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    LIG6 DNA LIGASE 6 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 842991, updated on 18-Sep-2024

    Summary

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    Official Symbol
    LIG6
    Official Full Name
    DNA LIGASE 6
    Primary source
    TAIR:AT1G66730
    Locus tag
    AT1G66730
    See related
    Araport:AT1G66730
    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
    AtLIG6; DNA LIGASE 6; F4N21.14; F4N21_14
    Summary
    Encodes a novel plant specific DNA ligase that is involved in seed germination and DNA repair.
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    Genomic context

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    See LIG6 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    19
    Sequence:
    Chromosome: 1; NC_003070.9 (24884681..24892046)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene S-adenosyl-L-methionine-dependent methyltransferases superfamily protein Neighboring gene ncRNA Neighboring gene ASF1 like histone chaperone Neighboring gene CDK-activating kinase 4

    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. Arabidopsis DNA polymerase lambda mutant is mildly sensitive to DNA double strand breaks but defective in integration of a transgene. Furukawa T, et al. Front Plant Sci, 2015. PMID 26074930, Free PMC Article
    2. A plant DNA ligase is an important determinant of seed longevity. Waterworth WM, et al. Plant J, 2010 Sep. PMID 20584150
    3. CENTRIN2 modulates homologous recombination and nucleotide excision repair in Arabidopsis. Molinier J, et al. Plant Cell, 2004 Jun. PMID 15155891, Free PMC Article
    4. Agrobacterium T-DNA integration into the plant genome can occur without the activity of key non-homologous end-joining proteins. Park SY, et al. Plant J, 2015 Mar. PMID 25641249
    5. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Theologis A, et al. Nature, 2000 Dec 14. PMID 11130712

    GeneRIFs: Gene References Into Functions

    General gene information

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    NM_105343.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA ligase (ATP) activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA integration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within double-strand break repair via nonhomologous end joining IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of cellular response to X-ray IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to UV-C IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to bleomycin IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to cold IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to molecule of bacterial origin IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to oxidative stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in seed development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in seed germination IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within seed germination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    DNA LIGASE 6
    NP_176845.2
    • DNA LIGASE 6 (LIG6); FUNCTIONS IN: DNA binding, DNA ligase (ATP) activity, ATP binding; INVOLVED IN: DNA repair, seed germination, DNA recombination, DNA replication; LOCATED IN: chloroplast; EXPRESSED IN: 16 plant structures; EXPRESSED DURING: 9 growth stages; CONTAINS InterPro DOMAIN/s: Nucleic acid-binding, OB-fold (InterPro:IPR012340), DNA ligase, N-terminal (InterPro:IPR012308), DNA repair metallo-beta-lactamase (InterPro:IPR011084), ATP dependent DNA ligase, central (InterPro:IPR012310), ATP dependent DNA ligase, C-terminal (InterPro:IPR012309), ATP-dependent DNA ligase (InterPro:IPR000977), ATP-dependent DNA ligase, conserved site (InterPro:IPR016059); BEST Arabidopsis thaliana protein match is: DNA ligase 1 (TAIR:AT1G08130.1); Has 4468 Blast hits to 4373 proteins in 907 species: Archae - 366; Bacteria - 1648; Metazoa - 644; Fungi - 681; Plants - 268; Viruses - 157; Other Eukaryotes - 704 (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
      24884681..24892046
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_105343.3 → NP_176845.2  DNA LIGASE 6 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_176845.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      F4HPZ9, Q9C9M5
      UniProtKB/TrEMBL
      A0A7G2E3R9
      Conserved Domains (6) summary
      cd07969
      Location:1241 → 1385
      OBF_DNA_ligase_I; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit
      cd07900
      Location:1002 → 1236
      Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I
      PRK01109
      Location:766 → 1389
      PRK01109; ATP-dependent DNA ligase; Provisional
      pfam04675
      Location:766 → 937
      DNA_ligase_A_N; DNA ligase N terminus
      pfam07522
      Location:276 → 380
      DRMBL; DNA repair metallo-beta-lactamase
      cd16273
      Location:42 → 204
      SNM1A-1C-like_MBL-fold; SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    F4HPZ9.1

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