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LIG4 Gene

protein-coding   GIFtS: 73
GCID: GC13M108859

Ligase IV, DNA, ATP-Dependent

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(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 IV, DNA, ATP-Dependent1 2     sealase1 2
Polydeoxyribonucleotide Synthase [ATP] 41 2 3     DNA Ligase IV2 3
DNA Joinase1 2     EC 6.5.1.13 8
DNA Repair Enzyme1 2     DNA Ligase 42
Polynucleotide Ligase1 2     

External Ids:    HGNC: 66011   Entrez Gene: 39812   Ensembl: ENSG000001744057   OMIM: 6018375   UniProtKB: P499173   

Export aliases for LIG4 gene to outside databases

Previous GC identifers: GC13M107220 GC13M103247 GC13M107696 GC13M106558 GC13M107657 GC13M089450


(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 LIG4 Gene:
The protein encoded by this gene is a DNA ligase that joins single-strand breaks in a double-stranded
polydeoxynucleotide in an ATP-dependent reaction. This protein is essential for V(D)J recombination and DNA
double-strand break (DSB) repair through nonhomologous end joining (NHEJ). This protein forms a complex with the
X-ray repair cross complementing protein 4 (XRCC4), and further interacts with the DNA-dependent protein kinase
(DNA-PK). Both XRCC4 and DNA-PK are known to be required for NHEJ. The crystal structure of the complex formed by
this protein and XRCC4 has been resolved. Defects in this gene are the cause of LIG4 syndrome. Alternatively
spliced transcript variants encoding the same protein have been observed. (provided by RefSeq, Jul 2008)

GeneCards Summary for LIG4 Gene:
LIG4 (ligase IV, DNA, ATP-dependent) is a protein-coding gene. Diseases associated with LIG4 include dna ligase iv deficiency, and severe combined immunodeficiency with sensitivity to ionizing radiation. GO annotations related to this gene include DNA ligase activity and protein C-terminus binding. An important paralog of this gene is LIG3.

UniProtKB/Swiss-Prot: DNLI4_HUMAN, P49917
Function: Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent
reaction. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J
recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining
activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent
protein kinase complex DNA-PK to these DNA ends

summary for LIG4 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).

Gene Wiki entry for LIG4 Gene


(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:
NC_000013.11  NT_009952.15  NC_018924.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the LIG4 gene promoter:
         RP58   p300   ZID   NF-AT1   NF-AT   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 5): LIG4 promoter sequence
   Search Chromatin IP Primers for LIG4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LIG4


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

Entrez Gene cytogenetic band: 13q33-q34   Ensembl cytogenetic band:  13q33.3   HGNC cytogenetic band: 13q33-q34

LIG4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LIG4 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M108859:  view genomic region     (about GC identifiers)

Start:
108,859,787 bp from pter      End:
108,870,716 bp from pter
Size:
10,930 bases      Orientation:
minus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: DNLI4_HUMAN, P49917 (See protein sequence)
Recommended Name: DNA ligase 4  
Size: 911 amino acids; 103971 Da
Cofactor: Magnesium (By similarity)
Subunit: Binds to XRCC4. The LIG4-XRCC4 complex has probably a 1:2 stoichiometry. The LIG4-XRCC4 heteromer
associates in a DNA-dependent manner with the DNA-dependent protein kinase complex DNA-PK, formed by the Ku
p70/p86 dimer (G22P1/G22P2) and PRKDC. Interacts with APLF
Sequence caution: Sequence=AAL77435.1; Type=Erroneous initiation; Sequence=CAA58467.1; Type=Erroneous initiation;
Selected PDB 3D structures from and Proteopedia for LIG4 (see all 9):
1IK9 (3D)        2E2W (3D)        3II6 (3D)        3VNN (3D)        3W1B (3D)        3W1G (3D)    
Secondary accessions: Q8IY66 Q8TEU5

Explore the universe of human proteins at neXtProt for LIG4: NX_P49917

Explore proteomics data for LIG4 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys184
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for LIG4 (P49917) (see all 10)
     DGERMQMH  TQTFMQKG  FYPAMRLI  ILCGTEKPE 


    See LIG4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001091738.1  NP_002303.2  NP_996820.1  

    ENSEMBL proteins: 
     ENSP00000349393   ENSP00000385955   ENSP00000402030  
    Reactome Protein details: P49917

    LIG4 Human Recombinant Protein Products:

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    OriGene Protein Over-expression Lysate for LIG4
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    Novus Biologicals LIG4 Protein
    Novus Biologicals LIG4 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for LIG4

    LIG4 Antibody Products:

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    LIG4 Assay Products:

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    Cloud-Clone Corp. ELISAs for LIG4
    Cloud-Clone Corp. CLIAs for LIG4


    (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
     IPR021536 DNA_ligase_IV
     IPR016059 DNA_ligase_ATP-dep_CS

    Graphical View of Domain Structure for InterPro Entry P49917

    ProtoNet protein and cluster: P49917

    2 Blocks protein domains:
    IPB001357 BRCT domain
    IPB012308 DNA ligase


    UniProtKB/Swiss-Prot: DNLI4_HUMAN, P49917
    Similarity: Belongs to the ATP-dependent DNA ligase family
    Similarity: Contains 2 BRCT domains


    LIG4 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DNLI4_HUMAN, P49917
    Function: Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent
    reaction. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J
    recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining
    activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent
    protein kinase complex DNA-PK to these DNA ends
    Catalytic activity: ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate +
    (deoxyribonucleotide)(n+m)

         Genatlas biochemistry entry for LIG4:
    DNA ligase IV,ATP-dependent,96kDa,the ligation responsible for DNA double-strand breaks repair by end joining (non
    homologous recombination) and V(D)J recombination

         Enzyme Number (IUBMB): EC 6.5.1.11 2

         Gene Ontology (GO): Selected molecular function terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IDA8798671
    GO:0003909DNA ligase activity TAS--
    GO:0003910DNA ligase (ATP) activity IDA8798671
    GO:0005515protein binding IPI16439205
    GO:0005524ATP binding IEA--
         
    LIG4 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for LIG4:
     Increased homologous recombina 

         13 MGI mutant phenotypes (inferred from 6 alleles(MGI details for Lig4):
     behavior/neurological  cellular  craniofacial  digestive/alimentary  growth/size/body 
     hematopoietic system  homeostasis/metabolism  immune system  liver/biliary system  mortality/aging 
     nervous system  reproductive system  tumorigenesis 

    LIG4 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for LIG4: Lig4tm1Fwa Lig4tm1Icrf

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LIG4
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for LIG4

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for LIG4
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for LIG4

    miRNA
    Products:
        
    miRTarBase miRNAs that target LIG4:
    hsa-mir-132-3p (MIRT021742), hsa-mir-26b-5p (MIRT028768), hsa-mir-16-5p (MIRT051082)

    Block miRNA regulation of human, mouse, rat LIG4 using miScript Target Protectors
    3 qRT-PCR Assays for microRNAs that regulate LIG4:
    hsa-miR-548am hsa-miR-548x hsa-miR-4282
    SwitchGear 3'UTR luciferase reporter plasmidLIG4 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for LIG4
    Predesigned siRNA for gene silencing in human, mouse, rat LIG4

    Gene Editing
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    DNA2.0 Custom Protein Engineering Service for LIG4

    Clone
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    OriGene ORF clones in mouse, rat for LIG4
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 3): LIG4 (NM_206937)
    Sino Biological Human cDNA Clone for LIG4
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LIG4
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LIG4

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for LIG4 
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LIG4


    (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
    DNLI4_HUMAN, P49917: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    plasma membrane4
    cytosol3
    cytoskeleton1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000793condensed chromosome IDA12589063
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm TAS--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--

    LIG4 for ontologies           About GeneDecksing


    (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 LIG4 About   (see all 7)  
    See pathways by source

    SuperPathContained pathways About
    1Non-homologous end-joining
    Non-homologous end-joining0.37
    DNA damage NHEJ mechanisms of DSBs repair0.37
    2HIV Life Cycle
    HIV Life Cycle0.91
    Integration of provirus0.00
    HIV Infection0.62
    2-LTR circle formation0.00
    Early Phase of HIV Life Cycle0.00
    3Homologous Recombination Repair
    Double-Strand Break Repair0.70
    Nonhomologous End-joining (NHEJ)0.00
    4Global Genomic NER (GG-NER)
    Nucleotide Excision Repair Pathway0.48
    5DNA Repair
    DNA Repair0.45

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for LIG4
        DNA Repair Mechanisms
    Nucleotide Excision Repair Pathway

    1 GeneGo (Thomson Reuters) Pathway for LIG4
        DNA damage NHEJ mechanisms of DSBs repair


    2 Reactome Pathways for LIG4
        Nonhomologous End-joining (NHEJ)
    2-LTR circle formation


    1 Kegg Pathway  (Kegg details for LIG4):
        Non-homologous end-joining


    LIG4 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including LIG4: 
              Cancer PathwayFinder in human mouse rat
              p53 Signaling Pathway in human mouse rat
              DNA Repair in human mouse rat
              Molecular Toxicology PathwayFinder 384HT in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for LIG4

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

    Selected Interacting proteins for LIG4 (P499171, 2, 3 ENSP000003493934) via UniProtKB, MINT, STRING, and/or I2D (see all 97)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NHEJ1Q9H9Q41, 3, ENSP000003493134EBI-847896,EBI-847807 I2D: score=3 STRING: ENSP00000349313
    APLFQ8IW191, 2, 3, ENSP000003070044EBI-847896,EBI-1256044 MINT-4790271 MINT-8412696 I2D: score=3 STRING: ENSP00000307004
    XRCC4Q134262, 3, ENSP000003420114MINT-8412696 I2D: score=4 STRING: ENSP00000342011
    H2AFXP161043, ENSP000003643104I2D: score=4 STRING: ENSP00000364310
    PRKDCP785273, ENSP000003134204I2D: score=3 STRING: ENSP00000313420
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 34):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000012single strand break repair IDA8798671
    GO:0001701in utero embryonic development ISS--
    GO:0002328pro-B cell differentiation ISS--
    GO:0006260DNA replication ----
    GO:0006266DNA ligation IDA12517771

    LIG4 for ontologies           About GeneDecksing



    (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 LIG4 available from Tocris Bioscience    About this table
    CompoundAction CAS #
    L189 DNA ligase I, III and IV inhibitor [64232-83-3]

    4 HMDB Compounds for LIG4    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--

    7 Novoseek inferred chemical compound relationships for LIG4 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    polynucleotide 72.3 8 2144612 (1), 8559059 (1), 18644470 (1), 18262407 (1) (see all 8)
    wortmannin 34.2 1 11292837 (1)
    alanine 3.59 2 15194694 (1)
    nacl 0 2 8798671 (1)
    phosphatidylinositol 0 1 10608806 (1)
    aspartate 0 1 12904551 (1)
    glutamate 0 1 12904551 (1)



    LIG4 for compounds           About GeneDecksing



    (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,
    Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for LIG4 gene (3 alternative transcripts): 
    NM_001098268.1  NM_002312.3  NM_206937.1  

    Unigene Cluster for LIG4:

    Ligase IV, DNA, ATP-dependent
    Hs.166091  [show with all ESTs]
    Unigene Representative Sequence: NM_002312
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000356922(uc010agg.1) ENST00000405925(uc001vqn.3 uc001vqo.3 uc010agf.3 uc001vqp.3)
    ENST00000442234
    Congresses - knowledge worth sharing:
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
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    Block miRNA regulation of human, mouse, rat LIG4 using miScript Target Protectors
    3 qRT-PCR Assays for microRNAs that regulate LIG4:
    hsa-miR-548am hsa-miR-548x hsa-miR-4282
    SwitchGear 3'UTR luciferase reporter plasmidLIG4 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat LIG4
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    GenScript: all cDNA clones in your preferred vector (see all 3): LIG4 (NM_206937)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LIG4
    Primer
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    OriGene qPCR primer pairs and template standards for LIG4
    OriGene qSTAR qPCR primer pairs in human, mouse for LIG4
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat LIG4
      QuantiTect SYBR Green Assays in human, mouse, rat LIG4
      QuantiFast Probe-based Assays in human, mouse, rat LIG4

    Additional mRNA sequence: 

    AK292419.1 AK314844.1 BC037491.2 BX648833.1 X83441.1 

    4 DOTS entries:

    DT.212191  DT.212190  DT.101975916  DT.92419742 

    Selected AceView cDNA sequences (see all 56):

    NM_206937 BC037491 Z42891 BU167518 AA831460 AA772198 AA687734 NM_002312 
    AI469486 CR618195 X83441 BX474719 CA441201 AL701039 H79100 R54358 
    BM803759 AW439586 BE348981 BI546008 AI809944 BX648833 BX474333 AA738148 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for LIG4    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4a · 4b · 4c · 4d
    SP1:                          -                                       
    SP2:                                                                  
    SP3:                          -           -                           
    SP4:        -     -     -     -     -     -                           


    ECgene alternative splicing isoforms for LIG4

    (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)
    About This Section

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    LIG4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CGATACTATG
    LIG4 Expression
    About this image


    LIG4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    LIG4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LIG4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.166091

    UniProtKB/Swiss-Prot: DNLI4_HUMAN, P49917
    Tissue specificity: Testis, thymus, prostate and heart

        Pathway & Disease-focused RT2 Profiler PCR Arrays including LIG4: 
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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 eukaryotes.

    Orthologs for LIG4 gene from Selected species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lig41 , 5 ligase IV, DNA, ATP-dependent1, 5 82.58(n)1
    87.05(a)1
      8 (4.52 cM)5
    3195831  NM_176953.31  NP_795927.21 
     99700205 
    chicken
    (Gallus gallus)
    Aves LIG41 ligase IV, DNA, ATP-dependent 75.04(n)
    77.11(a)
      418764  NM_001030816.1  NP_001025987.1 
    lizard
    (Anolis carolinensis)
    Reptilia LIG46
    ligase IV, DNA, ATP-dependent
    76(a)
    1 ↔ 1
    1(137058376-137061096)
    African clawed frog
    (Xenopus laevis)
    Amphibia lig4-A2 ligase IV, DNA, ATP-dependent 78.21(n)    AF393656.1 
    zebrafish
    (Danio rerio)
    Actinopterygii lig41 ligase IV, DNA, ATP-dependent 65.85(n)
    64.99(a)
      569525  NM_001103123.1  NP_001096593.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta ligase43
    Lig41
    DNA ligase (ATP)3
    Ligase41
    31(a)3
    45.17(n)1
    33.75(a)1
      12B23
    323221  NM_132679.31  NP_572907.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes DNL4(YOR005C)4
    DNL41
    DNA ligase required for nonhomologous end-joining (NHEJ), more4
    DNL41
    44.73(n)1
    30.29(a)1
      15(337343-334509)4
    8541661, 4  NP_014647.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons ATLIG41 ATLIG4 46.01(n)
    34.34(a)
      835822  NM_125098.3  NP_568851.2 


    ENSEMBL Gene Tree for LIG4 (if available)
    TreeFam Gene Tree for LIG4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LIG4 gene
    LIG32  

    LIG4 for paralogs           About GeneDecksing



    (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 LIG4 (see all 318)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0127744
    LIG4 syndrome (LIG4S)4--see VAR_0127742 R H mis40--------
    VAR_0127754
    LIG4 syndrome (LIG4S)4--see VAR_0127752 G E mis40--------
    rs1048944191,2
    Cpathogenic1108861177(-) TGTTTC/TGACGC 6 R * stg10--------
    rs1048944181,2
    Cpathogenic1108861879(-) TTCCAC/TGAATT 6 R * stg10--------
    rs1048944201,2
    Cpathogenic1108862211(-) TGGAGA/GATATT 6 E G mis10--------
    rs1048944211,2
    Cpathogenic1108862784(-) TGAACA/GTATGC 6 H R mis10--------
    rs18053881,2,,4
    C,F,O,Hpathogenic1108863591(-) ACAAAC/TTGTTG 6 T I mis140Minor allele frequency- N:0.00NA NS EA MN WA CSA EU 8920
    rs18053891,2,,4
    C,F,Hpathogenic1108863609(-) GGCTGC/TCTCAC 6 A V mis1 ese324Minor allele frequency- T:0.04NA NS MN EA EU 6587
    rs1117964841,2
    F--89450090(+) CACGAG/TATCAG 3 -- int11Minor allele frequency- T:0.50CSA 2
    rs1135547261,2
    F--89450091(+) ACGAGG/ATCAGG 3 -- int11Minor allele frequency- A:0.50CSA 2

    HapMap Linkage Disequilibrium report for LIG4 (108859787 - 108870716 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for LIG4: --
    Human Gene Mutation Database (HGMD): LIG4
    Locus Specific Mutation Databases (LSDB): LIG4

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601837   
    OMIM disorders: 606593  254500  602450  
    UniProtKB/Swiss-Prot: DNLI4_HUMAN, P49917
  • LIG4 syndrome (LIG4S) [MIM:606593]: Characterized by immunodeficiency and developmental and growth delay.
    Patients display unusual facial features, microcephaly, growth and/or developmental delay, pancytopenia, and
    various skin abnormalities. Note=The disease is caused by mutations affecting the gene represented in this entry
  • Severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-negative/NK-cell-positive
    with sensitivity to ionizing radiation (RSSCID) [MIM:602450]: A form of severe combined immunodeficiency, a
    genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both
    humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy
    with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID
    is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. Individuals affected by
    RS-SCID show defects in the DNA repair machinery necessary for coding joint formation and the completion of V(D)J
    recombination. A subset of cells from such patients show increased radiosensitivity. Note=The disease is caused
    by mutations affecting the gene represented in this entry

  • Selected diseases for LIG4 (see all 61):    
    About MalaCards
    dna ligase iv deficiency    severe combined immunodeficiency with sensitivity to ionizing radiation    multiple myeloma    dubowitz syndrome
    primary immunodeficiency disease    nijmegen breakage syndrome    acoustic neuroma    omenn syndrome
    seckel syndrome    neuroma    lynch syndrome    severe combined immunodeficiency
    autosomal recessive disease    stomach cancer    myeloma    pancytopenia
    ataxia telangiectasia    follicular lymphoma    lung cancer susceptibility    leukopenia

    5 diseases from the University of Copenhagen DISEASES database for LIG4:
    Primary immunodeficiency disease     Vaccinia     Dubowitz Syndrome     Microcephaly
    Autosomal recessive disease

    LIG4 for disorders           About GeneDecksing

    Selected Novoseek inferred disease relationships for LIG4 gene (see all 20)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    lig4 syndrome 97.4 38 15333585 (4), 16735143 (3), 17345618 (3), 19418549 (3) (see all 13)
    nijmegen breakage syndrome 76.5 6 16088910 (2), 15966765 (1), 12640452 (1), 18568480 (1)
    seckel syndrome 68.9 1 12640452 (1)
    omenn syndrome 66.4 1 18845326 (1)
    ataxia telangiectasia 65.8 11 16971555 (1), 17224058 (1), 19008195 (1), 15966765 (1) (see all 5)
    severe combined immunodeficiency 64.3 3 16358361 (1), 16357942 (1), 18568480 (1)
    microcephaly 56.7 8 16358361 (3), 20133615 (1), 16088910 (1), 19418549 (1)
    fanconis anemia 52.3 1 15966765 (1)
    growth retardation 46.4 8 20133615 (1), 19451691 (1), 16088910 (1), 17554302 (1) (see all 5)
    developmental delay 44.6 6 20133615 (1), 11779494 (1), 16358361 (1), 15333585 (1) (see all 5)

    Genetic Association Database (GAD): LIG4
    Human Genome Epidemiology (HuGE) Navigator: LIG4 (56 documents)

    Export disorders for LIG4 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 LIG4 gene, integrated from 10 sources (see all 251):
    (articles sorted by number of sources associating them with LIG4)
        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 Wei Y.-F.... Lindahl T. (Mol. Cell. Biol. 1995)
    2. DNA ligase IV from HeLa cell nuclei. (PubMed id 8798671)1, 2, 9 Robins P. and Lindahl T. (J. Biol. Chem. 1996)
    3. A new type of radiosensitive T-B-NK(+) severe combined immunodeficiency caused by a LIG4 mutation. (PubMed id 16357942)1, 2, 9 van der Burg M.... van Gent D.C. (J. Clin. Invest. 2006)
    4. Polymorphisms of LIG4 and XRCC4 involved in the NHEJ pathway interact to modify risk of glioma. (PubMed id 18165945)1, 4, 9 Liu Y....Zhou L. (Hum. Mutat. 2008)
    5. DNA ligase IV mutations identified in patients exhibiting developmental delay and immunodeficiency. (PubMed id 11779494)1, 2, 9 O'Driscoll M.... Concannon P. (Mol. Cell 2001)
    6. Lung cancer susceptibility and prognosis associated with polymorphisms in the nonhomologous end-joining pathway genes: a multiple genotype-phenotype study. (PubMed id 19408343)1, 4, 9 Tseng R.C....Wang Y.C. (Cancer 2009)
    7. Association between total immunoglobulin E and antibody responses to naturally acquired Ascaris lumbricoides infection and polymorphisms of immune system-related LIG4, TNFSF13B and IRS2 genes. (PubMed id 19604268)1, 4, 9 Acevedo N....Caraballo L. (Clin. Exp. Immunol. 2009)
    8. DNA ligase IV is essential for V(D)J recombination and DNA double- strand break repair in human precursor lymphocytes. (PubMed id 9809069)1, 2, 9 Grawunder U.... Lieber M.R. (Mol. Cell 1998)
    9. Association of DNA repair and steroid metabolism gene polymorphisms with clinical late toxicity in patients treated with conformal radiotherapy for prostate cancer. (PubMed id 16638864)1, 4, 9 Damaraju S....Parliament M. (Clin. Cancer Res. 2006)
    10. Cellular and biochemical impact of a mutation in DNA ligase IV conferring clinical radiosensitivity. (PubMed id 11349135)1, 2, 9 Riballo E.... Kysela B. (J. Biol. Chem. 2001)

    (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: 3981 HGNC: 6601 AceView: LIG4 Ensembl:ENSG00000174405 euGenes: HUgn3981
    ECgene: LIG4 Kegg: 3981 H-InvDB: LIG4

    (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 LIG4 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for LIG4 Genetics and Cytogenetics in Oncology and Haematology
    LIG4basehttp://bioinf.uta.fi/LIG4base/
    NIEHS-SNPshttp://egp.gs.washington.edu/data/lig4/
    Wikipedia http://en.wikipedia.org/wiki/DNA_ligase

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for LIG4 gene:
    Search GeneIP for patents involving LIG4

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



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