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    LIG4 DNA ligase 4 [ Homo sapiens (human) ]

    Gene ID: 3981, updated on 9-Jul-2021

    Summary

    Official Symbol
    LIG4provided by HGNC
    Official Full Name
    DNA ligase 4provided by HGNC
    Primary source
    HGNC:HGNC:6601
    See related
    Ensembl:ENSG00000174405 MIM:601837
    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
    LIG4S
    Summary
    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]
    Expression
    Ubiquitous expression in brain (RPKM 5.8), testis (RPKM 4.8) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See LIG4 in Genome Data Viewer
    Location:
    13q33.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (108207442..108218349, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (108859790..108870697, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene NALCN channel auxiliary factor 1 Neighboring gene uncharacterized LOC107984581 Neighboring gene NALF1 intronic transcript 1 Neighboring gene uncharacterized LOC112268111 Neighboring gene Sharpr-MPRA regulatory region 13792 Neighboring gene abhydrolase domain containing 13 Neighboring gene TNF superfamily member 13b Neighboring gene RNA, 5S ribosomal pseudogene 39

    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?

    Phenotypes

    Associated conditions

    Description Tests
    Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study.
    GeneReviews: Not available
    Lig4 syndrome
    MedGen: C1847827 OMIM: 606593 GeneReviews: Not available
    Compare labs
    Multiple myeloma
    MedGen: C0026764 OMIM: 254500 GeneReviews: Not available
    Compare labs

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA ligase (ATP) activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables DNA ligase (ATP) activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA ligase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA ligase activity TAS
    Traceable Author Statement
    more info
     
    enables ligase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein C-terminus binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in DNA ligation involved in DNA recombination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in DNA ligation involved in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in DNA ligation involved in DNA repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in DNA ligation involved in DNA repair ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in T cell differentiation in thymus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in T cell receptor V(D)J recombination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in V(D)J recombination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell population proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to ionizing radiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in cellular response to lithium ion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in central nervous system development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in chromosome organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in double-strand break repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in double-strand break repair ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in double-strand break repair via classical nonhomologous end joining IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in double-strand break repair via nonhomologous end joining IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in double-strand break repair via nonhomologous end joining IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in double-strand break repair via nonhomologous end joining IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in double-strand break repair via nonhomologous end joining IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in double-strand break repair via nonhomologous end joining ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in double-strand break repair via nonhomologous end joining TAS
    Traceable Author Statement
    more info
     
    involved_in establishment of integrated proviral latency TAS
    Traceable Author Statement
    more info
     
    involved_in immunoglobulin V(D)J recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in in utero embryonic development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in isotype switching ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of neuron apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuron apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in nucleotide-excision repair, DNA gap filling IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in nucleotide-excision repair, DNA gap filling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of chromosome organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of fibroblast proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of neurogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in pro-B cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in response to X-ray IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to gamma radiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in single strand break repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in somatic stem cell population maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    part_of DNA ligase IV complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of DNA ligase IV complex IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    part_of DNA-dependent protein kinase-DNA ligase 4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of DNA-dependent protein kinase-DNA ligase 4 complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of DNA-dependent protein kinase-DNA ligase 4 complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in chromosome, telomeric region IC
    Inferred by Curator
    more info
    PubMed 
    located_in condensed chromosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasmic ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
     
    part_of nonhomologous end joining complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    DNA ligase 4
    Names
    DNA joinase
    DNA ligase IV
    DNA repair enzyme
    ligase IV, DNA, ATP-dependent
    polydeoxyribonucleotide synthase [ATP] 4
    polynucleotide ligase
    sealase
    NP_001091738.1
    NP_001317524.1
    NP_001339527.1
    NP_001339528.1
    NP_001339529.1
    NP_001339530.1
    NP_001339531.1
    NP_001339532.1
    NP_001339533.1
    NP_001366024.1
    NP_002303.2
    NP_996820.1

    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_007396.1 RefSeqGene

      Range
      2167..13093
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_79

    mRNA and Protein(s)

    1. NM_001098268.2NP_001091738.1  DNA ligase 4 isoform 1

      See identical proteins and their annotated locations for NP_001091738.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1-3 and 5-10 all encode the same isoform (1).
      Source sequence(s)
      BC037491, BX648833
      Consensus CDS
      CCDS9508.1
      UniProtKB/Swiss-Prot
      P49917
      UniProtKB/TrEMBL
      A0A024RE06
      Related
      ENSP00000385955.1, ENST00000405925.2
      Conserved Domains (4) summary
      TIGR00574
      Location:81602
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      cd17717
      Location:813900
      BRCT_DNA_ligase_IV_rpt2; second BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      cd17722
      Location:658745
      BRCT_DNA_ligase_IV_rpt1; first BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      pfam11411
      Location:750783
      DNA_ligase_IV; DNA ligase IV
    2. NM_001330595.2NP_001317524.1  DNA ligase 4 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a dowstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AK292419, AL157762, BC037491, BX648833, DC372305
      Consensus CDS
      CCDS81779.1
      UniProtKB/Swiss-Prot
      P49917
      UniProtKB/TrEMBL
      A0A0C4DGV9, A8K8Q4
      Related
      ENSP00000480814.1, ENST00000614526.1
    3. NM_001352598.2NP_001339527.1  DNA ligase 4 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5), as well as variants 1-3 and 6-10, encodes isoform 1.
      Source sequence(s)
      AL157762
      Consensus CDS
      CCDS9508.1
      Conserved Domains (4) summary
      TIGR00574
      Location:81602
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      cd17717
      Location:813900
      BRCT_DNA_ligase_IV_rpt2; second BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      cd17722
      Location:658745
      BRCT_DNA_ligase_IV_rpt1; first BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      pfam11411
      Location:750783
      DNA_ligase_IV; DNA ligase IV
    4. NM_001352599.2NP_001339528.1  DNA ligase 4 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6), as well as variants 1-3, 5, and 7-10, encodes isoform 1.
      Source sequence(s)
      AL157762
      Consensus CDS
      CCDS9508.1
      Conserved Domains (4) summary
      TIGR00574
      Location:81602
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      cd17717
      Location:813900
      BRCT_DNA_ligase_IV_rpt2; second BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      cd17722
      Location:658745
      BRCT_DNA_ligase_IV_rpt1; first BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      pfam11411
      Location:750783
      DNA_ligase_IV; DNA ligase IV
    5. NM_001352600.2NP_001339529.1  DNA ligase 4 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7), as well as variants 1-3, 5, 6, and 8-10, encodes isoform 1.
      Source sequence(s)
      AL157762
      Consensus CDS
      CCDS9508.1
      Conserved Domains (4) summary
      TIGR00574
      Location:81602
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      cd17717
      Location:813900
      BRCT_DNA_ligase_IV_rpt2; second BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      cd17722
      Location:658745
      BRCT_DNA_ligase_IV_rpt1; first BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      pfam11411
      Location:750783
      DNA_ligase_IV; DNA ligase IV
    6. NM_001352601.2NP_001339530.1  DNA ligase 4 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8), as well as variants 1-3, 5-7, 9, and 10, encodes isoform 1.
      Source sequence(s)
      AL157762
      Consensus CDS
      CCDS9508.1
      Conserved Domains (4) summary
      TIGR00574
      Location:81602
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      cd17717
      Location:813900
      BRCT_DNA_ligase_IV_rpt2; second BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      cd17722
      Location:658745
      BRCT_DNA_ligase_IV_rpt1; first BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      pfam11411
      Location:750783
      DNA_ligase_IV; DNA ligase IV
    7. NM_001352602.2NP_001339531.1  DNA ligase 4 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9), as well as variants 1-3, 5-8, and 10, encodes isoform 1.
      Source sequence(s)
      AL157762
      Consensus CDS
      CCDS9508.1
      Conserved Domains (4) summary
      TIGR00574
      Location:81602
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      cd17717
      Location:813900
      BRCT_DNA_ligase_IV_rpt2; second BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      cd17722
      Location:658745
      BRCT_DNA_ligase_IV_rpt1; first BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      pfam11411
      Location:750783
      DNA_ligase_IV; DNA ligase IV
    8. NM_001352603.1NP_001339532.1  DNA ligase 4 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10), as well as variants 1-3 and 5-9, encodes isoform 1.
      Source sequence(s)
      AL157762
      Consensus CDS
      CCDS9508.1
      Conserved Domains (4) summary
      TIGR00574
      Location:81602
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      cd17717
      Location:813900
      BRCT_DNA_ligase_IV_rpt2; second BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      cd17722
      Location:658745
      BRCT_DNA_ligase_IV_rpt1; first BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      pfam11411
      Location:750783
      DNA_ligase_IV; DNA ligase IV
    9. NM_001352604.2NP_001339533.1  DNA ligase 4 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) encodes the longest isoform (3).
      Source sequence(s)
      AL157762
      Conserved Domains (3) summary
      TIGR00574
      Location:93614
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      pfam00533
      Location:668742
      BRCT; BRCA1 C Terminus (BRCT) domain
      pfam11411
      Location:762795
      DNA_ligase_IV; DNA ligase IV
    10. NM_001379095.1NP_001366024.1  DNA ligase 4 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL157762, DA211056
      Related
      ENSP00000484288.1, ENST00000611712.4
      Conserved Domains (4) summary
      TIGR00574
      Location:81602
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      cd17717
      Location:813900
      BRCT_DNA_ligase_IV_rpt2; second BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      cd17722
      Location:658745
      BRCT_DNA_ligase_IV_rpt1; first BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      pfam11411
      Location:750783
      DNA_ligase_IV; DNA ligase IV
    11. NM_002312.3NP_002303.2  DNA ligase 4 isoform 1

      See identical proteins and their annotated locations for NP_002303.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), as well as variants 2, 3, and 5-10, encodes isoform 1.
      Source sequence(s)
      AI809944, BC037491, CD102896, X83441
      Consensus CDS
      CCDS9508.1
      UniProtKB/Swiss-Prot
      P49917
      UniProtKB/TrEMBL
      A0A024RE06
      Conserved Domains (4) summary
      TIGR00574
      Location:81602
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      cd17717
      Location:813900
      BRCT_DNA_ligase_IV_rpt2; second BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      cd17722
      Location:658745
      BRCT_DNA_ligase_IV_rpt1; first BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      pfam11411
      Location:750783
      DNA_ligase_IV; DNA ligase IV
    12. NM_206937.2NP_996820.1  DNA ligase 4 isoform 1

      See identical proteins and their annotated locations for NP_996820.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1-3 and 5-10 all encode the same isoform (1).
      Source sequence(s)
      AL157762, BC037491, BX648833
      Consensus CDS
      CCDS9508.1
      UniProtKB/Swiss-Prot
      P49917
      UniProtKB/TrEMBL
      A0A024RE06
      Related
      ENSP00000402030.1, ENST00000442234.6
      Conserved Domains (4) summary
      TIGR00574
      Location:81602
      dnl1; DNA ligase I, ATP-dependent (dnl1)
      cd17717
      Location:813900
      BRCT_DNA_ligase_IV_rpt2; second BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      cd17722
      Location:658745
      BRCT_DNA_ligase_IV_rpt1; first BRCT domain of DNA ligase 4 (LIG4) and similar proteins
      pfam11411
      Location:750783
      DNA_ligase_IV; DNA ligase IV

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

      Range
      108207442..108218349 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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