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    LIG1 DNA ligase 1 [ Homo sapiens (human) ]

    Gene ID: 3978, updated on 11-Jun-2024

    Summary

    Official Symbol
    LIG1provided by HGNC
    Official Full Name
    DNA ligase 1provided by HGNC
    Primary source
    HGNC:HGNC:6598
    See related
    Ensembl:ENSG00000105486 MIM:126391; AllianceGenome:HGNC:6598
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LIGI; IMD96; hLig1
    Summary
    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]
    Expression
    Broad expression in bone marrow (RPKM 13.9), lymph node (RPKM 9.7) and 24 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See LIG1 in Genome Data Viewer
    Location:
    19q13.33
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (48115445..48170344, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (51109368..51164335, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (48618702..48673601, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene calcium binding protein 5 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48564610-48565203 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48565204-48565796 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:48565797-48566389 Neighboring gene phospholipase A2 group IVC Neighboring gene PLA2G4C antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10871 Neighboring gene uncharacterized LOC107985293 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:48673083-48673742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14872 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:48691653-48691885 Neighboring gene zinc finger SWIM-type containing 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48699771-48700283 Neighboring gene caspase recruitment domain family member 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14873 Neighboring gene uncharacterized LOC124904734

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC117397, MGC130025

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA ligase (ATP) activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA ligase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA ligase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables DNA ligase activity TAS
    Traceable Author Statement
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in DNA ligation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in DNA ligation TAS
    Traceable Author Statement
    more info
     
    involved_in DNA repair TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in Okazaki fragment processing involved in mitotic DNA replication IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    NOT involved_in V(D)J recombination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in anatomical structure morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in base-excision repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in base-excision repair, gap-filling TAS
    Traceable Author Statement
    more info
     
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lagging strand elongation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mismatch repair TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    DNA ligase 1
    Names
    ligase I, DNA, ATP-dependent
    polydeoxyribonucleotide synthase [ATP] 1
    NP_000225.1
    NP_001275992.1
    NP_001275993.1
    NP_001307899.1
    NP_001307900.1
    XP_047294789.1
    XP_047294790.1
    XP_054176994.1
    XP_054176995.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_007395.1 RefSeqGene

      Range
      4701..59859
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_78

    mRNA and Protein(s)

    1. NM_000234.3NP_000225.1  DNA ligase 1 isoform 1

      See identical proteins and their annotated locations for NP_000225.1

      Status: REVIEWED

      Source sequence(s)
      BC108318
      Consensus CDS
      CCDS12711.1
      UniProtKB/Swiss-Prot
      B2RAI8, B4DTU4, P18858, Q2TB12, Q32P23
      UniProtKB/TrEMBL
      A0A8V8TQQ7
      Related
      ENSP00000263274.6, ENST00000263274.12
      Conserved Domains (2) summary
      cl25417
      Location:164914
      CDC9; ATP-dependent DNA ligase [Replication, recombination and repair]
      cl25751
      Location:10275
      DUF4045; Domain of unknown function (DUF4045)
    2. NM_001289063.2NP_001275992.1  DNA ligase 1 isoform 2

      See identical proteins and their annotated locations for NP_001275992.1

      Status: REVIEWED

      Source sequence(s)
      AK300370, BC108318
      Consensus CDS
      CCDS74409.1
      UniProtKB/TrEMBL
      A0A8V8TQQ7
      Related
      ENSP00000442841.1, ENST00000427526.6
      Conserved Domains (4) summary
      cd07969
      Location:723868
      OBF_DNA_ligase_I; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit
      cd07900
      Location:500718
      Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I
      PLN03113
      Location:133883
      PLN03113; DNA ligase 1; Provisional
      pfam04675
      Location:257428
      DNA_ligase_A_N; DNA ligase N terminus
    3. NM_001289064.2NP_001275993.1  DNA ligase 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AK297296, BC108318
      Consensus CDS
      CCDS74410.1
      UniProtKB/TrEMBL
      B4DM52, F5GZ28, M0R1G7
      Related
      ENSP00000471861.2, ENST00000596549.6
      Conserved Domains (4) summary
      cd07969
      Location:686831
      OBF_DNA_ligase_I; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit
      cd07900
      Location:463681
      Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I
      PLN03113
      Location:103846
      PLN03113; DNA ligase 1; Provisional
      pfam04675
      Location:220391
      DNA_ligase_A_N; DNA ligase N terminus
    4. NM_001320970.2NP_001307899.1  DNA ligase 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC011466, BC108318, KC877741
      Consensus CDS
      CCDS92658.1
      UniProtKB/TrEMBL
      A0A8V8TQC4, A0A8V8TQQ7
      Related
      ENSP00000514663.1, ENST00000699866.1
      Conserved Domains (4) summary
      cd07969
      Location:753898
      OBF_DNA_ligase_I; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit
      cd07900
      Location:530748
      Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I
      PLN03113
      Location:163913
      PLN03113; DNA ligase 1; Provisional
      pfam04675
      Location:287458
      DNA_ligase_A_N; DNA ligase N terminus
    5. NM_001320971.2NP_001307900.1  DNA ligase 1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC011466, BC108318, KC877741
      Consensus CDS
      CCDS92657.1
      UniProtKB/TrEMBL
      A0A8V8TPH8, A0A8V8TQQ7
      Related
      ENSP00000514670.1, ENST00000699874.1
      Conserved Domains (4) summary
      cd07969
      Location:724869
      OBF_DNA_ligase_I; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit
      cd07900
      Location:501719
      Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I
      PLN03113
      Location:134884
      PLN03113; DNA ligase 1; Provisional
      pfam04675
      Location:258429
      DNA_ligase_A_N; DNA ligase N terminus

    RNA

    1. NR_110296.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AB208791, BC108318, BC110622
      Related
      ENST00000594759.5
    2. NR_135497.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC011466, BC108318, BC110622
      Related
      ENST00000601091.5
    3. NR_135498.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC011466, BC108318, KC877741
      Related
      ENST00000596672.6
    4. NR_135499.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC011466, BC108318, KC877741
      Related
      ENST00000699873.1
    5. NR_135500.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC011466, BC108318, KC877741
      Related
      ENST00000699872.1
    6. NR_135501.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC011466, BC108318, KC877741
      Related
      ENST00000699869.1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      48115445..48170344 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438833.1XP_047294789.1  DNA ligase 1 isoform X1

      UniProtKB/TrEMBL
      B4DUE1
      Related
      ENST00000594067.5
    2. XM_047438834.1XP_047294790.1  DNA ligase 1 isoform X2

      UniProtKB/TrEMBL
      A0A8V8TPH4
      Related
      ENSP00000514666.1, ENST00000699870.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      51109368..51164335 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321019.1XP_054176994.1  DNA ligase 1 isoform X1

      UniProtKB/TrEMBL
      B4DUE1
    2. XM_054321020.1XP_054176995.1  DNA ligase 1 isoform X2

      UniProtKB/TrEMBL
      A0A8V8TPH4