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 ... See more...

Aliases for LIG1 Gene

Aliases for LIG1 Gene

  • DNA Ligase 1 2 3 4 5
  • Polydeoxyribonucleotide Synthase [ATP] 1 3 4
  • Ligase I, DNA, ATP-Dependent 2 3
  • EC 6.5.1.1 4 51
  • DNA Ligase I 4
  • LIG1 5

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 Xeroderma Pigmentosum, Variant Type. Among its related pathways are Transcription-Coupled Nucleotide Excision Repair (TC-NER) and Telomere C-strand (Lagging Strand) Synthesis. 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 Summary 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 , Rfam classification and piRNA Summary for LIG1 Gene

Genomics for LIG1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LIG1 Gene
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LIG1

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

Genomic Locations for LIG1 Gene

Genomic Locations for LIG1 Gene
chr19:48,115,445-48,170,603
(GRCh38/hg38)
Size:
55,159 bases
Orientation:
Minus strand
chr19:48,618,702-48,673,860
(GRCh37/hg19)
Size:
55,159 bases
Orientation:
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:
    P18858-DNLI1_HUMAN
    Recommended name:
    DNA ligase 1
    Protein Accession:
    P18858
    Secondary Accessions:
    • B2RAI8
    • B4DTU4
    • Q2TB12
    • Q32P23

    Protein attributes for LIG1 Gene

    Size:
    919 amino acids
    Molecular mass:
    101736 Da
    Cofactor:
    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

    UniProtKB/Swiss-Prot:

neXtProt entry for LIG1 Gene

Selected DME Specific Peptides for LIG1 Gene

P18858:
  • ICKLGTGFS
  • VWEVKCADL
  • MILKQTFCE
  • KYPDIISRIPKIK
  • GLAEQSVL
  • EKKQIQPFQVLTTRKRK
  • NWLKLKKDY
  • TARKQLPKR
  • KAVAQATGRQLE
  • RFPRFIR

Post-translational modifications for LIG1 Gene

  • Ubiquitination at Lys226, Lys298, Lys407, and Lys795
  • Modification sites at PhosphoSitePlus

Antibody Products

Domains & Families for LIG1 Gene

Gene Families for LIG1 Gene

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

Suggested Antigen Peptide Sequences for LIG1 Gene

GenScript: Design optimal peptide antigens:
  • DNA ligase (B4DTU4_HUMAN)
  • cDNA FLJ52385, highly similar to DNA ligase 1 (EC 6.5.1.1) (B4E135_HUMAN)
  • Polydeoxyribonucleotide synthase [ATP] 1 (DNLI1_HUMAN)
  • DNA ligase (F5GZ28_HUMAN)
  • DNA ligase (Q2TB12_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P18858

UniProtKB/Swiss-Prot:

DNLI1_HUMAN :
  • Belongs to the ATP-dependent DNA ligase family.
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:
Reaction=ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.; EC=6.5.1.1; Evidence={ECO:0000255|PROSITE-ProRule:PRU10135};.
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:0000166 nucleotide binding IEA --
GO:0003677 DNA binding TAS,IEA --
GO:0003909 DNA ligase activity TAS --
GO:0003910 DNA ligase (ATP) activity IBA 21873635
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

CRISPR Products

miRNA for LIG1 Gene

miRTarBase miRNAs that target LIG1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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

COMPARTMENTS
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 4
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
golgi apparatus 1

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,IBA 21873635
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IBA 21873635
GO:0005739 mitochondrion IBA 21873635
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
  • Cell cycle Transition and termination of DNA replication
2 Qiagen pathways for LIG1 Gene
  • DNA Repair Mechanisms
  • Nucleotide Excision Repair Pathway

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 21873635
GO:0006281 NOT DNA repair TAS,IBA 21873635
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, ApexBio, DGIdb, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Bleomycin Approved, Investigational Pharma Target, inhibitor 172
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved, Investigational Nutra 0
ATP Investigational Nutra Agonist, Activator, Partial agonist, Antagonist, Full agonist, Gating inhibitor, Pore Blocker, Potentiation 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
pyrophosphate
  • [(ho)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • PYROphosphATE
14000-31-8

(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

Drug Products

Transcripts for LIG1 Gene

mRNA/cDNA for LIG1 Gene

5 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
21 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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: - - - - - -
SP2:
SP3: - -
SP4:
SP5: -
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:

ExUns: 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30 ^ 31
SP1: - - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for LIG1 Gene

GeneLoc Exon Structure for
LIG1

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, MaxQB, and MOPED for LIG1 Gene



Protein tissue co-expression partners for LIG1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LIG1

SOURCE GeneReport for Unigene cluster for LIG1 Gene:

Hs.1770

Evidence on tissue expression from TISSUES for LIG1 Gene

  • Blood(4.5)
  • Eye(4.1)
  • Nervous system(3.9)
  • Skin(2.7)
  • Intestine(2.5)
  • Bone marrow(2.3)
  • Liver(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
Chimpanzee
(Pan troglodytes)
Mammalia LIG1 30 31
  • 97.86 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LIG1 30 31
  • 86.2 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 86 (a)
OneToMany
-- 31
  • 63 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia LIG1 30 31
  • 85.68 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lig1 30 17 31
  • 82.39 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia LOC100911727 30
  • 81.85 (n)
Oppossum
(Monodelphis domestica)
Mammalia LIG1 31
  • 47 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LIG1 30 31
  • 68.96 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LIG1 31
  • 59 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lig1 30
  • 64.13 (n)
African clawed frog
(Xenopus laevis)
Amphibia ligI 30
Zebrafish
(Danio rerio)
Actinopterygii si:dkeyp-35b8.5 30
  • 63.6 (n)
LIG1 31
  • 52 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009222 30
  • 61.33 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta DNA-ligI 30 31
  • 56.52 (n)
OneToOne
CG5602 32
  • 47 (a)
caps 32
  • 30 (a)
trn 32
  • 29 (a)
Worm
(Caenorhabditis elegans)
Secernentea lig-1 30 31
  • 52.86 (n)
OneToOne
T21D12.9c 32
  • 32 (a)
T21D12.9a 32
  • 30 (a)
T21D12.9b 32
  • 30 (a)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ACL155W 30
  • 53.7 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12496g 30
  • 50.28 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CDC9 30 31 33
  • 48.88 (n)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons LIG1 30
  • 53.76 (n)
Rice
(Oryza sativa)
Liliopsida Os10g0489200 30
  • 52.91 (n)
Os.8285 30
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 52 (a)
OneToOne
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes cdc17 30
  • 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for LIG1 (if available)
TreeFam:
Gene Tree for LIG1 (if available)
Aminode:
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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LIG1 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
638467 Uncertain Significance: not provided 48,123,255(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
729211 Likely Benign: not provided 48,137,068(-) A/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
734140 Benign: not provided 48,161,475(-) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
764888 Likely Benign: not provided 48,137,570(-) G/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
773085 Benign: not provided 48,121,298(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for LIG1 Gene

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)
LIG1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIG1

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

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

- 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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 23
  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 23 41
  3. 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 23
  4. 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 23
  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 23

Products for LIG1 Gene