U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Lig3 DNA ligase 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 303369, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Lig3provided by RGD
    Official Full Name
    DNA ligase 3provided by RGD
    Primary source
    RGD:1309875
    See related
    EnsemblRapid:ENSRNOG00000021815 AllianceGenome:RGD:1309875
    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 base-excision repair, DNA ligation. Predicted to be located in mitochondrion; nucleoplasm; and synaptonemal complex. Predicted to be part of DNA ligase III-XRCC1 complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in mitochondrial DNA depletion syndrome 20 and pancreatic cancer. Orthologous to human LIG3 (DNA ligase 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Testes (RPKM 146.4), Thymus (RPKM 143.6) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Lig3 in Genome Data Viewer
    Location:
    10q26
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (68215371..68238705)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (67717808..67741141)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (70134734..70158051)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene chaperonin containing TCP1 subunit 6B Neighboring gene zinc finger protein 830 Neighboring gene uncharacterized LOC102547954 Neighboring gene ring finger and FYVE-like domain containing E3 ubiquitin protein ligase Neighboring gene RAD51 paralog D Neighboring gene U6 spliceosomal RNA Neighboring gene fibronectin type III domain containing 8

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Involvement of DNA ligase III and ribonuclease H1 in mitochondrial DNA replication in cultured human cells. Ruhanen H, et al. Biochim Biophys Acta, 2011 Dec. PMID 21878356, Free PMC Article
    2. Mammalian DNA ligase III: molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination. Chen J, et al. Mol Cell Biol, 1995 Oct. PMID 7565692, Free PMC Article
    3. The human DNA ligase III gene encodes nuclear and mitochondrial proteins. Lakshmipathy U, et al. Mol Cell Biol, 1999 May. PMID 10207110, Free PMC Article
    4. Early embryonic lethality due to targeted inactivation of DNA ligase III. Puebla-Osorio N, et al. Mol Cell Biol, 2006 May. PMID 16648486, Free PMC Article
    5. CircRNA Galntl6 sponges miR-335 to ameliorate stress-induced hypertension through upregulating Lig3 in rostral ventrolateral medulla. Zhang S, et al. Redox Biol, 2023 Aug. PMID 37315345, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CircRNA Galntl6 sponges miR-335 to ameliorate stress-induced hypertension through upregulating Lig3 in rostral ventrolateral medulla.
      Title: CircRNA Galntl6 sponges miR-335 to ameliorate stress-induced hypertension through upregulating Lig3 in rostral ventrolateral medulla.
    Submit: New GeneRIF Correction

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    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 ISO
    Inferred from Sequence Orthology
    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 zinc 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT involved_in V(D)J recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in base-excision repair, DNA ligation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in base-excision repair, DNA ligation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in base-excision repair, DNA ligation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in double-strand break repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair via alternative nonhomologous end joining ISO
    Inferred from Sequence Orthology
    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 mitochondrial DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mitochondrial DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mitochondrion organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of DNA recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of mitochondrial DNA replication ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of DNA ligase III-XRCC1 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in condensed nuclear chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in synaptonemal complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    DNA ligase 3
    Names
    DNA ligase (ATP) 3
    ligase III, DNA, ATP-dependent
    NP_001380964.1
    NP_001380965.1
    XP_008766242.2
    XP_008766243.2
    XP_038941956.1
    XP_038941957.1
    XP_038941958.1
    XP_038941959.2
    XP_063125149.1
    XP_063125150.1
    XP_063125151.1
    XP_063125152.1
    XP_063125153.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001394035.1 → NP_001380964.1  DNA ligase 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A0G2JV76, A6HHE1
      Conserved Domains (3) summary
      TIGR00574
      Location:320 → 832
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      pfam00645
      Location:97 → 182
      zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
      pfam16759
      Location:927 → 997
      LIG3_BRCT; DNA ligase 3 BRCT domain

    2. NM_001394036.1 → NP_001380965.1  DNA ligase 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A0G2JV76, A6HHE1
      Related
      ENSRNOP00000068489.3, ENSRNOT00000076739.4
      Conserved Domains (3) summary
      TIGR00574
      Location:320 → 832
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      pfam00645
      Location:97 → 182
      zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
      pfam16759
      Location:927 → 997
      LIG3_BRCT; DNA ligase 3 BRCT domain

    RNA

    1. NR_172067.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010

    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_086028.1 Reference GRCr8

      Range
      68215371..68238705
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039086031.2 → XP_038941959.2  DNA ligase 3 isoform X8

    2. XM_008768020.4 → XP_008766242.2  DNA ligase 3 isoform X2

      UniProtKB/TrEMBL
      A0A0G2JV76, A6HHE1

    3. XM_063269083.1 → XP_063125153.1  DNA ligase 3 isoform X7

      UniProtKB/TrEMBL
      Q5U2M4
      Related
      ENSRNOP00000069379.3, ENSRNOT00000084076.3

    4. XM_063269081.1 → XP_063125151.1  DNA ligase 3 isoform X5

      UniProtKB/TrEMBL
      Q5U2M4
      Related
      ENSRNOP00000052836.3, ENSRNOT00000055982.6

    5. XM_008768021.4 → XP_008766243.2  DNA ligase 3 isoform X4

      UniProtKB/TrEMBL
      A0A096MKE9

    6. XM_063269079.1 → XP_063125149.1  DNA ligase 3 isoform X1

      UniProtKB/TrEMBL
      A0A0G2JV76, A6HHE1

    7. XM_039086029.2 → XP_038941957.1  DNA ligase 3 isoform X3

      UniProtKB/TrEMBL
      A0A0G2JV76, A6HHE1
      Conserved Domains (3) summary
      TIGR00574
      Location:320 → 832
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      pfam00645
      Location:97 → 182
      zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
      pfam16759
      Location:927 → 997
      LIG3_BRCT; DNA ligase 3 BRCT domain

    8. XM_039086030.2 → XP_038941958.1  DNA ligase 3 isoform X3

      UniProtKB/TrEMBL
      A0A0G2JV76, A6HHE1
      Conserved Domains (3) summary
      TIGR00574
      Location:320 → 832
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      pfam00645
      Location:97 → 182
      zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
      pfam16759
      Location:927 → 997
      LIG3_BRCT; DNA ligase 3 BRCT domain

    9. XM_063269080.1 → XP_063125150.1  DNA ligase 3 isoform X3

      UniProtKB/TrEMBL
      A0A0G2JV76, A6HHE1

    10. XM_039086028.2 → XP_038941956.1  DNA ligase 3 isoform X3

      UniProtKB/TrEMBL
      A0A0G2JV76, A6HHE1
      Conserved Domains (3) summary
      TIGR00574
      Location:320 → 832
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      pfam00645
      Location:97 → 182
      zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
      pfam16759
      Location:927 → 997
      LIG3_BRCT; DNA ligase 3 BRCT domain

    11. XM_063269082.1 → XP_063125152.1  DNA ligase 3 isoform X6

      UniProtKB/TrEMBL
      Q5U2M4
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools