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    RNL RNAligase [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 837306, updated on 18-Sep-2024

    Summary

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    Official Symbol
    RNL
    Official Full Name
    RNAligase
    Primary source
    TAIR:AT1G07910
    Locus tag
    AT1G07910
    See related
    Araport:AT1G07910
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    ARABIDOPSIS THALIANA RNA LIGASE; AtRLG1; ATRNL; RNAligase; T6D22.1; T6D22_1; TRNA LIGASE
    Summary
    Encodes a tRNA ligase that resembles the yeast Trl1 RNA ligase in structure and function but very different in sequence. Like Trl1, AtRNL consists of two domains #Aei an N-terminal ligase component and a C-terminal 5'-kinase/2',3'-cyclic phosphodiesterase (CPD) component#Aei that can function in tRNA splicing in vivo when expressed as separate polypeptides. Requires a 2'-PO4 end for tRNA splicing in vivo.
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    Genomic context

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    See RNL in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    28
    Sequence:
    Chromosome: 1; NC_003070.9 (2445437..2454645)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene LOB domain-containing protein 1 Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein Neighboring gene GTP binding Elongation factor Tu family protein Neighboring gene pseudo Neighboring gene GTP binding Elongation factor Tu family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. ZYGOTE-ARREST 3 that encodes the tRNA ligase is essential for zygote division in Arabidopsis. Yang KJ, et al. J Integr Plant Biol, 2017 Sep. PMID 28631407
    2. Distinctive kinetics and substrate specificities of plant and fungal tRNA ligases. Remus BS, et al. RNA, 2014 Apr. PMID 24554441, Free PMC Article
    3. Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins. Englert M, et al. Nucleic Acids Res, 2005. PMID 15653639, Free PMC Article
    4. Meta-regulation of Arabidopsis auxin responses depends on tRNA maturation. Leitner J, et al. Cell Rep, 2015 Apr 28. PMID 25892242, Free PMC Article
    5. Structure-function analysis of the kinase-CPD domain of yeast tRNA ligase (Trl1) and requirements for complementation of tRNA splicing by a plant Trl1 homolog. Wang LK, et al. Nucleic Acids Res, 2006. PMID 16428247, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. essential for tRNA splicing and zygote division
      Title: ZYGOTE-ARREST 3 that encodes the tRNA ligase is essential for zygote division in Arabidopsis.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001331741.1
    NM_100665.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    enables RNA ligase (ATP) activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA ligase (ATP) activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables polynucleotide 5'-hydroxyl-kinase activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    NOT involved_in endoplasmic reticulum unfolded protein response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of auxin mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within tRNA splicing, via endonucleolytic cleavage and ligation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA splicing, via endonucleolytic cleavage and ligation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within tRNA splicing, via endonucleolytic cleavage and ligation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tRNA splicing, via endonucleolytic cleavage and ligation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within tRNA splicing, via endonucleolytic cleavage and ligation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    RNAligase
    NP_001318950.1
    • RNAligase (RNL); CONTAINS InterPro DOMAIN/s: tRNA ligase, phosphodiesterase, fungi (InterPro:IPR015965); Has 209 Blast hits to 196 proteins in 23 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 3; Plants - 200; Viruses - 0; Other Eukaryotes - 6 (source: NCBI BLink).
    NP_172269.2
    • RNAligase (RNL); CONTAINS InterPro DOMAIN/s: tRNA ligase, phosphodiesterase, fungi (InterPro:IPR015965); Has 209 Blast hits to 196 proteins in 23 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 3; Plants - 200; Viruses - 0; Other Eukaryotes - 6 (source: NCBI BLink).

    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_003070.9 Reference assembly

      Range
      2445437..2454645
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_100665.3 → NP_172269.2  RNAligase [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_172269.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WL81, Q0WVN4, Q0WWW5, Q96312, Q9LN14
      UniProtKB/TrEMBL
      A0A178WD33
      Conserved Domains (1) summary
      cl26784
      Location:942 → 1099
      tRNA_lig_CPD; Fungal tRNA ligase phosphodiesterase domain

    2. NM_001331741.1 → NP_001318950.1  RNAligase [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178WBC7, A0A2H1ZEA2
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q0WL81.1

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