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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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