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Aliases for LIG4 Gene

Aliases for LIG4 Gene

  • DNA Ligase 4 2 3
  • Polydeoxyribonucleotide Synthase [ATP] 4 2 3 4
  • Ligase IV, DNA, ATP-Dependent 2 3 5
  • Polynucleotide Ligase 2 3
  • DNA Repair Enzyme 2 3
  • DNA Ligase IV 3 4
  • DNA Joinase 2 3
  • EC 6.5.1.1 4 63
  • Sealase 2 3
  • LIG4S 3

External Ids for LIG4 Gene

Previous GeneCards Identifiers for LIG4 Gene

  • GC13M107220
  • GC13M103247
  • GC13M107696
  • GC13M106558
  • GC13M107657
  • GC13M108859
  • GC13M089450

Summaries for LIG4 Gene

Entrez Gene Summary for LIG4 Gene

  • The protein encoded by this gene is a DNA ligase that joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. This protein is essential for V(D)J recombination and DNA double-strand break (DSB) repair through nonhomologous end joining (NHEJ). This protein forms a complex with the X-ray repair cross complementing protein 4 (XRCC4), and further interacts with the DNA-dependent protein kinase (DNA-PK). Both XRCC4 and DNA-PK are known to be required for NHEJ. The crystal structure of the complex formed by this protein and XRCC4 has been resolved. Defects in this gene are the cause of LIG4 syndrome. Alternatively spliced transcript variants encoding the same protein have been observed. [provided by RefSeq, Jul 2008]

GeneCards Summary for LIG4 Gene

LIG4 (DNA Ligase 4) is a Protein Coding gene. Diseases associated with LIG4 include lig4 syndrome and multiple myeloma. Among its related pathways are HIV Life Cycle and Infectious disease. GO annotations related to this gene include ligase activity and DNA ligase activity.

UniProtKB/Swiss-Prot for LIG4 Gene

  • Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.

Tocris Summary for LIG4 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 LIG4 Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIG4 Gene

Genomics for LIG4 Gene

Regulatory Elements for LIG4 Gene

Promoters for LIG4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around LIG4 on UCSC Golden Path with GeneCards custom track

Genomic Location for LIG4 Gene

Chromosome:
13
Start:
108,207,439 bp from pter
End:
108,218,368 bp from pter
Size:
10,930 bases
Orientation:
Minus strand

Genomic View for LIG4 Gene

Genes around LIG4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIG4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIG4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIG4 Gene

Proteins for LIG4 Gene

  • Protein details for LIG4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P49917-DNLI4_HUMAN
    Recommended name:
    DNA ligase 4
    Protein Accession:
    P49917
    Secondary Accessions:
    • Q8IY66
    • Q8TEU5

    Protein attributes for LIG4 Gene

    Size:
    911 amino acids
    Molecular mass:
    103971 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Interacts with XRCC4. The LIG4-XRCC4 complex has probably a 1:2 stoichiometry. The LIG4-XRCC4 complex associates in a DNA-dependent manner with the DNA-PK complex composed of PRKDC, XRCC6/Ku70 and XRCC5/Ku86 to form the core non-homologous end joining (NHEJ) complex. Additional components of the NHEJ complex include NHEJ1/XLF and C9orf142/PAXX. Interacts with APLF.
    SequenceCaution:
    • Sequence=AAL77435.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAA58467.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LIG4 Gene

neXtProt entry for LIG4 Gene

Proteomics data for LIG4 Gene at MOPED

Post-translational modifications for LIG4 Gene

  • Ubiquitination at Lys 184
  • Modification sites at PhosphoSitePlus

Other Protein References for LIG4 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for LIG4 (LIG4)

Domains & Families for LIG4 Gene

Gene Families for LIG4 Gene

Suggested Antigen Peptide Sequences for LIG4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P49917

UniProtKB/Swiss-Prot:

DNLI4_HUMAN :
  • Contains 2 BRCT domains.
  • Belongs to the ATP-dependent DNA ligase family.
Domain:
  • Contains 2 BRCT domains.
Family:
  • Belongs to the ATP-dependent DNA ligase family.
genes like me logo Genes that share domains with LIG4: view

Function for LIG4 Gene

Molecular function for LIG4 Gene

GENATLAS Biochemistry:
DNA ligase IV,ATP-dependent,96kDa,the ligation responsible for DNA double-strand breaks repair by end joining (non homologous recombination) and V(D)J recombination
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
UniProtKB/Swiss-Prot Function:
Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.

Enzyme Numbers (IUBMB) for LIG4 Gene

genes like me logo Genes that share phenotypes with LIG4: view

Human Phenotype Ontology for LIG4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LIG4 Gene

MGI Knock Outs for LIG4:

Animal Model Products

miRNA for LIG4 Gene

miRTarBase miRNAs that target LIG4

No data available for Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for LIG4 Gene

Localization for LIG4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIG4 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LIG4 Gene COMPARTMENTS Subcellular localization image for LIG4 gene
Compartment Confidence
nucleus 5
plasma membrane 5
cytosol 3
cytoskeleton 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for LIG4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000793 condensed chromosome IDA 12589063
GO:0005654 nucleoplasm TAS --
GO:0070419 nonhomologous end joining complex IDA 20383123
genes like me logo Genes that share ontologies with LIG4: view

Pathways & Interactions for LIG4 Gene

genes like me logo Genes that share pathways with LIG4: view

Pathways by source for LIG4 Gene

1 KEGG pathway for LIG4 Gene
1 GeneGo (Thomson Reuters) pathway for LIG4 Gene

SIGNOR curated interactions for LIG4 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for LIG4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development ISS --
GO:0002328 pro-B cell differentiation ISS --
GO:0006260 DNA replication IEA --
GO:0006281 DNA repair IEA --
GO:0006297 nucleotide-excision repair, DNA gap filling IDA 12517771
genes like me logo Genes that share ontologies with LIG4: view

Drugs & Compounds for LIG4 Gene

(6) Drugs for LIG4 Gene - From: HMDB, ApexBio, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine monophosphate Approved Nutra 0
Adenosine triphosphate Approved Nutra 0
Diphosphate Experimental Pharma 0
SCR7 Pharma DNA ligase IV inhibitor 0

(7) Additional Compounds for LIG4 Gene - From: Tocris, Novoseek, and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
phosphoric acid
  • Acide phosphorique (FRENCH)
  • Acido fosforico [Italian]
  • Acidum phosphoricum
  • Diphosphate tetrasodium
  • Fosforzuuroplossingen [Dutch]
7664-38-2
L189
64232-83-3

(1) Tocris Compounds for LIG4 Gene

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

(1) ApexBio Compounds for LIG4 Gene

Compound Action Cas Number
SCR7 DNA ligase IV inhibitor 1533426-72-0
genes like me logo Genes that share compounds with LIG4: view

Transcripts for LIG4 Gene

Unigene Clusters for LIG4 Gene

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

Alternative Splicing Database (ASD) splice patterns (SP) for LIG4 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4a · 4b · 4c · 4d
SP1: -
SP2:
SP3: - -
SP4: - - - - - -

Relevant External Links for LIG4 Gene

GeneLoc Exon Structure for
LIG4
ECgene alternative splicing isoforms for
LIG4

Expression for LIG4 Gene

mRNA expression in normal human tissues for LIG4 Gene

Protein differential expression in normal tissues from HIPED for LIG4 Gene

This gene is overexpressed in Pancreas (24.0), Bone (18.0), and Blymphocyte (9.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for LIG4 Gene



SOURCE GeneReport for Unigene cluster for LIG4 Gene Hs.166091

mRNA Expression by UniProt/SwissProt for LIG4 Gene

P49917-DNLI4_HUMAN
Tissue specificity: Testis, thymus, prostate and heart.
genes like me logo Genes that share expression patterns with LIG4: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for LIG4 Gene

Orthologs for LIG4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LIG4 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LIG4 35
  • 85.14 (n)
  • 89.24 (a)
LIG4 36
  • 89 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LIG4 35
  • 89.39 (n)
  • 91 (a)
LIG4 36
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lig4 35
  • 82.58 (n)
  • 87.05 (a)
Lig4 16
Lig4 36
  • 87 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LIG4 35
  • 99.27 (n)
  • 99.45 (a)
LIG4 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lig4 35
  • 82.55 (n)
  • 86.17 (a)
oppossum
(Monodelphis domestica)
Mammalia LIG4 36
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 26 (a)
ManyToMany
chicken
(Gallus gallus)
Aves LIG4 35
  • 75.04 (n)
  • 77.11 (a)
LIG4 36
  • 75 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LIG4 36
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lig4 35
  • 71.5 (n)
  • 73.53 (a)
Str.4239 35
African clawed frog
(Xenopus laevis)
Amphibia lig4-A 35
zebrafish
(Danio rerio)
Actinopterygii lig4 35
  • 65.85 (n)
  • 64.99 (a)
lig4 36
  • 64 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta ligase4 37
  • 31 (a)
Lig4 35
  • 45.17 (n)
  • 33.75 (a)
Lig4 36
  • 27 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000623 35
  • 39.81 (n)
  • 32.64 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACR008W 35
  • 43.32 (n)
  • 28.43 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D01089g 35
  • 44.51 (n)
  • 30 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DNL4 35
  • 44.73 (n)
  • 30.29 (a)
DNL4 36
  • 20 (a)
OneToMany
DNL4 38
thale cress
(Arabidopsis thaliana)
eudicotyledons ATLIG4 35
  • 46.01 (n)
  • 34.34 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU06264 35
  • 44.02 (n)
  • 33.57 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lig4 35
  • 47.46 (n)
  • 33.66 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 44 (a)
OneToOne
Species with no ortholog for LIG4:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • 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 (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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LIG4 Gene

ENSEMBL:
Gene Tree for LIG4 (if available)
TreeFam:
Gene Tree for LIG4 (if available)

Paralogs for LIG4 Gene

No data available for Paralogs for LIG4 Gene

Variants for LIG4 Gene

Sequence variations from dbSNP and Humsavar for LIG4 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
VAR_012774 LIG4 syndrome (LIG4S)
VAR_012775 LIG4 syndrome (LIG4S)
rs3742212 - 108,209,652(-) ATTTT(A/T)TGTGG reference, missense
rs2232641 - 108,209,297(-) CTAAT(A/G)TATTT reference, missense
rs2232642 - 108,208,700(-) GTTTA(A/G)CTGAG reference, missense

Variation tolerance for LIG4 Gene

Residual Variation Intolerance Score: 54.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.69; 86.48% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LIG4 Gene

HapMap Linkage Disequilibrium report
LIG4
Human Gene Mutation Database (HGMD)
LIG4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for LIG4 Gene

Disorders for LIG4 Gene

MalaCards: The human disease database

(15) MalaCards diseases for LIG4 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
lig4 syndrome
  • dna ligase iv deficiency
multiple myeloma
  • plasma cell neoplasm
dubowitz syndrome
  • dubowitz's syndrome
omenn syndrome
  • reticuloendotheliosis familial with eosinophilia
severe combined immunodeficiency, athabascan type
  • severe combined immunodeficiency with sensitivity to ionizing radiation
- elite association - COSMIC cancer census association via MalaCards
Search LIG4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

DNLI4_HUMAN
  • LIG4 syndrome (LIG4S) [MIM:606593]: Characterized by immunodeficiency and developmental and growth delay. Patients display unusual facial features, microcephaly, growth and/or developmental delay, pancytopenia, and various skin abnormalities. {ECO:0000269 PubMed:11779494}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-negative/NK-cell-positive with sensitivity to ionizing radiation (RSSCID) [MIM:602450]: A form of severe combined immunodeficiency, a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. Individuals affected by RS-SCID show defects in the DNA repair machinery necessary for coding joint formation and the completion of V(D)J recombination. A subset of cells from such patients show increased radiosensitivity. {ECO:0000269 PubMed:16357942}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for LIG4

Genetic Association Database (GAD)
LIG4
Human Genome Epidemiology (HuGE) Navigator
LIG4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LIG4
genes like me logo Genes that share disorders with LIG4: view

No data available for Genatlas for LIG4 Gene

Publications for LIG4 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 Y.-F. … Lindahl T. (Mol. Cell. Biol. 1995) 2 3 4 67
  2. Polymorphisms of LIG4, BTBD2, HMGA2, and RTEL1 genes involved in the double-strand break repair pathway predict glioblastoma survival. (PMID: 20368557) Liu Y. … Bondy M. (J. Clin. Oncol. 2010) 3 23
  3. DNA repair gene polymorphisms and risk of pancreatic cancer. (PMID: 19147782) Li D. … Abbruzzese J.L. (Clin. Cancer Res. 2009) 3 23
  4. Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4. (PMID: 19332554) Wu P.Y. … Junop M.S. (Mol. Cell. Biol. 2009) 3 23
  5. Lung cancer susceptibility and prognosis associated with polymorphisms in the nonhomologous end-joining pathway genes: a multiple genotype-phenotype study. (PMID: 19408343) Tseng R.C. … Wang Y.C. (Cancer 2009) 3 23

Products for LIG4 Gene

Sources for LIG4 Gene

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