire of vertebrate IFN-stimulated genes. Briolat V, et al. J Immunol, 2014 May 1. PMID 24683187
    3. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA ligase (ATP) activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA ligase (GTP) activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA ligase (GTP) activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables RNA ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within 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
    		  
    acts_upstream_of_or_within tRNA splicing, via endonucleolytic cleavage and ligation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tRNA splicing, via endonucleolytic cleavage and ligation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    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
    		  

    General protein information

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    Preferred Names
    RNA-splicing ligase RtcB homolog
    Names
    3'-phosphate/5'-hydroxy nucleic acid ligase
    NP_998268.1

    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_213103.1 → NP_998268.1  RNA-splicing ligase RtcB homolog

      See identical proteins and their annotated locations for NP_998268.1

      Status: PROVISIONAL

      Source sequence(s)
      BC065987
      UniProtKB/Swiss-Prot
      Q6NZS4
      Related
      ENSDARP00000140069.1, ENSDART00000168167.2
      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

    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_007115.7 Reference GRCz11 Primary Assembly

      Range
      676710..685412 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6NZS4.1 GenPept UniProtKB/Swiss-Prot:Q6NZS4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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