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    Lig3 ligase III, DNA, ATP-dependent [ Mus musculus (house mouse) ]

    Gene ID: 16882, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Lig3provided by MGI
    Official Full Name
    ligase III, DNA, ATP-dependentprovided by MGI
    Primary source
    MGI:MGI:109152
    See related
    Ensembl:ENSMUSG00000020697 AllianceGenome:MGI:109152
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    D11Wsu78e
    Summary
    Predicted to enable DNA ligase (ATP) activity. Involved in double-strand break repair via alternative nonhomologous end joining and mitochondrion organization. Acts upstream of or within double-strand break repair via nonhomologous end joining; mitochondrial DNA repair; and negative regulation of DNA recombination. Located in synaptonemal complex. Is expressed in several structures, including early conceptus; gonad; hemolymphoid system gland; liver; and lung. 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, Nov 2024]
    Expression
    Ubiquitous expression in testis adult (RPKM 26.9), whole brain E14.5 (RPKM 12.7) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Lig3 in Genome Data Viewer
    Location:
    11 C; 11 50.23 cM
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (82671977..82695100)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (82781109..82804274)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E7027 Neighboring gene zinc finger protein 830 Neighboring gene predicted gene 11423 Neighboring gene ring finger and FYVE like domain containing protein Neighboring gene STARR-seq mESC enhancer starr_30179 Neighboring gene RAD51 paralog D Neighboring gene STARR-positive B cell enhancer ABC_E8433 Neighboring gene fibronectin type III domain containing 8

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Exploiting DNA Ligase III addiction of multiple myeloma by flavonoid Rhamnetin. Caracciolo D, et al. J Transl Med, 2022 Oct 22. PMID 36273153, Free PMC Article
    2. Time-dependent predominance of nonhomologous DNA end-joining pathways during embryonic development in mice. Chiruvella KK, et al. J Mol Biol, 2012 Mar 30. PMID 22306462
    3. Mitochondrial DNA ligase is dispensable for the viability of cultured cells but essential for mtDNA maintenance. Shokolenko IN, et al. J Biol Chem, 2013 Sep 13. PMID 23884459, 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. Two forms of mitochondrial DNA ligase III are produced in Xenopus laevis oocytes. Perez-Jannotti RM, et al. J Biol Chem, 2001 Dec 28. PMID 11598119

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Exploiting DNA Ligase III addiction of multiple myeloma by flavonoid Rhamnetin.
      Title: Exploiting DNA Ligase III addiction of multiple myeloma by flavonoid Rhamnetin.
    2. Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps.
      Title: Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps.
    3. Telomere-internal double-strand breaks (DSBs) are also repaired by a PARP1- and Ligase3-dependent reaction, suggesting alternative non-homologous end-joining (alt-NHEJ), which relies on microhomology at DSBs.
      Title: Telomere-Internal Double-Strand Breaks Are Repaired by Homologous Recombination and PARP1/Lig3-Dependent End-Joining.
    4. Results show that overexpression of DNA ligase III in mitochondria improves mitochondrial base excision repair and enhances cell survival after oxidative stress.
      Title: Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair.
    5. data confirm previous work showing that Lig3 is required to maintain mtDNA integrity and function, and highlight a new function of ATM in regulating DNA Lig3 stability and consequently mtDNA repair
      Title: Intrinsic mitochondrial DNA repair defects in Ataxia Telangiectasia.
    6. Lig3 has an essential role in mtDNA maintenance but is dispensable for the viability of cultured cells
      Title: Mitochondrial DNA ligase is dispensable for the viability of cultured cells but essential for mtDNA maintenance.
    7. results establish a role for Lig3 in mitochondria, but distinguish it from its interacting protein Xrcc1
      Title: Crucial role for DNA ligase III in mitochondria but not in Xrcc1-dependent repair.
    8. data reveal that the critical biological role of Lig3 is to maintain mtDNA integrity and not Xrcc1-dependent DNA repair
      Title: DNA ligase III is critical for mtDNA integrity but not Xrcc1-mediated nuclear DNA repair.
    9. Early embryonic lethality is due to targeted inactivation of DNA ligase III.
      Title: Early embryonic lethality due to targeted inactivation of DNA ligase III.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC78176

    Gene Ontology Provided by MGI

    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 (ATP) activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    		  
    involved_in DNA recombination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell division IEA
    Inferred from Electronic Annotation
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lagging strand elongation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within mitochondrial DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrial DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mitochondrion organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrion organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of DNA recombination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    DNA ligase 3
    Names
    DNA ligase (ATP) 3
    DNA ligase III
    polydeoxyribonucleotide synthase [ATP] 3
    NP_001278174.1
    NP_001278175.1
    NP_001278176.1
    NP_001390785.1
    NP_001390786.1
    NP_001390787.1
    NP_001390788.1
    NP_001390789.1
    NP_001390790.1
    NP_001390791.1
    NP_001390792.1
    NP_001390793.1
    NP_001390794.1
    NP_034846.2
    XP_006532411.1
    XP_006532416.1

    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_001291245.2 → NP_001278174.1  DNA ligase 3 isoform a

      See identical proteins and their annotated locations for NP_001278174.1

      Status: VALIDATED

      Source sequence(s)
      AL645594
      Consensus CDS
      CCDS25147.1
      UniProtKB/Swiss-Prot
      E9QL81, P97385, P97386
      UniProtKB/TrEMBL
      Q3U1F0, Q80ZH7
      Related
      ENSMUSP00000133805.2, ENSMUST00000173722.8
      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:936 → 1007
      LIG3_BRCT; DNA ligase 3 BRCT domain

    2. NM_001291246.2 → NP_001278175.1  DNA ligase 3 isoform b

      See identical proteins and their annotated locations for NP_001278175.1

      Status: VALIDATED

      Source sequence(s)
      AL645594
      Consensus CDS
      CCDS70266.1
      UniProtKB/TrEMBL
      Q3U1F0, Q3UC82
      Related
      ENSMUSP00000134300.2, ENSMUST00000173347.8
      Conserved Domains (6) summary
      cd07967
      Location:687 → 825
      OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
      cd07902
      Location:469 → 681
      Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
      TIGR00574
      Location:319 → 831
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      pfam00645
      Location:98 → 178
      zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
      pfam04675
      Location:265 → 430
      DNA_ligase_A_N; DNA ligase N terminus
      pfam16759
      Location:935 → 1006
      LIG3_BRCT; DNA ligase 3 BRCT domain

    3. NM_001291247.2 → NP_001278176.1  DNA ligase 3 isoform b

      See identical proteins and their annotated locations for NP_001278176.1

      Status: VALIDATED

      Source sequence(s)
      AL645594
      Consensus CDS
      CCDS70266.1
      UniProtKB/TrEMBL
      Q3U1F0, Q3UC82
      Related
      ENSMUSP00000133849.2, ENSMUST00000173727.8
      Conserved Domains (6) summary
      cd07967
      Location:687 → 825
      OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
      cd07902
      Location:469 → 681
      Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
      TIGR00574
      Location:319 → 831
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      pfam00645
      Location:98 → 178
      zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
      pfam04675
      Location:265 → 430
      DNA_ligase_A_N; DNA ligase N terminus
      pfam16759
      Location:935 → 1006
      LIG3_BRCT; DNA ligase 3 BRCT domain

    4. NM_001403856.1 → NP_001390785.1  DNA ligase 3 isoform a

      Status: VALIDATED

      Source sequence(s)
      AL645594
      UniProtKB/TrEMBL
      Q80ZH7

    5. NM_001403857.1 → NP_001390786.1  DNA ligase 3 isoform a

      Status: VALIDATED

      Source sequence(s)
      AL645594
      UniProtKB/TrEMBL
      Q80ZH7

    6. NM_001403858.1 → NP_001390787.1  DNA ligase 3 isoform b

      Status: VALIDATED

      Source sequence(s)
      AL645594
      UniProtKB/TrEMBL
      Q3UC82

    7. NM_001403859.1 → NP_001390788.1  DNA ligase 3 isoform c

      Status: VALIDATED

      Source sequence(s)
      AL645594

    8. NM_001403860.1 → NP_001390789.1  DNA ligase 3 isoform d

      Status: VALIDATED

      Source sequence(s)
      AL645594

    9. NM_001403861.1 → NP_001390790.1  DNA ligase 3 isoform e

      Status: VALIDATED

      Source sequence(s)
      AL645594

    10. NM_001403862.1 → NP_001390791.1  DNA ligase 3 isoform f

      Status: VALIDATED

      Source sequence(s)
      AL645594

    11. NM_001403863.1 → NP_001390792.1  DNA ligase 3 isoform g

      Status: VALIDATED

      Source sequence(s)
      AL645594
      UniProtKB/TrEMBL
      B1AT03
      Related
      ENSMUSP00000079317.6, ENSMUST00000080461.12

    12. NM_001403864.1 → NP_001390793.1  DNA ligase 3 isoform h

      Status: VALIDATED

      Source sequence(s)
      AL645594

    13. NM_001403865.1 → NP_001390794.1  DNA ligase 3 isoform i

      Status: VALIDATED

      Source sequence(s)
      AL645594

    14. NM_010716.4 → NP_034846.2  DNA ligase 3 isoform a

      See identical proteins and their annotated locations for NP_034846.2

      Status: VALIDATED

      Source sequence(s)
      AL645594
      Consensus CDS
      CCDS25147.1
      UniProtKB/Swiss-Prot
      E9QL81, P97385, P97386
      UniProtKB/TrEMBL
      Q3U1F0, Q80ZH7
      Related
      ENSMUSP00000090525.6, ENSMUST00000092849.12
      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:936 → 1007
      LIG3_BRCT; DNA ligase 3 BRCT domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      82671977..82695100
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006532353.5 → XP_006532416.1  DNA ligase 3 isoform X3

      UniProtKB/Swiss-Prot
      E9QL81, P97385, P97386
      Conserved Domains (2) summary
      TIGR00574
      Location:374 → 886
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      pfam00645
      Location:151 → 236
      zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region

    2. XM_006532348.5 → XP_006532411.1  DNA ligase 3 isoform X2

      UniProtKB/TrEMBL
      Q3U1F0
      Conserved Domains (3) summary
      TIGR00574
      Location:373 → 885
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      pfam00645
      Location:151 → 236
      zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
      pfam16759
      Location:989 → 1060
      LIG3_BRCT; DNA ligase 3 BRCT domain

    RNA

    1. XR_004936802.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P97386.2 GenPept UniProtKB/Swiss-Prot:P97386

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