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

Gene ID: 81513, updated on 27-Nov-2024

Summary

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Symbol
Lig1provided by RGD
Full Name
DNA ligase 1provided by RGD
Primary source
RGD:621424
See related
EnsemblRapid: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. Predicted to be located in nucleoplasm. Predicted to be active in mitochondrion and 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, Nov 2024]
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. The Role and Mechanism of Spinal NF-κB-CXCL1/CXCR2 in Rats with Nucleus Pulposus-induced Radicular Pain. Gao F, et al. Spine (Phila Pa 1976), 2024 Apr 1. PMID 38098294, Free PMC Article
  3. 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
  4. 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
  5. 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

See all (18) 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
  
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 IEA
Inferred from Electronic Annotation
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
    ENSRNOP00000106715.1, ENSRNOT00000144210.1
    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
    ENSRNOP00000089677.1, ENSRNOT00000109652.2
    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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