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Aliases for LIG1 Gene

Aliases for LIG1 Gene

  • DNA Ligase 1 2 3 3 5
  • Polydeoxyribonucleotide Synthase [ATP] 1 3 4
  • Ligase I, DNA, ATP-Dependent 2 3
  • DNA Ligase I 4
  • EC 4

External Ids for LIG1 Gene

Previous GeneCards Identifiers for LIG1 Gene

  • GC19M049263
  • GC19M048986
  • GC19M053294
  • GC19M053310
  • GC19M048618
  • GC19M045000

Summaries for LIG1 Gene

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 (DNA Ligase 1) is a Protein Coding gene. Diseases associated with LIG1 include Bloom Syndrome and Achalasia-Addisonianism-Alacrima Syndrome. Among its related pathways are Telomere C-strand (Lagging Strand) Synthesis and Cell Cycle, Mitotic. Gene Ontology (GO) annotations related to this gene include DNA ligase activity and DNA ligase (ATP) activity. An important paralog of this gene is LIG3.

UniProtKB/Swiss-Prot for LIG1 Gene

  • DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.

Tocris Summary for LIG1 Gene

  • Ligases are enzymes which 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 of enzymes, which also includes synthases and carboxylases.

Gene Wiki entry for LIG1 Gene

Additional gene information for LIG1 Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIG1 Gene

Genomics for LIG1 Gene

GeneHancer (GH) Regulatory Elements for LIG1 Gene

Promoters and enhancers for LIG1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J048168 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 658.1 +0.1 96 3.1 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF766 LIG1 ZSWIM9 BICRA KDELR1 GRWD1 CCDC9 PLA2G4C NOP53 NOP53-AS1 RPL18
GH19J047225 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 19.6 +941.2 941222 8.2 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 BBC3 BICRA ENSG00000268810 NOP53-AS1 CCDC9 NOP53 ENSG00000269321 SNORD23 PPP5D1 INAFM1
GH19J048958 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.1 -793.4 -793426 10.2 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF263 FTL GC19P048966 GC19P048967 ENSG00000267898 NUP62 PTOV1-AS2 IRF3 SNORD35A SNORD35B PRR12
GH19J048871 Promoter/Enhancer 2.6 EPDnew Ensembl ENCODE dbSUPER 10.1 -705.4 -705412 8.8 FEZF1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 MEF2D SSRP1 PPP1R15A GC19M048876 PRR12 SNRNP70 IRF3 GRWD1 SNORD35A PTOV1-AS2 SNORD35B PIH1D1
GH19J047607 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 10.1 +559.5 559534 6.9 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B ZNF207 ZNF143 SELENOW ENSG00000269321 ZC3H4 ZNF541 BICRA BSPH1 TPRX2P ELSPBP1 LOC105372430 MEIS3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LIG1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LIG1 gene promoter:
  • GATA-2
  • Nkx2-5
  • MAZR
  • MyoD
  • Elk-1
  • YY1
  • NF-E2 p45
  • NF-E2
  • E2F
  • E2F-1

Genomic Locations for LIG1 Gene

Genomic Locations for LIG1 Gene
55,160 bases
Minus strand
55,159 bases
Minus strand

Genomic View for LIG1 Gene

Genes around LIG1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIG1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIG1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIG1 Gene

Proteins for LIG1 Gene

  • Protein details for LIG1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    DNA ligase 1
    Protein Accession:
    Secondary Accessions:
    • B2RAI8
    • B4DTU4
    • Q2TB12
    • Q32P23

    Protein attributes for LIG1 Gene

    919 amino acids
    Molecular mass:
    101736 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Interacts with PCNA.

    Three dimensional structures from OCA and Proteopedia for LIG1 Gene

    Alternative splice isoforms for LIG1 Gene


neXtProt entry for LIG1 Gene

Post-translational modifications for LIG1 Gene

  • Ubiquitination at posLast=795795, posLast=422422, isoforms=2, 3407, posLast=298298, and isoforms=2, 3226
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LIG1 Gene

Domains & Families for LIG1 Gene

Gene Families for LIG1 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the ATP-dependent DNA ligase family.
  • Belongs to the ATP-dependent DNA ligase family.
genes like me logo Genes that share domains with LIG1: view

Function for LIG1 Gene

Molecular function for LIG1 Gene

UniProtKB/Swiss-Prot Function:
DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + (deoxyribonucleotide)(n)-3-hydroxyl + 5-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.
GENATLAS Biochemistry:
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 Numbers (IUBMB) for LIG1 Gene

Phenotypes From GWAS Catalog for LIG1 Gene

Gene Ontology (GO) - Molecular Function for LIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS,IEA --
GO:0003909 DNA ligase activity TAS --
GO:0003910 DNA ligase (ATP) activity IBA --
GO:0005524 ATP binding IEA --
GO:0016874 ligase activity IEA --
genes like me logo Genes that share ontologies with LIG1: view
genes like me logo Genes that share phenotypes with LIG1: view

Animal Models for LIG1 Gene

MGI Knock Outs for LIG1:

Animal Model Products

miRNA for LIG1 Gene

miRTarBase miRNAs that target LIG1

Clone Products

  • Addgene plasmids for LIG1

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LIG1 Gene

Localization for LIG1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIG1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LIG1 gene
Compartment Confidence
nucleus 5
mitochondrion 3
cytosol 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Golgi apparatus (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 8696349
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IBA --
GO:0005739 mitochondrion IBA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with LIG1: view

Pathways & Interactions for LIG1 Gene

genes like me logo Genes that share pathways with LIG1: view

Pathways by source for LIG1 Gene

1 GeneGo (Thomson Reuters) pathway for LIG1 Gene

SIGNOR curated interactions for LIG1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for LIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006260 DNA replication IEA --
GO:0006266 DNA ligation TAS --
GO:0006273 lagging strand elongation IBA --
GO:0006281 DNA repair TAS 8696349
GO:0006283 transcription-coupled nucleotide-excision repair TAS --
genes like me logo Genes that share ontologies with LIG1: view

Drugs & Compounds for LIG1 Gene

(12) Drugs for LIG1 Gene - From: DrugBank, DGIdb, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Bleomycin Approved, Investigational Pharma Target, inhibitor 162
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved, Investigational Nutra 0
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0
L189 Pharma inhibitor of human DNA ligases I, III and IV, DNA ligase I, III and IV inhibitor 0

(12) Additional Compounds for LIG1 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • [(ho)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • PYROphosphATE

(1) Tocris Compounds for LIG1 Gene

Compound Action Cas Number
L189 DNA ligase I, III and IV inhibitor 64232-83-3
genes like me logo Genes that share compounds with LIG1: view

Transcripts for LIG1 Gene

Unigene Clusters for LIG1 Gene

Ligase I, DNA, ATP-dependent:
Representative Sequences:

Clone Products

  • Addgene plasmids for LIG1

Alternative Splicing Database (ASD) splice patterns (SP) for LIG1 Gene

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: - - - - - -
SP3: - -
SP5: -
SP6: -

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

Relevant External Links for LIG1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LIG1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LIG1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LIG1 Gene

This gene is overexpressed in Fetal Brain (21.7), Lymph node (13.6), and Blymphocyte (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LIG1 Gene

Protein tissue co-expression partners for LIG1 Gene

NURSA nuclear receptor signaling pathways regulating expression of LIG1 Gene:


SOURCE GeneReport for Unigene cluster for LIG1 Gene:


Evidence on tissue expression from TISSUES for LIG1 Gene

  • Blood(4.3)
  • Eye(4.1)
  • Nervous system(3.4)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with LIG1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LIG1 Gene

Orthologs for LIG1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LIG1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LIG1 34 33
  • 97.86 (n)
(Canis familiaris)
Mammalia LIG1 34 33
  • 86.2 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 86 (a)
-- 34
  • 63 (a)
(Bos Taurus)
Mammalia LIG1 34 33
  • 85.68 (n)
(Mus musculus)
Mammalia Lig1 16 34 33
  • 82.39 (n)
(Rattus norvegicus)
Mammalia LOC100911727 33
  • 81.85 (n)
(Monodelphis domestica)
Mammalia LIG1 34
  • 47 (a)
(Gallus gallus)
Aves LIG1 34 33
  • 68.96 (n)
(Anolis carolinensis)
Reptilia LIG1 34
  • 59 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lig1 33
  • 64.13 (n)
African clawed frog
(Xenopus laevis)
Amphibia ligI 33
(Danio rerio)
Actinopterygii si:dkeyp-35b8.5 33
  • 63.6 (n)
LIG1 34
  • 52 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009222 33
  • 61.33 (n)
fruit fly
(Drosophila melanogaster)
Insecta DNA-ligI 34 33
  • 56.52 (n)
CG5602 35
  • 47 (a)
caps 35
  • 30 (a)
trn 35
  • 29 (a)
(Caenorhabditis elegans)
Secernentea lig-1 34 33
  • 52.86 (n)
T21D12.9c 35
  • 32 (a)
T21D12.9b 35
  • 30 (a)
T21D12.9a 35
  • 30 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL155W 33
  • 53.7 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12496g 33
  • 50.28 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CDC9 36 34 33
  • 48.88 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons LIG1 33
  • 53.76 (n)
(Oryza sativa)
Liliopsida Os10g0489200 33
  • 52.91 (n)
Os.8285 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 52 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes cdc17 33
  • 48.89 (n)
Species where no ortholog for LIG1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LIG1 Gene

Gene Tree for LIG1 (if available)
Gene Tree for LIG1 (if available)
Evolutionary constrained regions (ECRs) for LIG1: view image

Paralogs for LIG1 Gene

Paralogs for LIG1 Gene

genes like me logo Genes that share paralogs with LIG1: view

Variants for LIG1 Gene

Sequence variations from dbSNP and Humsavar for LIG1 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs121434560 pathogenic, DNA ligase I deficiency 48,133,011(-) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs121434561 pathogenic, DNA ligase I deficiency 48,121,244(-) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs780324684 A colorectal cancer sample 48,128,007(-) G/A/C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant, stop_gained
rs780748107 A colorectal cancer sample 48,153,884(-) T/C coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs13436 benign, not specified 48,117,779(-) C/G/T coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for LIG1 Gene

Variant ID Type Subtype PubMed ID
dgv1056e212 CNV loss 25503493
esv34181 CNV loss 18971310
esv3583450 CNV loss 25503493
esv3644577 CNV loss 21293372
esv3644578 CNV loss 21293372
nsv1125377 OTHER inversion 24896259
nsv833853 CNV loss 17160897
nsv953596 CNV deletion 24416366
nsv953597 CNV deletion 24416366
nsv9739 CNV gain+loss 18304495

Variation tolerance for LIG1 Gene

Residual Variation Intolerance Score: 22.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.47; 64.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LIG1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIG1 Gene

Disorders for LIG1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for LIG1 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
bloom syndrome
  • blm
achalasia-addisonianism-alacrima syndrome
  • aaa
lig4 syndrome
  • dna ligase iv deficiency
uv-sensitive syndrome
  • uv sensitive syndrome
acoustic neuroma
  • vestibular neurilemmoma
- elite association - COSMIC cancer census association via MalaCards
Search LIG1 in MalaCards View complete list of genes associated with diseases

Genatlas disease for LIG1 Gene

growth retardation,immunodeficiency and predisposition to malignancies,Bloom syndrome-like phenotype

Additional Disease Information for LIG1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LIG1: view

No data available for UniProtKB/Swiss-Prot for LIG1 Gene

Publications for LIG1 Gene

  1. Human DNA ligase I completely encircles and partially unwinds nicked DNA. (PMID: 15565146) Pascal JM … Ellenberger T (Nature 2004) 3 4 22 58
  2. Polymorphism of DNA ligase I and risk of lung cancer--a case-control analysis. (PMID: 12009232) Shen H … Wei Q (Lung cancer (Amsterdam, Netherlands) 2002) 3 22 44 58
  3. Assignment of the gene encoding DNA ligase I to human chromosome 19q13.2-13.3. (PMID: 1733856) Barnes DE … Mohrenweiser HW (Genomics 1992) 2 3 22 58
  4. Mutations in the DNA ligase I gene of an individual with immunodeficiencies and cellular hypersensitivity to DNA-damaging agents. (PMID: 1581963) Barnes DE … Lindahl T (Cell 1992) 3 4 22 58
  5. A wild-type DNA ligase I gene is expressed in Bloom's syndrome cells. (PMID: 1881902) Petrini JH … Weaver DT (Proceedings of the National Academy of Sciences of the United States of America 1991) 3 4 22 58

Products for LIG1 Gene