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    Lig1 DNA ligase 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 81513, updated on 2-May-2024

    Summary

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    Symbol
    Lig1provided by RGD
    Full Name
    DNA ligase 1provided by RGD
    Primary source
    RGD:621424
    See related
    Ensembl:ENSRNOG00000014193 AllianceGenome:RGD:621424
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables DNA ligase activity. Involved in DNA repair. Located in nucleus. Used to study epilepsy with generalized tonic-clonic seizures. Human ortholog(s) of this gene implicated in inherited metabolic disorder and primary immunodeficiency disease. Orthologous to human LIG1 (DNA ligase 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 163.8), Spleen (RPKM 108.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lig1 in Genome Data Viewer
    Location:
    1q21
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (83243043..83281707)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (74165688..74204400)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (75356212..75394757)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134485101 Neighboring gene vomeronasal 1 receptor 62 Neighboring gene zinc finger SWIM-type containing 9 Neighboring gene phospholipase A2 group IVC Neighboring gene pellino 1, pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Rat liver DNA ligases. Catalytic properties of a novel form of DNA ligase. Elder RH, et al. Eur J Biochem, 1992 Jan 15. PMID 1730240
    2. Growth retardation and immunodeficiency in a patient with mutations in the DNA ligase I gene. Webster AD, et al. Lancet, 1992 Jun 20. PMID 1351188
    3. Down-Regulation of Astrocytic Kir4.1 Channels during the Audiogenic Epileptogenesis in Leucine-Rich Glioma-Inactivated 1 (Lgi1) Mutant Rats. Kinboshi M, et al. Int J Mol Sci, 2019 Feb 26. PMID 30813600, Free PMC Article
    4. DNA ligase I null mouse cells show normal DNA repair activity but altered DNA replication and reduced genome stability. Bentley DJ, et al. J Cell Sci, 2002 Apr 1. PMID 11896201
    5. DNA ligase III promotes alternative nonhomologous end-joining during chromosomal translocation formation. Simsek D, et al. PLoS Genet, 2011 Jun. PMID 21655080, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Role and Mechanism of Spinal NF-kappaB-CXCL1/CXCR2 in Rats with Nucleus Pulposus-induced Radicular Pain.
      Title: The Role and Mechanism of Spinal NF-κB-CXCL1/CXCR2 in Rats with Nucleus Pulposus-induced Radicular Pain.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC105416

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA ligase (ATP) activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA ligase (ATP) activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA ligase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA ligase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding 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 ligation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA recombination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    NOT acts_upstream_of_or_within DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within DNA replication ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in Okazaki fragment processing involved in mitotic DNA replication IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    NOT involved_in V(D)J recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in base-excision repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in base-excision repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lagging strand elongation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within response to hydrogen peroxide ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    DNA ligase 1
    Names
    DNA ligase (ATP) 1
    DNA ligase I
    ligase I, DNA, ATP-dependent
    polydeoxyribonucleotide synthase [ATP] 1
    NP_001019439.1
    XP_038947878.1
    XP_038947883.1

    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_001024268.3 → NP_001019439.1  DNA ligase 1

      See identical proteins and their annotated locations for NP_001019439.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/Swiss-Prot
      Q9JHY8
      UniProtKB/TrEMBL
      F1M624, Q566D8
      Related
      ENSRNOP00000019799.7, ENSRNOT00000019799.7
      Conserved Domains (4) summary
      cd07969
      Location:749 → 894
      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:526 → 744
      Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I
      PLN03113
      Location:159 → 909
      PLN03113; DNA ligase 1; Provisional
      pfam04675
      Location:283 → 454
      DNA_ligase_A_N; DNA ligase N terminus

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      83243043..83281707
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039091950.2 → XP_038947878.1  DNA ligase 1 isoform X1

      UniProtKB/Swiss-Prot
      Q9JHY8
      UniProtKB/TrEMBL
      A0A8J8XFV7, A6KSM0
      Related
      ENSRNOP00000061228.3
      Conserved Domains (2) summary
      PTZ00121
      Location:2 → 270
      PTZ00121; MAEBL; Provisional
      PLN03113
      Location:174 → 924
      PLN03113; DNA ligase 1; Provisional

    2. XM_039091955.2 → XP_038947883.1  DNA ligase 1 isoform X1

      UniProtKB/Swiss-Prot
      Q9JHY8
      UniProtKB/TrEMBL
      A0A8J8XFV7, A6KSM0
      Conserved Domains (2) summary
      PTZ00121
      Location:2 → 270
      PTZ00121; MAEBL; Provisional
      PLN03113
      Location:174 → 924
      PLN03113; DNA ligase 1; Provisional
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9JHY8.1 GenPept UniProtKB/Swiss-Prot:Q9JHY8

    Gene LinkOut

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

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