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Aliases for LIG1 Gene

Aliases for LIG1 Gene

  • DNA Ligase 1 2 3 5
  • EC 4 61
  • Polydeoxyribonucleotide Synthase [ATP] 1 4
  • Ligase I, DNA, ATP-Dependent 2
  • DNA Ligase I 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 Vaccinia. Among its related pathways are Regulation of activated PAK-2p34 by proteasome mediated degradation and Chromosome Maintenance. 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

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

Genomics for LIG1 Gene

Regulatory Elements for LIG1 Gene

Enhancers for LIG1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19F048190 0.6 ENCODE 17 -20.0 -20026 0.8 FEZF1 RAD21 ZNF366 ZNF207 FOS CREM SP3 NFYA NFYC USF2 PLA2G4C LIG1 ENSG00000280353 ZNF114
GH19F048196 1.1 Ensembl 12.6 -26.5 -26498 0.6 MAZ FOSL1 ZFHX2 ZNF366 NCOR1 IKZF1 ZBTB33 KDM1A TRIM24 MLLT1 C19orf68 LIG1 ENSG00000280353 ZNF114
GH19F048368 0.4 ENCODE 10.2 -198.5 -198507 1.0 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 ZNF2 YY1 SLC30A9 ZNF766 CCDC114 CD37 CABP5 LIG1 SYNGR4 GRIN2D
GH19F048121 0.7 ENCODE 10.1 +47.6 47575 3.8 HDGF ATF1 PKNOX1 CREB3L1 ARID4B SIN3A YY1 SLC30A9 GLIS2 ZNF143 PLA2G4C LIG1 ENSG00000269534 ENSG00000269321
GH19F047728 0.2 ENCODE 10.1 +440.9 440945 3.1 PKNOX1 ARID4B SIN3A GLI4 ZNF2 GLIS2 ELK1 GATA2 FOS SP3 CCDC9 SELENOW CABP5 C5AR2 LIG1 GLTSCR2 KPTN PIR33748 GC19M047700
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around LIG1 on UCSC Golden Path with GeneCards custom track

Promoters for LIG1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for LIG1 Gene

48,115,444 bp from pter
48,170,603 bp from pter
55,160 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

Selected DME Specific Peptides for LIG1 Gene


Post-translational modifications for LIG1 Gene

  • Ubiquitination at Lys 226, Lys 298, Lys 407, Lys 422, and Lys 795
  • Modification sites at PhosphoSitePlus

Domains & Families for LIG1 Gene

Gene Families for LIG1 Gene

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

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

Enzyme Numbers (IUBMB) for LIG1 Gene

Gene Ontology (GO) - Molecular Function for LIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003909 DNA ligase activity IEA,TAS --
GO:0003910 DNA ligase (ATP) activity IEA,IBA --
GO:0003950 NAD+ ADP-ribosyltransferase activity IEA --
GO:0005524 ATP binding 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

Inhibitory RNA Products

Flow Cytometry Products

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

Jensen Localization Image for LIG1 Gene COMPARTMENTS Subcellular localization image for LIG1 gene
Compartment Confidence
golgi apparatus 5
nucleus 5
mitochondrion 4
cytosol 2

Gene Ontology (GO) - Cellular Components for LIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,TAS 8696349
GO:0005654 nucleoplasm IDA,TAS --
GO:0005739 mitochondrion IBA --
GO:0005794 Golgi apparatus IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with LIG1: view

Pathways & Interactions for LIG1 Gene

SuperPathways for LIG1 Gene

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

Pathways by source 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:0000722 telomere maintenance via recombination TAS --
GO:0006259 DNA metabolic process TAS 2204063
GO:0006260 DNA replication IEA --
GO:0006266 DNA ligation IEA --
GO:0006281 DNA repair IEA,TAS 8696349
genes like me logo Genes that share ontologies with LIG1: view

Drugs & Compounds for LIG1 Gene

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Bleomycin Approved Pharma Target, inhibitor 153
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved Nutra 0
Adenosine triphosphate Approved Nutra 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
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi

(1) Tocris Compounds for LIG1 Gene

Compound Action Cas Number
L189 DNA ligase I, III and IV inhibitor 64232-83-3

(1) ApexBio Compounds for LIG1 Gene

Compound Action Cas Number
L189 inhibitor of human DNA ligases I, III and IV 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:

Inhibitory RNA Products

Flow Cytometry Products

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 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, PaxDb, 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:

genes like me logo Genes that share expression patterns with LIG1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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 35
  • 97.86 (n)
(Canis familiaris)
Mammalia LIG1 34 35
  • 86.2 (n)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 86 (a)
-- 35
  • 63 (a)
(Bos Taurus)
Mammalia LIG1 34 35
  • 85.68 (n)
(Mus musculus)
Mammalia Lig1 34 16 35
  • 82.39 (n)
(Rattus norvegicus)
Mammalia LOC100911727 34
  • 81.85 (n)
(Monodelphis domestica)
Mammalia LIG1 35
  • 47 (a)
(Gallus gallus)
Aves LIG1 34 35
  • 68.96 (n)
(Anolis carolinensis)
Reptilia LIG1 35
  • 59 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lig1 34
  • 64.13 (n)
African clawed frog
(Xenopus laevis)
Amphibia ligI 34
(Danio rerio)
Actinopterygii si:dkeyp-35b8.5 34
  • 63.6 (n)
LIG1 35
  • 52 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009222 34
  • 61.33 (n)
fruit fly
(Drosophila melanogaster)
Insecta DNA-ligI 34 35
  • 56.52 (n)
CG5602 36
  • 47 (a)
caps 36
  • 30 (a)
trn 36
  • 29 (a)
(Caenorhabditis elegans)
Secernentea lig-1 34 35
  • 52.86 (n)
T21D12.9c 36
  • 32 (a)
T21D12.9a 36
  • 30 (a)
T21D12.9b 36
  • 30 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL155W 34
  • 53.7 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12496g 34
  • 50.28 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CDC9 34 35 37
  • 48.88 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons LIG1 34
  • 53.76 (n)
(Oryza sativa)
Liliopsida Os10g0489200 34
  • 52.91 (n)
Os.8285 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 52 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes cdc17 34
  • 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)

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 Sequence Context AA Info Type
rs780324684 A colorectal cancer sample 48,128,007(+) TGACC(A/G/T)ATGGG nc-transcript-variant, reference, missense, stop-gained
rs780748107 A colorectal cancer sample 48,153,884(+) CTCCT(C/T)CTTCC intron-variant, nc-transcript-variant, reference, missense
rs121434560 Pathogenic 48,133,011(-) CCTGC(A/G)AATAC nc-transcript-variant, reference, missense
rs121434561 Pathogenic 48,121,244(-) GGAAG(C/T)GGGCC nc-transcript-variant, reference, missense
rs102347 -- 48,130,277(-) GTGAC(A/G)GAGAG intron-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)

Relevant External Links for LIG1 Gene

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

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: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
bloom syndrome
  • bloom-torre-machacek syndrome
achalasia-addisonianism-alacrimia syndrome
  • triple-a syndrome
lig4 syndrome
  • dna ligase iv deficiency
uv-sensitive syndrome
  • uv sensitive syndrome
- 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

Relevant External Links for LIG1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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 J.M. … Ellenberger T. (Nature 2004) 3 4 22 64
  2. Polymorphism of DNA ligase I and risk of lung cancer--a case-control analysis. (PMID: 12009232) Shen H. … Wei Q. (Lung Cancer 2002) 3 22 46 64
  3. Assignment of the gene encoding DNA ligase I to human chromosome 19q13.2-13.3. (PMID: 1733856) Barnes D.E. … Mohrenweiser H.W. (Genomics 1992) 2 3 22 64
  4. Mutations in the DNA ligase I gene of an individual with immunodeficiencies and cellular hypersensitivity to DNA-damaging agents. (PMID: 1581963) Barnes D.E. … Lindahl T. (Cell 1992) 3 4 22 64
  5. A wild-type DNA ligase I gene is expressed in Bloom's syndrome cells. (PMID: 1881902) Petrini J.H.J. … Weaver D.T. (Proc. Natl. Acad. Sci. U.S.A. 1991) 3 4 22 64

Products for LIG1 Gene

Sources for LIG1 Gene

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