This gene is a member of the DNA ligase family. Each member of this family encodes a protein that catalyzes the joining of DNA ends but they each have a distinct role in DNA metabolism. The protein encoded by this gene is involved in excision repair and is located in both the mitochondria and nucleus, with translation initiation from the upstream start codon allowing for transp... See more...

Aliases for LIG3 Gene

Aliases for LIG3 Gene

  • DNA Ligase 3 2 3 4 5
  • Polydeoxyribonucleotide Synthase [ATP] 3 3 4
  • Ligase III, DNA, ATP-Dependent 2 3
  • Ligase II, DNA, ATP-Dependent 2 3
  • EC 6.5.1.1 4 51
  • LIG3alpha 2 3
  • DNA Ligase III 4
  • LIG2 3
  • LIG3 5

External Ids for LIG3 Gene

Previous HGNC Symbols for LIG3 Gene

  • LIG2

Previous GeneCards Identifiers for LIG3 Gene

  • GC17P033077
  • GC17P035343
  • GC17P033453
  • GC17P030331
  • GC17P033307
  • GC17P029493

Summaries for LIG3 Gene

Entrez Gene Summary for LIG3 Gene

  • This gene is a member of the DNA ligase family. Each member of this family encodes a protein that catalyzes the joining of DNA ends but they each have a distinct role in DNA metabolism. The protein encoded by this gene is involved in excision repair and is located in both the mitochondria and nucleus, with translation initiation from the upstream start codon allowing for transport to the mitochondria and translation initiation from a downstream start codon allowing for transport to the nucleus. Additionally, alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

GeneCards Summary for LIG3 Gene

LIG3 (DNA Ligase 3) is a Protein Coding gene. Diseases associated with LIG3 include Bloom Syndrome and Vaginal Carcinosarcoma. 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 LIG1.

UniProtKB/Swiss-Prot Summary for LIG3 Gene

  • Isoform 3 functions as heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. Isoform 1 is targeted to mitochondria, where it functions as DNA ligase in mitochondrial base-excision DNA repair (PubMed:10207110, PubMed:24674627).

Tocris Summary for LIG3 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.

Additional gene information for LIG3 Gene

No data available for CIViC Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LIG3 Gene

Genomics for LIG3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LIG3 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 LIG3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LIG3

Top Transcription factor binding sites by QIAGEN in the LIG3 gene promoter:
  • AML1a
  • FOXO3
  • FOXO3a
  • LyF-1
  • p53
  • Pax-2
  • Pax-2a

Genomic Locations for LIG3 Gene

Genomic Locations for LIG3 Gene
chr17:34,980,498-35,009,743
(GRCh38/hg38)
Size:
29,246 bases
Orientation:
Plus strand
chr17:33,307,513-33,332,088
(GRCh37/hg19)
Size:
24,576 bases
Orientation:
Plus strand

Genomic View for LIG3 Gene

Genes around LIG3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIG3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIG3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIG3 Gene

Proteins for LIG3 Gene

  • Protein details for LIG3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P49916-DNLI3_HUMAN
    Recommended name:
    DNA ligase 3
    Protein Accession:
    P49916
    Secondary Accessions:
    • E5KLB5
    • E5KLB6
    • Q16714
    • Q6NVK3

    Protein attributes for LIG3 Gene

    Size:
    1009 amino acids
    Molecular mass:
    112907 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Isoform 3 interacts (via BRCT domain) with the nuclear DNA-repair protein XRCC1.
    Miscellaneous:
    • [Isoform 1]: Produced by alternative splicing.
    • [Isoform 2]: Produced by alternative splicing.
    • [Isoform 3]: Produced by alternative initiation of isoform 1.
    • [Isoform 4]: Produced by alternative initiation of isoform 2.

    Three dimensional structures from OCA and Proteopedia for LIG3 Gene

    Alternative splice isoforms for LIG3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LIG3 Gene

Selected DME Specific Peptides for LIG3 Gene

P49916:
  • PVQPMLA
  • DGERVQVH

Post-translational modifications for LIG3 Gene

  • Ubiquitination at Lys728 and Lys765
  • Modification sites at PhosphoSitePlus

Domains & Families for LIG3 Gene

Gene Families for LIG3 Gene

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

Protein Domains for LIG3 Gene

Suggested Antigen Peptide Sequences for LIG3 Gene

GenScript: Design optimal peptide antigens:
  • Ligase III, DNA, ATP-dependent (C4B7Q3_HUMAN)
  • Polydeoxyribonucleotide synthase [ATP] 3 (DNLI3_HUMAN)
  • DNA ligase (E5KLB6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P49916

UniProtKB/Swiss-Prot:

DNLI3_HUMAN :
  • The PARP-type zinc finger is required for DNA ligase activity.
  • Belongs to the ATP-dependent DNA ligase family.
Domain:
  • The PARP-type zinc finger is required for DNA ligase activity.
Family:
  • Belongs to the ATP-dependent DNA ligase family.
genes like me logo Genes that share domains with LIG3: view

Function for LIG3 Gene

Molecular function for LIG3 Gene

UniProtKB/Swiss-Prot Function:
Isoform 3 functions as heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. Isoform 1 is targeted to mitochondria, where it functions as DNA ligase in mitochondrial base-excision DNA repair (PubMed:10207110, PubMed:24674627).
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, ECO:0000269|PubMed:10207110, ECO:0000269|PubMed:20518483};.
GENATLAS Biochemistry:
DNA ligase III,ATP-dependent,103kDa,complexing with LIG3,involved in DNA replication,recombination and DNA repair,highly expressed in testes

Enzyme Numbers (IUBMB) for LIG3 Gene

Phenotypes From GWAS Catalog for LIG3 Gene

Gene Ontology (GO) - Molecular Function for LIG3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003677 DNA binding IEA --
GO:0003909 DNA ligase activity TAS --
GO:0003910 DNA ligase (ATP) activity IEA,IBA 21873635
GO:0005515 protein binding IPI 15744309
genes like me logo Genes that share ontologies with LIG3: view
genes like me logo Genes that share phenotypes with LIG3: view

Animal Models for LIG3 Gene

MGI Knock Outs for LIG3:
  • Lig3 Lig3<tm1Czhu>

Animal Model Products

  • Taconic Biosciences Mouse Models for LIG3

CRISPR Products

miRNA for LIG3 Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIG3

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LIG3 Gene

Localization for LIG3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIG3 Gene

[Isoform 1]: Mitochondrion. Note=Contains an N-terminal mitochondrial transit peptide. {ECO:0000269 PubMed:10207110}.
[Isoform 2]: Mitochondrion. Note=Contains an N-terminal mitochondrial transit peptide. {ECO:0000305 PubMed:10207110}.
[Isoform 3]: Nucleus. Note=Lacks the N-terminal mitochondrial transit peptide. {ECO:0000269 PubMed:10207110}.
[Isoform 4]: Nucleus. Note=Lacks the N-terminal mitochondrial transit peptide. {ECO:0000305 PubMed:10207110}.

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 LIG3 gene
Compartment Confidence
nucleus 5
mitochondrion 4
plasma membrane 2
extracellular 2
cytoskeleton 2
cytosol 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LIG3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005654 nucleoplasm IDA,TAS --
GO:0005737 cytoplasm IBA 21873635
GO:0005739 mitochondrion IBA --
GO:0070421 DNA ligase III-XRCC1 complex IBA 21873635
genes like me logo Genes that share ontologies with LIG3: view

Pathways & Interactions for LIG3 Gene

genes like me logo Genes that share pathways with LIG3: view

Pathways by source for LIG3 Gene

2 Qiagen pathways for LIG3 Gene
  • DNA Repair Mechanisms
  • Nucleotide Excision Repair Pathway

SIGNOR curated interactions for LIG3 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for LIG3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination TAS --
GO:0006260 DNA replication IEA --
GO:0006266 DNA ligation IEA,IBA 21873635
GO:0006273 lagging strand elongation IBA 21873635
GO:0006281 DNA repair IEA,IBA 21873635
genes like me logo Genes that share ontologies with LIG3: view

Drugs & Compounds for LIG3 Gene

(9) Drugs for LIG3 Gene - From: DrugBank, PharmGKB, ApexBio, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Bleomycin Approved, Investigational Pharma Target, inhibitor 172
Cisplatin Approved Pharma Inhibits DNA synthesis,chemotherapy drug, Potent pro-apoptotic anticancer agent; activates caspase-3, Platinum 3412
Cyclophosphamide Approved, Investigational Pharma Nitrogen mustard alkylating agent and prodrug. 3670
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved, Investigational Nutra 0

(6) Additional Compounds for LIG3 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 LIG3 Gene

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

(1) ApexBio Compounds for LIG3 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 LIG3: view

Drug Products

Transcripts for LIG3 Gene

mRNA/cDNA for LIG3 Gene

2 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
16 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 LIG3

Alternative Splicing Database (ASD) splice patterns (SP) for LIG3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^
SP1: - - - - -
SP2: - - - - -
SP3: - - - - -
SP4:
SP5:
SP6: -
SP7: -
SP8:

ExUns: 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for LIG3 Gene

GeneLoc Exon Structure for
LIG3

Expression for LIG3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LIG3 Gene

Protein differential expression in normal tissues from HIPED for LIG3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (15.9) and Pancreas (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LIG3 Gene



Protein tissue co-expression partners for LIG3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LIG3

SOURCE GeneReport for Unigene cluster for LIG3 Gene:

Hs.100299

mRNA Expression by UniProt/SwissProt for LIG3 Gene:

P49916-DNLI3_HUMAN
Tissue specificity: Testis, thymus, prostate and heart.

Evidence on tissue expression from TISSUES for LIG3 Gene

  • Pancreas(4.4)
  • Nervous system(3.5)
  • Skin(2.9)
  • Blood(2.9)
  • Kidney(2.6)
  • Muscle(2.6)
  • Intestine(2.6)
  • Heart(2.5)
  • Liver(2.5)
  • Bone marrow(2.5)
  • Thyroid gland(2.3)
  • Lung(2.3)
  • Spleen(2.3)
  • Eye(2.2)
  • Lymph node(2.1)
  • Gall bladder(2)
genes like me logo Genes that share expression patterns with LIG3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for LIG3 Gene

Orthologs for LIG3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for LIG3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LIG3 30 31
  • 99.7 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LIG3 30 31
  • 89.18 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LIG3 30 31
  • 88.49 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lig3 30
  • 88.14 (n)
Mouse
(Mus musculus)
Mammalia Lig3 30 17 31
  • 87.64 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LIG3 31
  • 78 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LIG3 31
  • 53 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LIG3 30 31
  • 74.1 (n)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lig3 30
  • 69.73 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC398275 30
Zebrafish
(Danio rerio)
Actinopterygii lig3 30 31
  • 67.9 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta lig3 30 31
  • 54.2 (n)
OneToOne
CG17227 32
  • 45 (a)
Worm
(Caenorhabditis elegans)
Secernentea K07C5.3 32
  • 28 (a)
lig-4 31
  • 15 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DNL4 31
  • 13 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 53 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.12130 30
Species where no ortholog for LIG3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • 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 (Oryza sativa)
  • 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)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for LIG3 Gene

ENSEMBL:
Gene Tree for LIG3 (if available)
TreeFam:
Gene Tree for LIG3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LIG3: view image

Paralogs for LIG3 Gene

Paralogs for LIG3 Gene

(1) SIMAP similar genes for LIG3 Gene using alignment to 8 proteins:

  • DNLI3_HUMAN
  • C4B7Q3_HUMAN
  • E5KLB6_HUMAN
  • K7EJR4_HUMAN
  • K7ELY6_HUMAN
  • K7ENR9_HUMAN
  • K7EQB6_HUMAN
  • K7ERZ5_HUMAN
genes like me logo Genes that share paralogs with LIG3: view

Variants for LIG3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LIG3 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
715083 Benign: not provided 34,992,620(+) G/A SYNONYMOUS_VARIANT
717561 Likely Benign: not provided 35,002,795(+) G/A INTRON_VARIANT
782153 Benign: not provided 34,986,110(+) C/T MISSENSE_VARIANT
rs114522796 Benign: not provided 35,001,292(+) C/T SYNONYMOUS_VARIANT
rs1319167353 Uncertain Significance: not provided 35,004,499(+) C/T MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for LIG3 Gene

Structural Variations from Database of Genomic Variants (DGV) for LIG3 Gene

Variant ID Type Subtype PubMed ID
esv3640436 CNV loss 21293372
nsv2035 CNV deletion 18451855
nsv472770 CNV novel sequence insertion 20440878
nsv960095 CNV duplication 23825009

Variation tolerance for LIG3 Gene

Residual Variation Intolerance Score: 6.69% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.54; 44.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LIG3 Gene

Human Gene Mutation Database (HGMD)
LIG3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIG3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIG3 Gene

Disorders for LIG3 Gene

MalaCards: The human disease database

(26) MalaCards diseases for LIG3 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
bloom syndrome
  • bls
vaginal carcinosarcoma
  • malignant vaginal mixed epithelial and mesenchymal tumor
vaginal adenosarcoma
lymphoid interstitial pneumonia
  • lip
chronic inflammation of lacrimal passage
- elite association - COSMIC cancer census association via MalaCards
Search LIG3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LIG3

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 LIG3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LIG3 Gene

Publications for LIG3 Gene

  1. Molecular cloning and expression of human cDNAs encoding a novel DNA ligase IV and DNA ligase III, an enzyme active in DNA repair and recombination. (PMID: 7760816) Wei YF … Schär P (Molecular and cellular biology 1995) 2 3 4 23
  2. Mammalian DNA ligase III: molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination. (PMID: 7565692) Chen J … Husain I (Molecular and cellular biology 1995) 3 4 23
  3. Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair. (PMID: 24674627) Akbari M … Bohr VA (DNA repair 2014) 3 4
  4. Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing. (PMID: 20843780) Wang W … Scharfe C (Nucleic acids research 2011) 3 4
  5. Comprehensive screen of genetic variation in DNA repair pathway genes and postmenopausal breast cancer risk. (PMID: 20496165) Monsees GM … Han J (Breast cancer research and treatment 2011) 3 41

Products for LIG3 Gene

  • Signalway ELISA kits for LIG3
  • Signalway Proteins for LIG3

Sources for LIG3 Gene