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LIG3 Gene

protein-coding   GIFtS: 70
GCID: GC17P033307

Ligase III, DNA, ATP-Dependent

(Previous names: ligase II, DNA, ATP-dependent)
(Previous symbol: LIG2)
  See LIG3-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Ligase III, DNA, ATP-Dependent1 2     EC 6.5.1.13 8
LIG21 2     DNA Ligase 32
Ligase II, DNA, ATP-Dependent1 2     DNA Ligase III3
Polydeoxyribonucleotide Synthase [ATP] 32 3     

External Ids:    HGNC: 66001   Entrez Gene: 39802   Ensembl: ENSG000000051567   OMIM: 6009405   UniProtKB: P499163   

Export aliases for LIG3 gene to outside databases

Previous GC identifers: GC17P033077 GC17P035343 GC17P033453 GC17P030331 GC17P029493


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for LIG3 Gene:
This gene is a member of the DNA ligase family. Each member of this family encodes a protein that catalyzes the
joining of DNA ends but they each have a distinct role in DNA metabolism. The protein encoded by this gene is
involved in excision repair and is located in both the mitochondria and nucleus, with translation initiation from
the upstream start codon allowing for transport to the mitochondria and translation initiation from a downstream
start codon allowing for transport to the nucleus. Additionally, alternate transcriptional splice variants,
encoding different isoforms, have been characterized. (provided by RefSeq, Jul 2008)

GeneCards Summary for LIG3 Gene:
LIG3 (ligase III, DNA, ATP-dependent) is a protein-coding gene. Diseases associated with LIG3 include bloom syndrome. GO annotations related to this gene include DNA ligase activity and DNA ligase (ATP) activity. An important paralog of this gene is LIG4.

UniProtKB/Swiss-Prot: DNLI3_HUMAN, P49916
Function: Interacts with DNA-repair protein XRCC1 and can correct defective DNA strand-break repair and sister
chromatid exchange following treatment with ionizing radiation and alkylating agents

summary for LIG3 Gene:
Ligases catalyze the joining of two molecules with concomitant hydrolysis of the diphosphate bond in ATP or
a similar triphosphate. They belong to the E.C. 6 class, which also includes synthases and carboxylases. DNA
ligases play an integral role in DNA repair and replication: they catalyze the formation of phosphodiester
bonds, using ATP as a co-factor. These enzymes are divided into three classes: DNA ligase I, III and IV. DNA
ligase I links Okazaki fragments to form a continuous strand of DNA. DNA ligase III is involved in base
excision repair. Finally, DNA ligase IV is involved in the repair of DNA double-strand breaks by
non-homologous end joining (NHEJ).




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000017.10  NT_010783.16  NC_018928.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the LIG3 gene promoter:
         AML1a   p53   FOXO3   FOXO3a   Pax-2   Pax-2a   LyF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLIG3 promoter sequence
   Search Chromatin IP Primers for LIG3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LIG3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17q11.2-q12   Ensembl cytogenetic band:  17q12   HGNC cytogenetic band: 17q11.2-q12

LIG3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LIG3 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P033307:  view genomic region     (about GC identifiers)

Start:
33,307,513 bp from pter      End:
33,332,088 bp from pter
Size:
24,576 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: DNLI3_HUMAN, P49916 (See protein sequence)
Recommended Name: DNA ligase 3  
Size: 1009 amino acids; 112907 Da
Cofactor: Magnesium (By similarity)
Sequence caution: Sequence=AAA85022.1; Type=Erroneous initiation; Sequence=AAL91592.1; Type=Erroneous initiation;
Sequence=CAA59230.1; Type=Erroneous initiation;
Selected PDB 3D structures from and Proteopedia for LIG3 (see all 7):
1IMO (3D)        1IN1 (3D)        1UW0 (3D)        3L2P (3D)        3PC7 (3D)        3PC8 (3D)    
Secondary accessions: Q16714 Q6NVK3
Alternative splicing: 2 isoforms:  P49916-1   P49916-2   

Explore the universe of human proteins at neXtProt for LIG3: NX_P49916

Explore proteomics data for LIG3 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys728, Lys765
  • Modification sites at PhosphoSitePlus
  • 2 DME Specific Peptides for LIG3 (P49916)
     PVQPMLA  DGERVQVH 


    See LIG3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_002302.2  NP_039269.2  

    ENSEMBL proteins: 
     ENSP00000367787   ENSP00000468479   ENSP00000262327   ENSP00000467063   ENSP00000467757  
     ENSP00000466278   ENSP00000465288  
    Reactome Protein details: P49916

    LIG3 Human Recombinant Protein Products:

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    Novus Biologicals LIG3 Proteins
    Novus Biologicals LIG3 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for LIG3 

     
    antibodies-online proteins for LIG3 (3 products) 

     
    antibodies-online peptides for LIG3

    LIG3 Antibody Products:

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    antibodies-online antibodies for LIG3 (56 products) 

    LIG3 Assay Products:

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    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for LIG3 
    antibodies-online kits for LIG3 (4 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    Selected InterPro protein domains (see all 8):
     IPR012340 NA-bd_OB-fold
     IPR012308 DNA_ligase_ATP-dep_N
     IPR012310 DNA_ligase_ATP-dep_cent
     IPR001510 Znf_PARP
     IPR016059 DNA_ligase_ATP-dep_CS

    Graphical View of Domain Structure for InterPro Entry P49916

    ProtoNet protein and cluster: P49916

    3 Blocks protein domains:
    IPB001357 BRCT domain
    IPB001510 Zn-finger
    IPB012308 DNA ligase


    UniProtKB/Swiss-Prot: DNLI3_HUMAN, P49916
    Similarity: Belongs to the ATP-dependent DNA ligase family
    Similarity: Contains 1 BRCT domain
    Similarity: Contains 1 PARP-type zinc finger


    Find genes that share domains with LIG3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DNLI3_HUMAN, P49916
    Function: Interacts with DNA-repair protein XRCC1 and can correct defective DNA strand-break repair and sister
    chromatid exchange following treatment with ionizing radiation and alkylating agents
    Catalytic activity: ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate +
    (deoxyribonucleotide)(n+m)

         Genatlas biochemistry entry for LIG3:
    DNA ligase III,ATP-dependent,103kDa,complexing with LIG3,involved in DNA replication,recombination and DNA
    repair,highly expressed in testes

         Enzyme Number (IUBMB): EC 6.5.1.11 2

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003909DNA ligase activity IDA9809069
    GO:0003910DNA ligase (ATP) activity IBA--
    GO:0005515protein binding IPI15744309
    GO:0005524ATP binding IEA--
         
    Find genes that share ontologies with LIG3           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for LIG3:
     Synthetic lethal with Ras 

         10 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Lig3):
     behavior/neurological  cardiovascular system  cellular  craniofacial  embryogenesis 
     growth/size/body  homeostasis/metabolism  mortality/aging  muscle  nervous system 

    Find genes that share phenotypes with LIG3           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Lig3tm1Czhu for LIG3

       genOway: Develop your customized and physiologically relevant rodent model for LIG3

    miRNA
    Products:
        
    miRTarBase miRNAs that target LIG3:
    hsa-mir-30a-5p (MIRT028636), hsa-mir-149-5p (MIRT045688)

    Block miRNA regulation of human, mouse, rat LIG3 using miScript Target Protectors
    6 qRT-PCR Assays for microRNAs that regulate LIG3:
    hsa-miR-221* hsa-miR-579 hsa-miR-3128 hsa-miR-3065-3p hsa-miR-3662 hsa-miR-3156-5p
    SwitchGear 3'UTR luciferase reporter plasmidLIG3 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for LIG3
    Predesigned siRNA for gene silencing in human, mouse, rat LIG3

    Gene Editing
    Products:
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    Clone
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    OriGene ORF clones in mouse, rat for LIG3
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    GenScript: all cDNA clones in your preferred vector (see all 2): LIG3 (NM_002311)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LIG3
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LIG3

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for LIG3 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LIG3


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    DNLI3_HUMAN, P49916: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    mitochondrion2

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000794condensed nuclear chromosome ----
    GO:0000795synaptonemal complex IEA--
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm TAS--
    GO:0005694chromosome IBA--

    Find genes that share ontologies with LIG3           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for LIG3 About    
    See pathways by source

    SuperPathContained pathways About
    1Resolution of Abasic Sites (AP sites)
    Resolution of Abasic Sites (AP sites)0.89
    Resolution of AP sites via the single-nucleotide replacement pathway0.00
    Base excision repair0.53
    Base Excision Repair0.00
    2Global Genomic NER (GG-NER)
    Nucleotide Excision Repair Pathway0.48
    3DNA Repair
    DNA Repair0.45
    4Chks in Checkpoint Regulation
    DNA Repair Mechanisms0.32
    5Meiosis (EMD)
    Meiosis


    Find genes that share SuperPaths with LIG3           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for LIG3
        DNA Repair Mechanisms
    Nucleotide Excision Repair Pathway

    1 Reactome Pathway for LIG3
        Resolution of AP sites via the single-nucleotide replacement pathway


    1 Kegg Pathway  (Kegg details for LIG3):
        Base excision repair

        Pathway & Disease-focused RT2 Profiler PCR Array including LIG3: 
              DNA Repair in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for LIG3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for LIG3 (P499162, 3 ENSP000003677874) via UniProtKB, MINT, STRING, and/or I2D (see all 67)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PIK3R1P279862, 3, ENSP000002743354MINT-8111871 I2D: score=2 STRING: ENSP00000274335
    PLCG1P191742, 3, ENSP000002440074MINT-8112471 I2D: score=2 STRING: ENSP00000244007
    ENSG00000206454Q018603I2D: score=1 
    ENSG00000229094Q018603I2D: score=1 
    ENSG00000230336Q018603I2D: score=1 
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    Gene Ontology (GO): Selected biological process terms (see all 15):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006260DNA replication ----
    GO:0006273lagging strand elongation IBA--
    GO:0006281DNA repair TAS--
    GO:0006284base-excision repair TAS--
    GO:0006288base-excision repair, DNA ligation IEA--

    Find genes that share ontologies with LIG3           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Compounds for LIG3 available from Tocris Bioscience    About this table
    CompoundAction CAS #
    L189 DNA ligase I, III and IV inhibitor [64232-83-3]

    4 HMDB Compounds for LIG3    About this table
    CompoundSynonyms CAS #PubMed Ids
    Adenosine monophosphate5'-AMP (see all 28)61-19-8--
    Adenosine triphosphate5'-(tetrahydrogen triphosphate) Adenosine (see all 24)56-65-5--
    Phosphoric acidacide phosphorique (FRENCH) (see all 20)7664-38-2--
    Pyrophosphate(4-)Diphosphoric acid ion (see all 10)14000-31-8--

    1 DrugBank Compound for LIG3    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    BleomycinBleocin (see all 8)11056-06-7targetinhibitor17202402

    7 Novoseek inferred chemical compound relationships for LIG3 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    poly(ra).oligo(dt) 82.5 1 7510367 (1)
    polynucleotide 76.2 3 11163244 (1), 20099873 (1), 15367657 (1)
    adpribose 46.5 3 8948628 (2), 11016934 (1)
    camptothecin 43 2 9739812 (2)
    methylmethanesulfonate 42.5 1 9379914 (1)
    arsenite 29 1 9379914 (1)
    zinc 26.2 12 10419478 (3), 12897160 (3), 9776738 (2), 17054425 (1) (see all 5)

    2 PharmGKB related drug/compound annotations for LIG3 gene    About this table
    Drug/compound PharmGKB Annotation
    cisplatinCA  
    cyclophosphamideCA  



    Find genes that share compounds with LIG3           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for LIG3 gene (2 alternative transcripts): 
    NM_002311.4  NM_013975.3  

    Unigene Cluster for LIG3:

    Ligase III, DNA, ATP-dependent
    Hs.100299  [show with all ESTs]
    Unigene Representative Sequence: NM_013975
    16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000378526(uc002hik.2) ENST00000585941 ENST00000262327(uc002hii.3 uc002hij.3 uc010cth.1)
    ENST00000592690 ENST00000585740 ENST00000590181 ENST00000586407 ENST00000588109
    ENST00000586435 ENST00000590630 ENST00000586058 ENST00000588713 ENST00000593099
    ENST00000586119 ENST00000585370 ENST00000592244
    miRNA
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    hsa-miR-221* hsa-miR-579 hsa-miR-3128 hsa-miR-3065-3p hsa-miR-3662 hsa-miR-3156-5p
    SwitchGear 3'UTR luciferase reporter plasmidLIG3 3' UTR sequence
    Inhib. RNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat LIG3
      QuantiFast Probe-based Assays in human, mouse, rat LIG3

    Additional mRNA sequence: 

    AK127668.1 AK300363.1 AK308407.1 BC009026.1 BC068005.1 U40671.1 X84740.1 

    15 DOTS entries:

    DT.313674  DT.95088103  DT.100784860  DT.100784857  DT.120964172  DT.91749274  DT.95358707  DT.120964053 
    DT.100784856  DT.120964009  DT.120964125  DT.91704022  DT.91824684  DT.91837080  DT.100008759 

    Selected AceView cDNA sequences (see all 150):

    BX470676 U40671 CA426477 BP873049 BQ691150 BE901311 CB127294 BM467239 
    BM927151 BU171391 AL528176 BX280780 BQ024078 AW950125 AW236716 AK125853 
    AI682152 NM_002311 CR616389 BC068005 BF881950 BC009026 NM_013975 AA953450 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for LIG3 (see all 8)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^
    SP1:                                      -                 -                 -                                               -           -                     
    SP2:                                      -                 -                 -                                               -           -                     
    SP3:                          -     -     -                 -                 -                                                                                 
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21
    SP1:                                -         
    SP2:                                          
    SP3:                                          
    SP4:                                          
    SP5:                                          


    ECgene alternative splicing isoforms for LIG3

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    LIG3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGAAAGAAAA
    LIG3 Expression
    About this image


    LIG3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Testis (Reproductive System)
    LIG3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LIG3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.100299

    UniProtKB/Swiss-Prot: DNLI3_HUMAN, P49916
    Tissue specificity: Testis, thymus, prostate and heart

        Pathway & Disease-focused RT2 Profiler PCR Array including LIG3: 
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for LIG3 gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lig31 , 5 ligase III, DNA, ATP-dependent1, 5 87.64(n)1
    88.4(a)1
      11 (50.23 cM)5
    168821  NM_010716.21  NP_034846.21 
     827811085 
    chicken
    (Gallus gallus)
    Aves LIG31 ligase III, DNA, ATP-dependent 74.1(n)
    80.16(a)
      417530  NM_001006215.1  NP_001006215.1 
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3982752 DNA ligase III isoform alpha 76.11(n)    AF393654.1 
    zebrafish
    (Danio rerio)
    Actinopterygii lig31 ligase III, DNA, ATP-dependent 67.9(n)
    70.96(a)
      563276  NM_001030174.2  NP_001025345.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG172273
    lig31
    DNA ligase (ATP)3
    DNA ligase III1
    45(a)3
    54.2(n)1
    49.92(a)1
      87B93
    415181  NM_141930.31  NP_650187.21 
    worm
    (Caenorhabditis elegans)
    Secernentea K07C5.33 DNA ligase like domain 28(a)   V(10345621-10347943)   --
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes DNL46
    DNA ligase required for nonhomologous end-joining ...
    13(a)
    1 → many
    XV(334509-337343) YOR005C


    ENSEMBL Gene Tree for LIG3 (if available)
    TreeFam Gene Tree for LIG3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LIG3 gene
    LIG42  
    1 SIMAP similar gene for LIG3 using alignment to 8 protein entries:     DNLI3_HUMAN (see all proteins):
    PARP1

    Find genes that share paralogs with LIG3           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for LIG3 (see all 590)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0365134
    A colorectal cancer sample4--see VAR_0365132 D N mis40--------
    rs1939226901,2
    Cprobable-non-pathogenic133382069(+) ACACCT/CGTGCA 4 /P syn11Minor allele frequency- C:0.00EU 1305
    rs573114841,2
    C--33307701(+) GCGGG-/CCCGGG 2 -- int10--------
    rs31360081,2
    C--33325181(+) CTCAC-/TCAC  
            
    CACCT
    2 -- int11Minor allele frequency- TCAC:0.01NS 176
    rs1127886481,2
    C,F--33327524(+) TGCCCG/ACCTCA 2 -- int11Minor allele frequency- A:0.50NA 2
    rs31360191,2
    C,F--33328059(+) gctggG/Aactac 2 -- int11Minor allele frequency- A:0.01NS 162
    rs98951351,2
    C,F--33367967(+) gtggcG/Aggtgc 2 -- us2k14Minor allele frequency- A:0.25NA 8
    rs713646881,2
    C--33368098(+) GTCGC-/AAAAAA 2 -- us2k11Minor allele frequency- A:0.50NA 2
    rs1473454671,2
    --33368376(+) TATATA/GCTGTA 2 -- us2k10--------
    rs1861418591,2
    --33368491(+) GGATTG/TTTCAG 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for LIG3 (33307513 - 33332088 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for LIG3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv2035CNV Loss18451855

    Human Gene Mutation Database (HGMD): LIG3
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing LIG3
    DNA2.0 Custom Variant and Variant Library Synthesis for LIG3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 600940    OMIM disorders: --

    1 disease for LIG3:    
    About MalaCards
    bloom syndrome

    1 disease from the University of Copenhagen DISEASES database for LIG3:
    Vaccinia

    Find genes that share disorders with LIG3           About GenesLikeMe

    2 Novoseek inferred disease relationships for LIG3 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    bloom syndrome 63.3 4 8532526 (1), 8265359 (1)
    cancer 0 1 15257099 (1)

    Genetic Association Database (GAD): LIG3
    Human Genome Epidemiology (HuGE) Navigator: LIG3 (37 documents)

    Export disorders for LIG3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for LIG3 gene, integrated from 10 sources (see all 153):
    (articles sorted by number of sources associating them with LIG3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and expression of human cDNAs encoding a novel DNA ligase IV and DNA ligase III, an enzyme active in DNA repair and recombination. (PubMed id 7760816)1, 2, 3, 9 Wei Y.-F.... Lindahl T. (Mol. Cell. Biol. 1995)
    2. Mammalian DNA ligase III: molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination. (PubMed id 7565692)1, 2, 9 Chen J.... Husain I. (Mol. Cell. Biol. 1995)
    3. Comprehensive screen of genetic variation in DNA repair pathway genes and postmenopausal breast cancer risk. (PubMed id 20496165)1, 4 Monsees G.M....Han J. (Breast Cancer Res. Treat. 2011)
    4. Polymorphisms in DNA repair genes and risk of non-Hodgkin lymphoma in a pooled analysis of three studies. (PubMed id 20813000)1, 4 Shen M....Zheng T. (Br. J. Haematol. 2010)
    5. A Large-scale genetic association study of esophageal adenocarcinoma risk. (PubMed id 20453000)1, 4 Liu C.Y....Christiani D.C. (Carcinogenesis 2010)
    6. Polymorphisms in the base excision repair pathway and graft-versus-host disease. (PubMed id 20574454)1, 4 Arora M....Thyagarajan B. (Leukemia 2010)
    7. Genetic susceptibility to distinct bladder cancer subphenotypes. (PubMed id 19692168)1, 4 Guey L.T....Malats N. (Eur. Urol. 2010)
    8. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    9. Comprehensive analysis of DNA repair gene polymorphisms and survival in patients with early stage non-small-cell lung cancer. (PubMed id 20731661)1, 4 Kim M....Park J.Y. (Cancer Sci. 2010)
    10. Variation within DNA repair pathway genes and risk of multiple sclerosis. (PubMed id 20522537)1, 4 Briggs F.B....Barcellos L.F. (Am. J. Epidemiol. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 3980 HGNC: 6600 AceView: LIG3 Ensembl:ENSG00000005156 euGenes: HUgn3980
    ECgene: LIG3 Kegg: 3980 H-InvDB: LIG3

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for LIG3 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for LIG3 Genetics and Cytogenetics in Oncology and Haematology
    Wikipedia http://en.wikipedia.org/wiki/DNA_ligase
    NIEHS-SNPshttp://egp.gs.washington.edu/data/mpg/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LIG3 gene:
    Search GeneIP for patents involving LIG3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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