Free for academic non-profit institutions. Other users need a Commercial license

Aliases for LIG1 Gene

Aliases for LIG1 Gene

  • DNA Ligase 1 2 3 5
  • EC 6.5.1.1 4 61
  • Polydeoxyribonucleotide Synthase [ATP] 1 4
  • Ligase I, DNA, ATP-Dependent 2
  • DNA Ligase I 4

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 Vaccinia. Among its related pathways are Telomere C-strand (Lagging Strand) Synthesis and Nucleotide excision repair. 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 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

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIG1 Gene

Genomics for LIG1 Gene

Regulatory Elements for LIG1 Gene

Enhancers for LIG1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19G048958 2.1 FANTOM5 Ensembl ENCODE dbSUPER 10.1 -793.4 -793427 10.2 MLX CREB3L1 AGO1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 PPP1R15A PRR12 NUP62 IZUMO1 RUVBL2 CA11 SEC1P SNORD35B C19orf68 ALDH16A1
GH19G048871 1.7 Ensembl ENCODE dbSUPER 10.1 -705.4 -705412 8.8 CREB3L1 AGO1 FEZF1 YY1 SLC30A9 ZNF143 ZNF263 SP3 TBX21 MEF2D FLT3LG PRR12 TULP2 HSD17B14 SNORD35B ALDH16A1 SNORD35A RPS11 PIH1D1 RPL18
GH19G048612 1.7 Ensembl ENCODE dbSUPER 10.1 -446.2 -446160 7.8 CREB3L1 AGO1 ZFP64 DMAP1 FEZF1 YY1 SLC30A9 ZNF143 SP3 NFYC PRR12 SNORD35A KDELR1 SNORD35B ALDH16A1 GRWD1 SEC1P NOP53-AS1 RPS11 PIH1D1
GH19G047607 1.6 Ensembl ENCODE dbSUPER 10.1 +559.5 559517 6.9 HDGF PKNOX1 CREB3L1 AGO1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF541 PRKD2 LIG1 KPTN ENSG00000277383 BICRA-AS1
GH19G048190 0.9 ENCODE 17 -20.0 -20026 0.8 SIN3A FEZF1 ZNF207 FOS SP3 NFYC REST ZNF518A MBD2 GLIS1 PLA2G4C LIG1 BICRA CYTH2 ENSG00000280353 C19orf68
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LIG1 on UCSC Golden Path with GeneCards custom track

Promoters for LIG1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000110666 303 1801 HDGF PKNOX1 CREB3L1 ARNT AGO1 ARID4B SIN3A DMAP1 ZNF2 YY1

Genomic Location for LIG1 Gene

Chromosome:
19
Start:
48,115,444 bp from pter
End:
48,170,603 bp from pter
Size:
55,160 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 posLast=226226, isoforms=2, 3298, posLast=407407, isoforms=2, 3422, and isoforms=3795
  • Modification sites at PhosphoSitePlus

Antibody Products

Domains & Families for LIG1 Gene

Gene Families for LIG1 Gene

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

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
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + (deoxyribonucleotide)(n)-3-hydroxyl + 5-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.
UniProtKB/Swiss-Prot Function:
DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.

Enzyme Numbers (IUBMB) for LIG1 Gene

Gene Ontology (GO) - Molecular Function for LIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS,IEA --
GO:0003909 DNA ligase activity TAS --
GO:0003910 DNA ligase (ATP) activity IBA --
GO:0005524 ATP binding IEA --
GO:0016874 ligase activity 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

Clone Products

  • Addgene plasmids for LIG1
  • Applied Biological Materials Clones 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 3
cytosol 2
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for LIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 8696349
GO:0005654 nucleoplasm TAS --
GO:0005739 mitochondrion IBA --
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

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:0006259 DNA metabolic process TAS 2204063
GO:0006260 DNA replication IEA --
GO:0006266 DNA ligation TAS --
GO:0006281 DNA repair TAS 8696349
GO:0006283 transcription-coupled nucleotide-excision repair TAS --
genes like me logo Genes that share ontologies with LIG1: view

Drugs & Compounds for LIG1 Gene

(13) 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 Pharma Target, inhibitor 159
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved Nutra 0
Adenosine triphosphate Approved Nutra 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: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
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

Unigene Clusters for LIG1 Gene

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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for LIG1
  • Applied Biological Materials Clones 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
ECgene alternative splicing isoforms for
LIG1

Expression for LIG1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for LIG1 Gene



Protein tissue co-expression partners for LIG1 Gene

NURSA nuclear receptor signaling pathways regulating expression of LIG1 Gene:

LIG1

SOURCE GeneReport for Unigene cluster for LIG1 Gene:

Hs.1770

Evidence on tissue expression from TISSUES for LIG1 Gene

  • Blood(4.3)
  • Eye(4.1)
  • Nervous system(3.4)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with LIG1: view

Primer Products

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 34 35
  • 97.86 (n)
dog
(Canis familiaris)
Mammalia LIG1 34 35
  • 86.2 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 86 (a)
OneToMany
-- 35
  • 63 (a)
OneToMany
cow
(Bos Taurus)
Mammalia LIG1 34 35
  • 85.68 (n)
mouse
(Mus musculus)
Mammalia Lig1 34 16 35
  • 82.39 (n)
rat
(Rattus norvegicus)
Mammalia LOC100911727 34
  • 81.85 (n)
oppossum
(Monodelphis domestica)
Mammalia LIG1 35
  • 47 (a)
OneToOne
chicken
(Gallus gallus)
Aves LIG1 34 35
  • 68.96 (n)
lizard
(Anolis carolinensis)
Reptilia LIG1 35
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lig1 34
  • 64.13 (n)
African clawed frog
(Xenopus laevis)
Amphibia ligI 34
zebrafish
(Danio rerio)
Actinopterygii si:dkeyp-35b8.5 34
  • 63.6 (n)
LIG1 35
  • 52 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009222 34
  • 61.33 (n)
fruit fly
(Drosophila melanogaster)
Insecta DNA-ligI 34 35
  • 56.52 (n)
CG5602 36
  • 47 (a)
caps 36
  • 30 (a)
trn 36
  • 29 (a)
worm
(Caenorhabditis elegans)
Secernentea lig-1 34 35
  • 52.86 (n)
T21D12.9c 36
  • 32 (a)
T21D12.9a 36
  • 30 (a)
T21D12.9b 36
  • 30 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL155W 34
  • 53.7 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D12496g 34
  • 50.28 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CDC9 34 35 37
  • 48.88 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons LIG1 34
  • 53.76 (n)
rice
(Oryza sativa)
Liliopsida Os10g0489200 34
  • 52.91 (n)
Os.8285 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 52 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes cdc17 34
  • 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 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)

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 from dbSNP and Humsavar for LIG1 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs780324684 A colorectal cancer sample 48,128,007(+) TGACC(A/G/T)ATGGG nc-transcript-variant, reference, missense, stop-gained
rs780748107 A colorectal cancer sample 48,153,884(+) CTCCT(C/T)CTTCC intron-variant, nc-transcript-variant, reference, missense
rs121434560 Pathogenic 48,133,011(-) CCTGC(A/G)AATAC nc-transcript-variant, reference, missense
rs121434561 Pathogenic 48,121,244(-) GGAAG(C/T)GGGCC nc-transcript-variant, reference, missense
rs1000048604 -- 48,171,696(+) TAGAG(G/T)CACCA intron-variant, upstream-variant-2KB

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)

Relevant External Links for LIG1 Gene

Human Gene Mutation Database (HGMD)
LIG1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIG1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIG1 Gene

Disorders for LIG1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
bloom syndrome
  • bloom-torre-machacek syndrome
vaccinia
achalasia-addisonianism-alacrimia syndrome
  • triple-a syndrome
lig4 syndrome
  • dna ligase iv deficiency
uv-sensitive syndrome
  • uv sensitive syndrome
- 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

Relevant External Links for LIG1

Genetic Association Database (GAD)
LIG1
Human Genome Epidemiology (HuGE) Navigator
LIG1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LIG1
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 J.M. … Ellenberger T. (Nature 2004) 3 4 22 64
  2. Polymorphism of DNA ligase I and risk of lung cancer--a case-control analysis. (PMID: 12009232) Shen H. … Wei Q. (Lung Cancer 2002) 3 22 46 64
  3. Mutations in the DNA ligase I gene of an individual with immunodeficiencies and cellular hypersensitivity to DNA-damaging agents. (PMID: 1581963) Barnes D.E. … Lindahl T. (Cell 1992) 3 4 22 64
  4. Assignment of the gene encoding DNA ligase I to human chromosome 19q13.2-13.3. (PMID: 1733856) Barnes D.E. … Mohrenweiser H.W. (Genomics 1992) 2 3 22 64
  5. A wild-type DNA ligase I gene is expressed in Bloom's syndrome cells. (PMID: 1881902) Petrini J.H.J. … Weaver D.T. (Proc. Natl. Acad. Sci. U.S.A. 1991) 3 4 22 64

Products for LIG1 Gene

  • Addgene plasmids for LIG1

Sources for LIG1 Gene