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LIG3 DNA ligase 3 [ Homo sapiens (human) ]

Gene ID: 3980, updated on 7-Apr-2024

Summary

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Official Symbol
LIG3provided by HGNC
Official Full Name
DNA ligase 3provided by HGNC
Primary source
HGNC:HGNC:6600
See related
Ensembl:ENSG00000005156 MIM:600940; AllianceGenome:HGNC:6600
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LIG2; MTDPS20; LIG3alpha
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 7.0), thyroid (RPKM 4.6) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
17q12
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (34980512..35010872)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (35928368..35957659)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (33307531..33336762)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene chaperonin containing TCP1 subunit 6B Neighboring gene Sharpr-MPRA regulatory region 18 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12049 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12050 Neighboring gene zinc finger protein 830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8432 Neighboring gene RAD51L3-RFFL readthrough Neighboring gene oligosaccharyltransferase complex subunit pseudogene 7 Neighboring gene ring finger and FYVE like domain containing E3 ubiquitin protein ligase Neighboring gene ReSE screen-validated silencer GRCh37_chr17:33354498-33354674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12054 Neighboring gene small nucleolar RNA U13 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:33390277-33391476 Neighboring gene ribosomal protein L37 pseudogene 22

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. LIG3 gene polymorphisms and risk of gastric cancer in a Southern Chinese population. Hua RX, et al. Gene, 2019 Jul 15. PMID 31034940
  2. Polymorphism rs1052536 in Base Excision Repair Gene Is a Risk Factor in a High-Risk Area of Neural Tube Defects in China. Li G, et al. Med Sci Monit, 2018 Jul 19. PMID 30022792, Free PMC Article
  3. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining. Kukshal V, et al. Nucleic Acids Res, 2015 Aug 18. PMID 26130724, Free PMC Article
  4. Polymorphism of the LIG3 gene in keratoconus and Fuchs endothelial corneal dystrophy. Synowiec E, et al. Cell Mol Biol (Noisy-le-grand), 2015 Mar 28. PMID 25817347
  5. Escape from telomere-driven crisis is DNA ligase III dependent. Jones RE, et al. Cell Rep, 2014 Aug 21. PMID 25127141

See all (191) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Toxicity and therapy outcome associations in LIG3, SLCO1B3, ABCB1, OPRM1 and GSTP1 in high-grade serous ovarian cancer.
    Title: Toxicity and therapy outcome associations in LIG3, SLCO1B3, ABCB1, OPRM1 and GSTP1 in high-grade serous ovarian cancer.
  2. Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity.
    Title: Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity.
  3. Rac GTPase activating protein 1 promotes gallbladder cancer via binding DNA ligase 3 to reduce apoptosis.
    Title: Rac GTPase activating protein 1 promotes gallbladder cancer via binding DNA ligase 3 to reduce apoptosis.
  4. Biallelic variants in LIG3 cause a novel mitochondrial neurogastrointestinal encephalomyopathy.
    Title: Biallelic variants in LIG3 cause a novel mitochondrial neurogastrointestinal encephalomyopathy.
  5. Human DNA ligases in replication and repair.
    Title: Human DNA ligases in replication and repair.
  6. Altered DNA ligase activity in human disease.
    Title: Altered DNA ligase activity in human disease.
  7. An atypical BRCT-BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIalpha within a flexible DNA repair complex.
    Title: An atypical BRCT-BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex.
  8. MM express elevated MALAT1 and involve in alternative non-homozygous end joining (A-NHEJ) pathway by binding to PARP1 and LIG3, two key components of the A-NHEJ protein complex.
    Title: Targeting the MALAT1/PARP1/LIG3 complex induces DNA damage and apoptosis in multiple myeloma.
  9. Data report that polymorphisms in LIG3 gene are not associated with the susceptibility to gastric cancer. The study helps to provide novel insight into the role of LIG3 polymorphisms in gastric cancer risk.
    Title: LIG3 gene polymorphisms and risk of gastric cancer in a Southern Chinese population.
  10. High lig3 expression is associated with multiple myeloma.
    Title: miR-22 suppresses DNA ligase III addiction in multiple myeloma.
Submit: New GeneRIF Correction See all GeneRIFs (44)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Mitochondrial DNA depletion syndrome 20 (mngie type)
MedGen: C5676934 OMIM: 619780 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Common variants at ten loci influence QT interval duration in the QTGEN Study.
EBI GWAS Catalog
Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, ligase III, DNA, ATP-dependent (LIG3), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with LIG3 is increased by RRE PubMed
Tat tat Both HIV-1 Tat 47-59 and FITC-labeled Tat 47-59 peptides downregulate gene expression of ligase III, DNA, ATP-dependent (LIG3) in U-937 macrophages PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA ligase (ATP) activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA ligase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
NOT involved_in V(D)J recombination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in base-excision repair, DNA ligation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in base-excision repair, DNA ligation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in base-excision repair, DNA ligation TAS
Traceable Author Statement
more info
  
involved_in base-excision repair, gap-filling TAS
Traceable Author Statement
more info
  
involved_in cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in double-strand break repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in double-strand break repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in double-strand break repair via homologous recombination TAS
Traceable Author Statement
more info
  
involved_in lagging strand elongation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of mitochondrial DNA replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of DNA ligase III-XRCC1 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
DNA ligase 3
Names
ligase II, DNA, ATP-dependent
ligase III, DNA, ATP-dependent
polydeoxyribonucleotide synthase [ATP] 3
NP_002302.2
NP_039269.2
XP_005258027.1
XP_006721959.1
XP_016880113.1
XP_047291924.1
XP_047291925.1
XP_047291926.1
XP_047291927.1
XP_047291928.1
XP_054172026.1
XP_054172027.1
XP_054172028.1
XP_054172029.1
XP_054172030.1
XP_054172031.1
XP_054172032.1
XP_054172033.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029221.2 RefSeqGene

    Range
    5002..34233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002311.5 → NP_002302.2  DNA ligase 3 isoform beta precursor

    See identical proteins and their annotated locations for NP_002302.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (beta) contains an alternate in-frame exon in the coding region which includes an in-frame stop codon, compared to variant alpha. This isoform (beta) is shorter and has a distinct C-terminus, compared to isoform alpha.
    Source sequence(s)
    BG470103, DB100562, U40671
    Consensus CDS
    CCDS11285.2
    UniProtKB/Swiss-Prot
    P49916
    Related
    ENSP00000262327.4, ENST00000262327.9
    Conserved Domains (5) summary
    cd07967
    Location:686 → 824
    OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
    cd07902
    Location:468 → 680
    Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
    TIGR00574
    Location:318 → 830
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97 → 179
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam04675
    Location:264 → 429
    DNA_ligase_A_N; DNA ligase N terminus

  2. NM_013975.4 → NP_039269.2  DNA ligase 3 isoform alpha precursor

    See identical proteins and their annotated locations for NP_039269.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (alpha) represents the longer transcript and encodes the longer isoform (alpha).
    Source sequence(s)
    AA872458, AC004223, AW166526, BC068005, BM726768, DB100562
    Consensus CDS
    CCDS11284.2
    UniProtKB/Swiss-Prot
    E5KLB5, E5KLB6, P49916, Q16714, Q6NVK3
    Related
    ENSP00000367787.3, ENST00000378526.9
    Conserved Domains (3) summary
    TIGR00574
    Location:318 → 830
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:96 → 181
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:933 → 1004
    LIG3_BRCT; DNA ligase 3 BRCT domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    34980512..35010872
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047435969.1 → XP_047291925.1  DNA ligase 3 isoform X2

  2. XM_047435968.1 → XP_047291924.1  DNA ligase 3 isoform X1

  3. XM_047435971.1 → XP_047291927.1  DNA ligase 3 isoform X5

  4. XM_047435972.1 → XP_047291928.1  DNA ligase 3 isoform X7

    UniProtKB/TrEMBL
    B7Z6I3

  5. XM_005257970.5 → XP_005258027.1  DNA ligase 3 isoform X3

    Conserved Domains (6) summary
    cd07967
    Location:695 → 833
    OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
    cd07902
    Location:477 → 689
    Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
    TIGR00574
    Location:327 → 839
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:106 → 188
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam04675
    Location:273 → 438
    DNA_ligase_A_N; DNA ligase N terminus
    pfam16759
    Location:942 → 1013
    LIG3_BRCT; DNA ligase 3 BRCT domain

  6. XM_006721896.4 → XP_006721959.1  DNA ligase 3 isoform X6

    Conserved Domains (5) summary
    cd07967
    Location:695 → 833
    OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
    cd07902
    Location:477 → 689
    Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
    TIGR00574
    Location:327 → 839
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:106 → 188
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam04675
    Location:273 → 438
    DNA_ligase_A_N; DNA ligase N terminus

  7. XM_017024624.2 → XP_016880113.1  DNA ligase 3 isoform X4

    UniProtKB/Swiss-Prot
    E5KLB5, E5KLB6, P49916, Q16714, Q6NVK3
    Conserved Domains (3) summary
    TIGR00574
    Location:318 → 830
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:96 → 181
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:933 → 1004
    LIG3_BRCT; DNA ligase 3 BRCT domain

  8. XM_047435970.1 → XP_047291926.1  DNA ligase 3 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    35928368..35957659
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316054.1 → XP_054172029.1  DNA ligase 3 isoform X3

  2. XM_054316057.1 → XP_054172032.1  DNA ligase 3 isoform X6

  3. XM_054316051.1 → XP_054172026.1  DNA ligase 3 isoform X1

  4. XM_054316056.1 → XP_054172031.1  DNA ligase 3 isoform X5

  5. XM_054316058.1 → XP_054172033.1  DNA ligase 3 isoform X7

    UniProtKB/TrEMBL
    B7Z6I3

  6. XM_054316052.1 → XP_054172027.1  DNA ligase 3 isoform X2

  7. XM_054316055.1 → XP_054172030.1  DNA ligase 3 isoform X4

    UniProtKB/Swiss-Prot
    E5KLB5, E5KLB6, P49916, Q16714, Q6NVK3

  8. XM_054316053.1 → XP_054172028.1  DNA ligase 3 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P49916.2 GenPept UniProtKB/Swiss-Prot:P49916

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