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LIG1 Gene

protein-coding   GIFtS: 75
GCID: GC19M048618

Ligase I, DNA, ATP-Dependent

  See LIG1-related diseases
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 I, DNA, ATP-Dependent1 2
Polydeoxyribonucleotide Synthase [ATP] 12 3
EC 6.5.1.13 8
DNA Ligase 12
DNA Ligase I3

External Ids:    HGNC: 65981   Entrez Gene: 39782   Ensembl: ENSG000001054867   OMIM: 1263915   UniProtKB: P188583   

Export aliases for LIG1 gene to outside databases

Previous GC identifers: GC19M049263 GC19M048986 GC19M053294 GC19M053310 GC19M045000


(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 LIG1 Gene:
This gene encodes a member of the ATP-dependent DNA ligase protein family. The encoded protein functions in DNA
replication, recombination, and the base excision repair process. Mutations in this gene that lead to DNA ligase
I deficiency result in immunodeficiency and increased sensitivity to DNA-damaging agents. Disruption of this gene
may also be associated with a variety of cancers. Alternative splicing results in multiple transcript variants.
(provided by RefSeq, Jan 2014)

GeneCards Summary for LIG1 Gene:
LIG1 (ligase I, DNA, ATP-dependent) is a protein-coding gene. Diseases associated with LIG1 include dna ligase i deficiency, and bloom syndrome. GO annotations related to this gene include DNA ligase activity and DNA ligase (ATP) activity.

UniProtKB/Swiss-Prot: DNLI1_HUMAN, P18858
Function: DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA
repair

summary for LIG1 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 LIG1 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 at NCBI GenBank:
NC_000019.9  NT_011109.17  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the LIG1 gene promoter:
         Elk-1   MAZR   MyoD   Nkx2-5   NF-E2 p45   YY1   GATA-2   E2F-1   E2F   NF-E2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidLIG1 promoter sequence
   Search Chromatin IP Primers for LIG1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LIG1


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

Entrez Gene cytogenetic band: 19q13.2-q13.3   Ensembl cytogenetic band:  19q13.33   HGNC cytogenetic band: 19q13.2-q13.3

LIG1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LIG1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M048618:  view genomic region     (about GC identifiers)

Start:
48,618,702 bp from pter      End:
48,673,860 bp from pter
Size:
55,159 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, 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, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: DNLI1_HUMAN, P18858 (See protein sequence)
Recommended Name: DNA ligase 1  
Size: 919 amino acids; 101736 Da
Cofactor: Magnesium
1 PDB 3D structure from and Proteopedia for LIG1:
1X9N (3D)    
Secondary accessions: B2RAI8 Q32P23

Explore the universe of human proteins at neXtProt for LIG1: NX_P18858

Explore proteomics data for LIG1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys226, Lys298, Lys407, Lys422, Lys795
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for LIG1 (P18858) (see all 10)
     RFPRFIR  GLAEQSVL  NWLKLKKDY  VWEVKCADL 


    See LIG1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_000225.1  NP_001275992.1  NP_001275993.1  

    ENSEMBL proteins: 
     ENSP00000263274   ENSP00000471380   ENSP00000442841   ENSP00000471836   ENSP00000472331  
     ENSP00000445928   ENSP00000471861   ENSP00000469638   ENSP00000472085   ENSP00000441531  
    Reactome Protein details: P18858

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    Cloud-Clone Corp. Proteins for LIG1

     
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    antibodies-online proteins for LIG1 (2 products) 

     
    antibodies-online peptides for LIG1

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    antibodies-online antibodies for LIG1 (75 products) 

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    (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 6):
     IPR012340 NA-bd_OB-fold
     IPR012308 DNA_ligase_ATP-dep_N
     IPR012310 DNA_ligase_ATP-dep_cent
     IPR016059 DNA_ligase_ATP-dep_CS
     IPR012309 DNA_ligase_ATP-dep_C

    Graphical View of Domain Structure for InterPro Entry P18858

    ProtoNet protein and cluster: P18858

    1 Blocks protein domain: IPB012308 DNA ligase

    UniProtKB/Swiss-Prot: DNLI1_HUMAN, P18858
    Similarity: Belongs to the ATP-dependent DNA ligase family


    Find genes that share domains with LIG1           About GenesLikeMe


    (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, 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: DNLI1_HUMAN, P18858
    Function: DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA
    repair
    Catalytic activity: ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate +
    (deoxyribonucleotide)(n+m)

         Genatlas biochemistry entry for LIG1:
    DNA ligase I,ATP-dependent,yeast cdc9 homolog,interacting with FEN1 to inhibit DNA synthesis by DNA polymerase
    delta/PCNA complex,required for fetal liver erythropoiesis

         Enzyme Number (IUBMB): EC 6.5.1.11 2

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003909DNA ligase activity IDA9809069
    GO:0003910DNA ligase (ATP) activity IBA--
    GO:0005524ATP binding IEA--
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with LIG1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for LIG1:
     Upregulation of Wnt/beta-caten 

         10 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Lig1):
     cellular  embryogenesis  growth/size/body  hematopoietic system  homeostasis/metabolism 
     immune system  integument  liver/biliary system  mortality/aging  tumorigenesis 

    Find genes that share phenotypes with LIG1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for LIG1: Lig1tm2Dwm Lig1tm1Dwm

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LIG1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for LIG1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for LIG1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for LIG1

    miRNA
    Products:
        
    miRTarBase miRNAs that target LIG1:
    hsa-mir-26b-5p (MIRT030288), hsa-mir-149-5p (MIRT045653), hsa-mir-615-3p (MIRT040334)

    Block miRNA regulation of human, mouse, rat LIG1 using miScript Target Protectors
    1 qRT-PCR Assays for microRNA that regulate LIG1:
    hsa-miR-944
    SwitchGear 3'UTR luciferase reporter plasmidLIG1 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Predesigned siRNA for gene silencing in human, mouse, rat LIG1

    Gene Editing
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    Clone
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    OriGene ORF clones in mouse, rat for LIG1
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    GenScript: all cDNA clones in your preferred vector: LIG1 (NM_000234)
    Browse Sino Biological Human cDNA Clones
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LIG1


    (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
    DNLI1_HUMAN, P18858: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    mitochondrion3
    cytosol2

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005654nucleoplasm TAS--
    GO:0005694chromosome IBA--
    GO:0005730NOT nucleolus IDA--
    GO:0005739mitochondrion IBA--

    Find genes that share ontologies with LIG1           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 LIG1 About   (see all 14)  
    See pathways by source

    SuperPathSelected contained pathways About (see all per SuperPath)
    1Telomere C-strand (Lagging Strand) Synthesis
    Gap-filling DNA repair synthesis and ligation in TC-NER0.94
    Processive synthesis on the lagging strand0.00
    Telomere C-strand (Lagging Strand) Synthesis0.79
    Mismatch repair0.00
    Extension of Telomeres0.79
    Lagging Strand Synthesis0.00
    Mismatch repair0.56
    Processive synthesis on the C-strand of the telomere0.00
    2Global Genomic NER (GG-NER)
    Global Genomic NER (GG-NER)0.69
    Nucleotide Excision Repair Pathway0.48
    Nucleotide excision repair0.69
    3Resolution of Abasic Sites (AP sites)
    Resolution of Abasic Sites (AP sites)0.89
    Base Excision Repair0.00
    Resolution of AP sites via the multiple-nucleotide patch replacement pathway0.89
    Removal of DNA patch containing abasic residue0.00
    Base excision repair0.53
    4DNA strand elongation
    DNA strand elongation0.63
    DNA replication0.63
    5HIV Life Cycle
    HIV Life Cycle0.91
    Early Phase of HIV Life Cycle0.00
    HIV Infection0.62


    Find genes that share SuperPaths with LIG1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for LIG1
        DNA Repair Mechanisms
    Nucleotide Excision Repair Pathway

    1 GeneGo (Thomson Reuters) Pathway for LIG1
        Cell cycle Transition and termination of DNA replication

    2 BioSystems Pathways for LIG1
        Mismatch repair
    Integrated Pancreatic Cancer Pathway

    Selected Reactome Pathways for LIG1 (see all 7)
        Processive synthesis on the lagging strand
    Removal of DNA patch containing abasic residue
    Gap-filling DNA repair synthesis and ligation in GG-NER
    Processive synthesis on the C-strand of the telomere
    Resolution of AP sites via the multiple-nucleotide patch replacement pathway


    4 Kegg Pathways  (Kegg details for LIG1):
        DNA replication
    Base excision repair
    Nucleotide excision repair
    Mismatch repair

        Pathway & Disease-focused RT2 Profiler PCR Arrays including LIG1: 
              DNA Damage Signaling Pathway in human mouse rat
              DNA Repair in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for LIG1

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

    Selected Interacting proteins for LIG1 (P188582, 3 ENSP000002632744) via UniProtKB, MINT, STRING, and/or I2D (see all 101)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    INPP1P494412, 3, ENSP000003254234MINT-63777 I2D: score=4 STRING: ENSP00000325423
    RGS2P412202, 3, ENSP000002353824MINT-8268834 I2D: score=2 STRING: ENSP00000235382
    PCNAP120043, ENSP000003684384I2D: score=8 STRING: ENSP00000368438
    CDC34P494273, ENSP000002155744I2D: score=3 STRING: ENSP00000215574
    CSNK2A1P684003, ENSP000002172444I2D: score=2 STRING: ENSP00000217244
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 22):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000278mitotic cell cycle TAS--
    GO:0000722telomere maintenance via recombination TAS--
    GO:0000723telomere maintenance TAS--
    GO:0000724double-strand break repair via homologous recombination TAS--
    GO:0006259DNA metabolic process TAS2204063

    Find genes that share ontologies with LIG1           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 LIG1 available from Tocris Bioscience    About this table
    CompoundAction CAS #
    L189 DNA ligase I, III and IV inhibitor [64232-83-3]

    4 HMDB Compounds for LIG1    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 LIG1    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    BleomycinBleocin (see all 8)11056-06-7targetinhibitor17202402

    Selected Novoseek inferred chemical compound relationships for LIG1 gene (see all 19)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    f-ara-atp 79.6 6 1310314 (4), 8698042 (1), 7881348 (1)
    phosphodiester 57.3 1 9371766 (1)
    aphidicolin 50.2 9 12372342 (4), 11452007 (1)
    3-aminobenzamide 49.4 2 8565116 (1)
    polynucleotide 42.3 4 9742240 (2), 8471077 (1)
    nad+ 38.3 2 16361267 (1), 15901723 (1)
    danazol 27.2 1 1939197 (1)
    atp 21.8 3 1508676 (1), 17688957 (1), 15901723 (1), 1569068 (1)
    adpribose 19.8 1 7898478 (1)
    cytarabine 18 8 12372342 (4), 11948132 (1)



    Find genes that share compounds with LIG1           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 LIG1 gene (3 alternative transcripts): 
    NM_000234.2  NM_001289063.1  NM_001289064.1  

    Unigene Cluster for LIG1:

    Ligase I, DNA, ATP-dependent
    Hs.1770  [show with all ESTs]
    Unigene Representative Sequence: AB208791
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 20):
    ENST00000263274(uc010xze.1 uc002phz.1 uc002pia.1 uc002pib.1 uc010xzf.1 uc010xzg.1)
    ENST00000597146 ENST00000599322 ENST00000594759 ENST00000427526 ENST00000594067
    ENST00000601091 ENST00000596672 ENST00000596332 ENST00000596457 ENST00000597901
    ENST00000542460(uc010xzh.1) ENST00000595758 ENST00000596104 ENST00000599165
    ENST00000596549 ENST00000593425 ENST00000600055
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat LIG1
      QuantiFast Probe-based Assays in human, mouse, rat LIG1

    Additional mRNA sequence: 

    AB208791.1 AK225863.1 AK297296.1 AK300370.1 AK300607.1 AK303644.1 AK314210.1 BC108318.1 
    BC110622.2 M36067.1 

    13 DOTS entries:

    DT.448549  DT.97796314  DT.100821564  DT.91866213  DT.100678667  DT.100802814  DT.40132859  DT.98131741 
    DT.121446143  DT.91760966  DT.91760975  DT.121446147  DT.97773816 

    Selected AceView cDNA sequences (see all 277):

    BQ221492 CR599472 BM548700 BE794374 AI867071 CA773455 BG257399 BF437306 
    AU120985 BU154275 BI916625 BU170774 AL710126 AL042689 BM472230 AU143382 
    CB529685 CB155211 BX325045 BQ231386 M36067 AA306774 CB270211 CR619348 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for LIG1 (see all 11)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b · 11c ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^
    SP1:              -                             -           -     -           -                                                           -                     
    SP2:                                                                                                                                                            
    SP3:                                                              -           -                                                                                 
    SP4:                                                                                                                                                            
    SP5:                                                                          -                                                                                 

    ExUns: 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30 ^ 31
    SP1:              -                             -                             -                           
    SP2:                                                                                                      
    SP3:                                                                                                      
    SP4:                                                                                                      
    SP5:                                                                                                      


    ECgene alternative splicing isoforms for LIG1

    (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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    LIG1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGTTGGACGG
    LIG1 Expression
    About this image


    LIG1 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 5 entries
             Cerebral Cortex
     
     Neural Tube (Nervous System)    fully expand to see all 4 entries
             Metencephalon
     
     Thymus (Hematopoietic System)
             Thymus
     
     Kidney (Urinary System)
             Metanephros
     
     Lower Urinary Tract (Urinary System)
             Ureter
    LIG1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LIG1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.1770
        Pathway & Disease-focused RT2 Profiler PCR Arrays including LIG1: 
              DNA Damage Signaling Pathway in human mouse rat
              DNA Repair in human mouse rat

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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 LIG1 gene from Selected species (see all 23)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lig11 , 5 ligase I, DNA, ATP-dependent1, 5 82.39(n)1
    84.35(a)1
      7 (7.82 cM)5
    168811  NM_001083188.11  NP_001076657.11 
     132772835 
    chicken
    (Gallus gallus)
    Aves LIG11 ligase I, DNA, ATP-dependent 68.96(n)
    68.55(a)
      430516  XM_003643130.2  XP_003643178.2 
    lizard
    (Anolis carolinensis)
    Reptilia LIG16
    ligase I, DNA, ATP-dependent
    59(a)
    1 ↔ 1
    GL343253.1(1532059-1556199)
    African clawed frog
    (Xenopus laevis)
    Amphibia ligI2 ligase I 71.87(n)    L43496.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BM532575.12   -- 72.16(n)    BM532575.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG56023
    DNA-ligI1
    DNA ligase (ATP)3
    DNA ligase I1
    47(a)
    (best of 3)3
    56.52(n)1
    51.52(a)1
      60A83
    377911  NM_137999.21  NP_611843.21 
    worm
    (Caenorhabditis elegans)
    Secernentea T21D12.9c3
    lig-11
    lig-11 32(a)
    (best of 3)3
    52.86(n)1
    50.72(a)1
      IV(274626-278272)3
    1795021  NM_171537.31  NP_741625.21 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes CDC9(YDL164C)4
    CDC91
    DNA ligase found in the nucleus and mitochondria, an more4
    CDC91
    48.88(n)1
    46.14(a)1
      4(167254-164987)4
    8513911, 4  NP_010117.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons LIG11 LIG1 53.76(n)
    51.29(a)
      837333  NM_100689.4  NP_172293.2 
    rice
    (Oryza sativa)
    Liliopsida Os.82852 Oryza sativa (japonica cultivar-group) putative DNA more 70.14(n)    AK120278.1 


    ENSEMBL Gene Tree for LIG1 (if available)
    TreeFam Gene Tree for LIG1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section

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      --

    (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)
    About This Section

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    Selected SNPs for LIG1 (see all 1612)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0365124
    A colorectal cancer sample4--see VAR_0365122 S L mis40--------
    VAR_0365114
    A colorectal cancer sample4--see VAR_0365112 K E mis40--------
    rs1904588611,2
    --44999996(+) CTTAGG/TGGGGC 1 -- ds50010--------
    rs1834080651,2
    --45000093(+) TTAGCC/GAGGCG 1 -- ds50010--------
    rs37310511,2
    C,F--45000094(-) acgccT/Cggcta 1 -- ds50011Minor allele frequency- C:0.02NS 108
    rs37310501,2
    C,F--45000100(-) gacacC/Tacgcc 1 -- ds50011Minor allele frequency- T:0.02NS 106
    rs1399988861,2
    --45000103(+) GTGGTA/GTCACA 1 -- ds50010--------
    rs1863290241,2
    --45000224(+) AGAGCA/GAGACT 1 -- ds50010--------
    rs1113206791,2
    C--45000239(+) CTCAAG/AACAAA 1 -- ds50011Minor allele frequency- A:0.50CSA 2
    rs1908870801,2
    --45000304(+) GGGCTC/TGGGCA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for LIG1 (48618702 - 48673860 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for LIG1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv833853CNV Loss17160897
    nsv912217CNV Loss21882294
    esv34181CNV Loss18971310
    nsv9739CNV Gain+Loss18304495

    Human Gene Mutation Database (HGMD): LIG1
    Locus Specific Mutation Databases (LSDB): LIG1

    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, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 126391    OMIM disorders: --

    2 diseases for LIG1:    
    About MalaCards
    dna ligase i deficiency    bloom syndrome

    2 diseases from the University of Copenhagen DISEASES database for LIG1:
    Vaccinia     Autosomal recessive disease

    Find genes that share disorders with LIG1           About GenesLikeMe

    Selected Novoseek inferred disease relationships for LIG1 gene (see all 14)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    bloom syndrome 82.1 7 1900268 (2), 7683758 (1), 1881902 (1), 7480643 (1) (see all 6)
    nijmegen breakage syndrome 46.3 1 15966765 (1)
    ataxia telangiectasia 45 1 15966765 (1)
    xeroderma pigmentosum 21.9 1 15966765 (1)
    pancreatic carcinoma 10.8 2 12408985 (1)
    tumors 4.58 18 11751514 (6), 11948132 (2), 16940149 (1), 8144677 (1)
    pancreatic cancer 3.95 1 12372342 (1)
    immunodeficiency 2.47 2 1351188 (1), 8907308 (1)
    growth retardation 1.04 1 1351188 (1)
    shock 0 1 10970827 (1)

    Genatlas disease: LIG1
    growth retardation,immunodeficiency and predisposition to malignancies,Bloom syndrome-like phenotype

    Genetic Association Database (GAD): LIG1
    Human Genome Epidemiology (HuGE) Navigator: LIG1 (37 documents)

    Export disorders for LIG1 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 LIG1 gene, integrated from 10 sources (see all 227):
    (articles sorted by number of sources associating them with LIG1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Polymorphism of DNA ligase I and risk of lung cancer--a case-control analysis. (PubMed id 12009232)1, 4, 9 Shen H....Wei Q. (Lung Cancer 2002)
    2. A wild-type DNA ligase I gene is expressed in Bloom's syndrome cells. (PubMed id 1881902)1, 2, 9 Petrini J.H.J.... Weaver D.T. (Proc. Natl. Acad. Sci. U.S.A. 1991)
    3. Human DNA ligase I completely encircles and partially unwinds nicked DNA. (PubMed id 15565146)1, 2, 9 Pascal J.M.... Ellenberger T. (Nature 2004)
    4. Human DNA ligase I cDNA: cloning and functional expression in Saccharomyces cerevisiae. (PubMed id 2204063)1, 2, 9 Barnes D.E....Lindahl T. (Proc. Natl. Acad. Sci. U.S.A. 1990)
    5. No association of DNA ligase-I polymorphism with the risk of lung cancer in north-Indian population. (PubMed id 16907646)1, 4, 9 Sobti R.C....Raimondi S. (DNA Cell Biol. 2006)
    6. Mutations in the DNA ligase I gene of an individual with immunodeficiencies and cellular hypersensitivity to DNA-damaging agents. (PubMed id 1581963)1, 2, 9 Barnes D.E.... Lindahl T. (Cell 1992)
    7. 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)
    8. 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)
    9. A Large-scale genetic association study of esophageal adenocarcinoma risk. (PubMed id 20453000)1, 4 Liu C.Y....Christiani D.C. (Carcinogenesis 2010)
    10. DNA repair gene polymorphisms and risk of adult meningioma, glioma, and acoustic neuroma. (PubMed id 20150366)1, 4 Rajaraman P....Inskip P.D. (Neuro-oncology 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: 3978 HGNC: 6598 AceView: LIG1 Ensembl:ENSG00000105486 euGenes: HUgn3978
    ECgene: LIG1 Kegg: 3978 H-InvDB: LIG1

    (According to HUGE)
    About This Section

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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 LIG1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for LIG1 Genetics and Cytogenetics in Oncology and Haematology
    LIG1basehttp://bioinf.uta.fi/LIG1base/
    NIEHS-SNPshttp://egp.gs.washington.edu/data/lig1/
    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 LIG1 gene:
    Search GeneIP for patents involving LIG1

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



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