Atlas of Genetics and Cytogenetics in Oncology and Haematology

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LIG3 (DNA ligase 3)

Identity

Alias_namesLIG2
ligase II, DNA, ATP-dependent
ligase III, DNA, ATP-dependent
Other aliasLIG3alpha
HGNC (Hugo) LIG3
LocusID (NCBI) 3980
Atlas_Id 41155
Location 17q12  [Link to chromosome band 17q12]
Location_base_pair Starts at 34980498 and ends at 35005069 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
KIAA1210 (Xq24) / LIG3 (17q12)LIG3 (17q12) / FLOT1 (6p21.33)LIG3 (17q12) / HAP1 (17q21.2)
LIG3 (17q12) / KXD1 (19p13.11)LIG3 (17q12) / LIG3 (17q12)LIG3 (17q12) / ZFAT (8q24.22)
LIG3 17q12 C19orf50LIG3 17q12 / HAP1 17q21.2LIG3 17q12 / ZFAT 8q24.22

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 3 ]
  t(8;17)(q24;q12) LIG3/ZFAT
t(17;17)(q12;q21) LIG3/HAP1
t(17;19)(q12;p13) LIG3/KXD1

External links

Nomenclature
HGNC (Hugo)LIG3   6600
Cards
Entrez_Gene (NCBI)LIG3  3980  DNA ligase 3
AliasesLIG2; LIG3alpha
GeneCards (Weizmann)LIG3
Ensembl hg19 (Hinxton)ENSG00000005156 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000005156 [Gene_View]  ENSG00000005156 [Sequence]  chr17:34980498-35005069 [Contig_View]  LIG3 [Vega]
ICGC DataPortalENSG00000005156
TCGA cBioPortalLIG3
AceView (NCBI)LIG3
Genatlas (Paris)LIG3
WikiGenes3980
SOURCE (Princeton)LIG3
Genetics Home Reference (NIH)LIG3
Genomic and cartography
GoldenPath hg38 (UCSC)LIG3  -     chr17:34980498-35005069 +  17q12   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LIG3  -     17q12   [Description]    (hg19-Feb_2009)
LIG3 - 17q12 [CytoView hg19]  LIG3 - 17q12 [CytoView hg38]
Mapping of homologs : NCBILIG3 [Mapview hg19]  LIG3 [Mapview hg38]
OMIM600940   
Gene and transcription
Genbank (Entrez)AA872458 AK091492 AK125853 AK300363 AK308407
RefSeq transcript (Entrez)NM_002311 NM_013975
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LIG3
Cluster EST : UnigeneHs.556108 [ NCBI ]
CGAP (NCI)Hs.556108
Alternative Splicing GalleryENSG00000005156
Gene ExpressionLIG3 [ NCBI-GEO ]   LIG3 [ EBI - ARRAY_EXPRESS ]   LIG3 [ SEEK ]   LIG3 [ MEM ]
Gene Expression Viewer (FireBrowse)LIG3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3980
GTEX Portal (Tissue expression)LIG3
Human Protein AtlasENSG00000005156-LIG3 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP49916   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP49916  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP49916
Splice isoforms : SwissVarP49916
PhosPhoSitePlusP49916
Domaine pattern : Prosite (Expaxy)BRCT (PS50172)    DNA_LIGASE_A1 (PS00697)    DNA_LIGASE_A2 (PS00333)    DNA_LIGASE_A3 (PS50160)    PARP_ZN_FINGER_1 (PS00347)    PARP_ZN_FINGER_2 (PS50064)   
Domains : Interpro (EBI)BRCT_dom    BRCT_dom_sf    DNA_ligase_ATP-dep    DNA_ligase_ATP-dep_C    DNA_ligase_ATP-dep_cent    DNA_ligase_ATP-dep_CS    DNA_ligase_ATP-dep_N    DNA_ligase_N_sf    LIG3_BRCT    NA-bd_OB-fold    Znf_PARP    Znf_PARP_sf   
Domain families : Pfam (Sanger)DNA_ligase_A_C (PF04679)    DNA_ligase_A_M (PF01068)    DNA_ligase_A_N (PF04675)    LIG3_BRCT (PF16759)    zf-PARP (PF00645)   
Domain families : Pfam (NCBI)pfam04679    pfam01068    pfam04675    pfam16759    pfam00645   
Domain families : Smart (EMBL)BRCT (SM00292)  zf-PARP (SM01336)  
Conserved Domain (NCBI)LIG3
DMDM Disease mutations3980
Blocks (Seattle)LIG3
PDB (RSDB)1IMO    1IN1    1UW0    3L2P    3PC7    3PC8    3QVG   
PDB Europe1IMO    1IN1    1UW0    3L2P    3PC7    3PC8    3QVG   
PDB (PDBSum)1IMO    1IN1    1UW0    3L2P    3PC7    3PC8    3QVG   
PDB (IMB)1IMO    1IN1    1UW0    3L2P    3PC7    3PC8    3QVG   
Structural Biology KnowledgeBase1IMO    1IN1    1UW0    3L2P    3PC7    3PC8    3QVG   
SCOP (Structural Classification of Proteins)1IMO    1IN1    1UW0    3L2P    3PC7    3PC8    3QVG   
CATH (Classification of proteins structures)1IMO    1IN1    1UW0    3L2P    3PC7    3PC8    3QVG   
SuperfamilyP49916
Human Protein Atlas [tissue]ENSG00000005156-LIG3 [tissue]
Peptide AtlasP49916
HPRD02966
IPIIPI00029081   IPI00000156   
Protein Interaction databases
DIP (DOE-UCLA)P49916
IntAct (EBI)P49916
FunCoupENSG00000005156
BioGRIDLIG3
STRING (EMBL)LIG3
ZODIACLIG3
Ontologies - Pathways
QuickGOP49916
Ontology : AmiGOdouble-strand break repair via homologous recombination  DNA binding  DNA ligase activity  DNA ligase activity  DNA ligase (ATP) activity  protein binding  ATP binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  mitochondrion  lagging strand elongation  transcription-coupled nucleotide-excision repair  base-excision repair, DNA ligation  base-excision repair, DNA ligation  base-excision repair, DNA ligation  nucleotide-excision repair, DNA gap filling  double-strand break repair  cell cycle  zinc ion binding  V(D)J recombination  mitochondrial DNA repair  cell division  DNA biosynthetic process  negative regulation of mitochondrial DNA replication  double-strand break repair via alternative nonhomologous end joining  
Ontology : EGO-EBIdouble-strand break repair via homologous recombination  DNA binding  DNA ligase activity  DNA ligase activity  DNA ligase (ATP) activity  protein binding  ATP binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  mitochondrion  lagging strand elongation  transcription-coupled nucleotide-excision repair  base-excision repair, DNA ligation  base-excision repair, DNA ligation  base-excision repair, DNA ligation  nucleotide-excision repair, DNA gap filling  double-strand break repair  cell cycle  zinc ion binding  V(D)J recombination  mitochondrial DNA repair  cell division  DNA biosynthetic process  negative regulation of mitochondrial DNA replication  double-strand break repair via alternative nonhomologous end joining  
Pathways : KEGGBase excision repair   
NDEx NetworkLIG3
Atlas of Cancer Signalling NetworkLIG3
Wikipedia pathwaysLIG3
Orthology - Evolution
OrthoDB3980
GeneTree (enSembl)ENSG00000005156
Phylogenetic Trees/Animal Genes : TreeFamLIG3
HOGENOMP49916
Homologs : HomoloGeneLIG3
Homology/Alignments : Family Browser (UCSC)LIG3
Gene fusions - Rearrangements
Fusion : MitelmanLIG3/HAP1 [17q12/17q21.2]  
Fusion : MitelmanLIG3/KXD1 [17q12/19p13.11]  [t(17;19)(q12;p13)]  
Fusion : MitelmanLIG3/ZFAT [17q12/8q24.22]  [t(8;17)(q24;q12)]  
Fusion PortalLIG3 17q12 C19orf50 BRCA
Fusion PortalLIG3 17q12 HAP1 17q21.2 BRCA
Fusion PortalLIG3 17q12 ZFAT 8q24.22 BRCA
Fusion : QuiverLIG3
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLIG3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LIG3
dbVarLIG3
ClinVarLIG3
1000_GenomesLIG3 
Exome Variant ServerLIG3
ExAC (Exome Aggregation Consortium)ENSG00000005156
GNOMAD BrowserENSG00000005156
Varsome BrowserLIG3
Genetic variants : HAPMAP3980
Genomic Variants (DGV)LIG3 [DGVbeta]
DECIPHERLIG3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLIG3 
Mutations
ICGC Data PortalLIG3 
TCGA Data PortalLIG3 
Broad Tumor PortalLIG3
OASIS PortalLIG3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLIG3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLIG3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LIG3
DgiDB (Drug Gene Interaction Database)LIG3
DoCM (Curated mutations)LIG3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LIG3 (select a term)
intoGenLIG3
Cancer3DLIG3(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600940   
Orphanet
DisGeNETLIG3
MedgenLIG3
Genetic Testing Registry LIG3
NextProtP49916 [Medical]
TSGene3980
GENETestsLIG3
Target ValidationLIG3
Huge Navigator LIG3 [HugePedia]
snp3D : Map Gene to Disease3980
BioCentury BCIQLIG3
ClinGenLIG3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3980
Chemical/Pharm GKB GenePA30374
Clinical trialLIG3
Miscellaneous
canSAR (ICR)LIG3 (select the gene name)
DataMed IndexLIG3
Probes
Litterature
PubMed118 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLIG3
EVEXLIG3
GoPubMedLIG3
iHOPLIG3
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Thu Mar 21 15:53:11 CET 2019
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