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LIG1 DNA ligase 1 [ Homo sapiens (human) ]

Gene ID: 3978, updated on 7-Dec-2018

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
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
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

Genomic context

See LIG1 in Genome Data Viewer
Location:
19q13.33
Exon count:
29
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (48115445..48170603, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (48618702..48673852, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene calcium binding protein 5 Neighboring gene phospholipase A2 group IVC Neighboring gene PLA2G4C antisense RNA 1 Neighboring gene uncharacterized LOC107985293 Neighboring gene zinc finger SWIM-type containing 9 Neighboring gene caspase recruitment domain family member 8 Neighboring gene vomeronasal 1 receptor 97 pseudogene

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Base Excision Repair, organism-specific biosystem (from REACTOME)
    Base Excision Repair, organism-specific biosystemOf the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of ...
  • Base excision repair, organism-specific biosystem (from KEGG)
    Base excision repair, organism-specific biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
  • Base excision repair, conserved biosystem (from KEGG)
    Base excision repair, conserved biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
  • Cell Cycle, organism-specific biosystem (from REACTOME)
    Cell Cycle, organism-specific biosystem
    Cell Cycle
  • Cell Cycle, Mitotic, organism-specific biosystem (from REACTOME)
    Cell Cycle, Mitotic, organism-specific biosystemThe replication of the genome and the subsequent segregation of chromosomes into daughter cells are controlled by a series of events collectively known as the cell cycle. DNA replication is carried o...
  • Chromosome Maintenance, organism-specific biosystem (from REACTOME)
    Chromosome Maintenance, organism-specific biosystemChromosome maintenance is critical for stable chromosome function in mammalian and other eukaryotic cells. Aspects of telomere maintenance and nucleosome assembly are covered here.
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • DNA Replication, organism-specific biosystem (from REACTOME)
    DNA Replication, organism-specific biosystemStudies in the past decade have suggested that the basic mechanism of DNA replication initiation is conserved in all kingdoms of life. Initiation in unicellular eukaryotes, in particular Saccharomyce...
  • DNA replication, organism-specific biosystem (from KEGG)
    DNA replication, organism-specific biosystemA complex network of interacting proteins and enzymes is required for DNA replication. Generally, DNA replication follows a multistep enzymatic pathway. At the DNA replication fork, a DNA helicase (D...
  • DNA replication, conserved biosystem (from KEGG)
    DNA replication, conserved biosystemA complex network of interacting proteins and enzymes is required for DNA replication. Generally, DNA replication follows a multistep enzymatic pathway. At the DNA replication fork, a DNA helicase (D...
  • DNA strand elongation, organism-specific biosystem (from REACTOME)
    DNA strand elongation, organism-specific biosystemAccurate and efficient genome duplication requires coordinated processes to replicate two template strands at eucaryotic replication forks. Knowledge of the fundamental reactions involved in replicat...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Early Phase of HIV Life Cycle, organism-specific biosystem (from REACTOME)
    Early Phase of HIV Life Cycle, organism-specific biosystemIn the early phase of HIV lifecycle, an active virion binds and enters a target cell mainly by specific interactions of the viral envelope proteins with host cell surface receptors. The virion core...
  • Extension of Telomeres, organism-specific biosystem (from REACTOME)
    Extension of Telomeres, organism-specific biosystemTelomerase acts as reverse transcriptase in the elongation of telomeres (Smogorzewska and de Lange 2004).
  • Gap-filling DNA repair synthesis and ligation in GG-NER, organism-specific biosystem (from REACTOME)
    Gap-filling DNA repair synthesis and ligation in GG-NER, organism-specific biosystemGlobal genome nucleotide excision repair (GG-NER) is completed by DNA repair synthesis that fills the single stranded gap created after dual incision of the damaged DNA strand and excision of the ~27...
  • Gap-filling DNA repair synthesis and ligation in TC-NER, organism-specific biosystem (from REACTOME)
    Gap-filling DNA repair synthesis and ligation in TC-NER, organism-specific biosystemIn transcription-coupled nucleotide excision repair (TC-NER), similar to global genome nucleotide excision repair (GG-NER), DNA polymerases delta or epsilon, or the Y family DNA polymerase kappa, fil...
  • Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystem (from REACTOME)
    Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystemThe DNA damage in GG-NER is recognized by the joint action of two protein complexes. The first complex is composed of XPC, RAD23A or RAD23B and CETN2. The second complex, known as the UV-DDB complex,...
  • HIV Infection, organism-specific biosystem (from REACTOME)
    HIV Infection, organism-specific biosystemThe global pandemic of Human Immunodeficiency Virus (HIV) infection has resulted in tens of millions of people infected by the virus and millions more affected. UNAIDS estimates around 40 million ...
  • HIV Life Cycle, organism-specific biosystem (from REACTOME)
    HIV Life Cycle, organism-specific biosystemThe life cycle of HIV-1 is divided into early and late phases, shown schematically in the figure. In the early phase, an HIV-1 virion binds to receptors and co-receptors on the human host cell surfac...
  • Infectious disease, organism-specific biosystem (from REACTOME)
    Infectious disease, organism-specific biosystem
    Infectious disease
  • Integrated Pancreatic Cancer Pathway, organism-specific biosystem (from WikiPathways)
    Integrated Pancreatic Cancer Pathway, organism-specific biosystemAn integrated pathway model which displays the protein-protein interactions (PPIs) among the relevant proteins for pancreatic cancer. This pathway is a collection of different mechanistic protein pat...
  • Lagging Strand Synthesis, organism-specific biosystem (from REACTOME)
    Lagging Strand Synthesis, organism-specific biosystemDue to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching...
  • Mismatch Repair, organism-specific biosystem (from REACTOME)
    Mismatch Repair, organism-specific biosystemThe mismatch repair (MMR) system corrects single base mismatches and small insertion and deletion loops (IDLs) of unpaired bases. MMR is primarily associated with DNA replication and is highly conser...
  • Mismatch repair, organism-specific biosystem (from KEGG)
    Mismatch repair, organism-specific biosystemDNA mismatch repair (MMR) is a highly conserved biological pathway that plays a key role in maintaining genomic stability. MMR corrects DNA mismatches generated during DNA replication, thereby preven...
  • Mismatch repair, organism-specific biosystem (from WikiPathways)
    Mismatch repair, organism-specific biosystemDNA mismatch repair is a system for recognizing and repairing erroneous insertion, deletion and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairin...
  • Mismatch repair, conserved biosystem (from KEGG)
    Mismatch repair, conserved biosystemDNA mismatch repair (MMR) is a highly conserved biological pathway that plays a key role in maintaining genomic stability. MMR corrects DNA mismatches generated during DNA replication, thereby preven...
  • Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta), organism-specific biosystem (from REACTOME)
    Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta), organism-specific biosystemMSH2:MSH3 (MutSbeta) binds unpaired loops of 2 or more nucleotides (Palombo et al. 1996, Genschel et al. 1998). Human cells contain about 6-fold more MSH2:MSH6 than MSH2:MSH3 (MutSbeta) and an imbala...
  • Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha), organism-specific biosystem (from REACTOME)
    Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha), organism-specific biosystemMSH2:MSH6 (MutSalpha) binds single base mismatches and unpaired loops of 1-2 nucleotides (reviewed in Edelbrock et al. 2013). Human cells contain about 6-fold more MSH2:MSH6 than MSH2:MSH3 (MutSbeta)...
  • Nucleotide Excision Repair, organism-specific biosystem (from REACTOME)
    Nucleotide Excision Repair, organism-specific biosystemNucleotide excision repair (NER) was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recove...
  • Nucleotide excision repair, organism-specific biosystem (from KEGG)
    Nucleotide excision repair, organism-specific biosystemNucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the ...
  • Nucleotide excision repair, conserved biosystem (from KEGG)
    Nucleotide excision repair, conserved biosystemNucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the ...
  • PCNA-Dependent Long Patch Base Excision Repair, organism-specific biosystem (from REACTOME)
    PCNA-Dependent Long Patch Base Excision Repair, organism-specific biosystemLong-patch base excision repair (BER) can proceed through PCNA-dependent DNA strand displacement synthesis by replicative DNA polymerases - DNA polymerase delta complex (POLD) or DNA polymerase epsil...
  • POLB-Dependent Long Patch Base Excision Repair, organism-specific biosystem (from REACTOME)
    POLB-Dependent Long Patch Base Excision Repair, organism-specific biosystemDuring POLB-dependent long patch base excision repair (BER), PARP1 and/or PARP2 is recruited to the BER site along with flap endonuclease FEN1. PARP1 and/or PARP2 and FEN1 facilitate POLB-mediated st...
  • Processive synthesis on the C-strand of the telomere, organism-specific biosystem (from REACTOME)
    Processive synthesis on the C-strand of the telomere, organism-specific biosystemOnce polymerase switching from pol alpha to pol delta is complete the processive synthesis of a short run of DNA called an Okazaki fragment begins. DNA synthesis is discontinuous and as the extending...
  • Processive synthesis on the lagging strand, organism-specific biosystem (from REACTOME)
    Processive synthesis on the lagging strand, organism-specific biosystemThe key event that allows the processive synthesis on the lagging strand, is polymerase switching from pol alpha to pol delta, as on the leading strand. However, the processive synthesis on the laggi...
  • Resolution of AP sites via the multiple-nucleotide patch replacement pathway, organism-specific biosystem (from REACTOME)
    Resolution of AP sites via the multiple-nucleotide patch replacement pathway, organism-specific biosystemWhile the single nucleotide replacement pathway appears to facilitate the repair of most damaged bases, an alternative BER pathway is evoked when the structure of the 5'-terminal sugar phosphate is s...
  • Resolution of Abasic Sites (AP sites), organism-specific biosystem (from REACTOME)
    Resolution of Abasic Sites (AP sites), organism-specific biosystemResolution of AP sites can occur through the single nucleotide replacement pathway or through the multiple nucleotide patch replacement pathway, also known as the long-patch base excision repair (BER...
  • S Phase, organism-specific biosystem (from REACTOME)
    S Phase, organism-specific biosystemDNA synthesis occurs in the S phase, or the synthesis phase, of the cell cycle. The cell duplicates its hereditary material, and two copies of the chromosome are formed. As DNA replication continues,...
  • Synthesis of DNA, organism-specific biosystem (from REACTOME)
    Synthesis of DNA, organism-specific biosystemThe actual synthesis of DNA occurs in the S phase of the cell cycle. This includes the initiation of DNA replication, when the first nucleotide of the new strand is laid down during the synthesis of ...
  • Telomere C-strand (Lagging Strand) Synthesis, organism-specific biosystem (from REACTOME)
    Telomere C-strand (Lagging Strand) Synthesis, organism-specific biosystemDue to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching...
  • Telomere Maintenance, organism-specific biosystem (from REACTOME)
    Telomere Maintenance, organism-specific biosystemTelomeres are protein-DNA complexes at the ends of linear chromosomes that are important for genome stability. Telomeric DNA in humans, as in many eukaryotic organisms, consists of tandem repeats (B...
  • Transcription-Coupled Nucleotide Excision Repair (TC-NER), organism-specific biosystem (from REACTOME)
    Transcription-Coupled Nucleotide Excision Repair (TC-NER), organism-specific biosystemDNA damage in transcribed strands of active genes is repaired through a specialized nucleotide excision repair (NER) pathway known as transcription-coupled nucleotide excision repair (TC-NER). TC-NER...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC117397, MGC130025

Gene Ontology Provided by GOA

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

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_024307281.1

NCBI Reference Sequences (RefSeq)

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
    P18858
    Related
    ENSP00000263274.6, ENST00000263274.11
    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_001289063.1NP_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/Swiss-Prot
    P18858
    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_001289064.1NP_001275993.1  DNA ligase 1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AK297296, BC108318
    Consensus CDS
    CCDS74410.1
    UniProtKB/Swiss-Prot
    P18858
    UniProtKB/TrEMBL
    B4DM52, F5GZ28
    Related
    ENSP00000441531.1, ENST00000536218.5
    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_001320970.1NP_001307899.1  DNA ligase 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, KC877741
    UniProtKB/Swiss-Prot
    P18858
    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_001320971.1NP_001307900.1  DNA ligase 1 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, KC877741
    UniProtKB/Swiss-Prot
    P18858
    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_110296.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AB208791, BC108318, BC110622
    Related
    ENST00000594759.5
  2. NR_135497.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, BC110622
    Related
    ENST00000601091.5
  3. NR_135498.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, KC877741
  4. NR_135499.1 RNA Sequence

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, KC877741

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    48115445..48170603 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024451513.1XP_024307281.1  DNA ligase 1 isoform X1

    Conserved Domains (2) summary
    cl25417
    Location:119878
    CDC9; ATP-dependent DNA ligase [Replication, recombination and repair]
    cl25574
    Location:10211
    TOP2c; TopoisomeraseII

RNA

  1. XR_002958316.1 RNA Sequence

  2. XR_002958315.1 RNA Sequence

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