U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LIG1 DNA ligase 1 [ Homo sapiens (human) ]

Gene ID: 3978, updated on 23-Nov-2023

Summary

Official Symbol
LIG1provided by HGNC
Official Full Name
DNA ligase 1provided by HGNC
Primary source
HGNC:HGNC:6598
See related
Ensembl:ENSG00000105486 MIM:126391; AllianceGenome:HGNC:6598
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
LIGI; IMD96; hLig1
Summary
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]
Expression
Broad expression in bone marrow (RPKM 13.9), lymph node (RPKM 9.7) and 24 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See LIG1 in Genome Data Viewer
Location:
19q13.33
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (48115445..48170344, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (51109368..51164335, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (48618702..48673601, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene calcium binding protein 5 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48564610-48565203 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48565204-48565796 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:48565797-48566389 Neighboring gene phospholipase A2 group IVC Neighboring gene PLA2G4C antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10871 Neighboring gene uncharacterized LOC107985293 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:48673083-48673742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14872 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:48691653-48691885 Neighboring gene zinc finger SWIM-type containing 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48699771-48700283 Neighboring gene caspase recruitment domain family member 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14873 Neighboring gene uncharacterized LOC124904734

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC117397, MGC130025

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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables DNA ligase activity TAS
Traceable Author Statement
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
involved_in DNA ligation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in DNA ligation TAS
Traceable Author Statement
more info
 
involved_in DNA repair TAS
Traceable Author Statement
more info
PubMed 
involved_in Okazaki fragment processing involved in mitotic DNA replication IBA
Inferred from Biological aspect of Ancestor
more info
 
NOT involved_in V(D)J recombination IDA
Inferred from Direct Assay
more info
PubMed 
involved_in anatomical structure morphogenesis TAS
Traceable Author Statement
more info
PubMed 
involved_in base-excision repair IDA
Inferred from Direct Assay
more info
PubMed 
involved_in base-excision repair, gap-filling TAS
Traceable Author Statement
more info
 
involved_in cell division IEA
Inferred from Electronic Annotation
more info
 
involved_in lagging strand elongation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in mismatch repair TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
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

Preferred Names
DNA ligase 1
Names
ligase I, DNA, ATP-dependent
polydeoxyribonucleotide synthase [ATP] 1
NP_000225.1
NP_001275992.1
NP_001275993.1
NP_001307899.1
NP_001307900.1
XP_047294789.1
XP_047294790.1
XP_054176994.1
XP_054176995.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_007395.1 RefSeqGene

    Range
    4701..59859
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_78

mRNA and Protein(s)

  1. NM_000234.3NP_000225.1  DNA ligase 1 isoform 1

    See identical proteins and their annotated locations for NP_000225.1

    Status: REVIEWED

    Source sequence(s)
    BC108318
    Consensus CDS
    CCDS12711.1
    UniProtKB/Swiss-Prot
    B2RAI8, B4DTU4, P18858, Q2TB12, Q32P23
    UniProtKB/TrEMBL
    A0A8V8TQQ7
    Related
    ENSP00000263274.6, ENST00000263274.12
    Conserved Domains (2) summary
    cl25417
    Location:164914
    CDC9; ATP-dependent DNA ligase [Replication, recombination and repair]
    cl25751
    Location:10275
    DUF4045; Domain of unknown function (DUF4045)
  2. NM_001289063.2NP_001275992.1  DNA ligase 1 isoform 2

    See identical proteins and their annotated locations for NP_001275992.1

    Status: REVIEWED

    Source sequence(s)
    AK300370, BC108318
    Consensus CDS
    CCDS74409.1
    UniProtKB/TrEMBL
    A0A8V8TQQ7
    Related
    ENSP00000442841.1, ENST00000427526.6
    Conserved Domains (4) summary
    cd07969
    Location:723868
    OBF_DNA_ligase_I; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit
    cd07900
    Location:500718
    Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I
    PLN03113
    Location:133883
    PLN03113; DNA ligase 1; Provisional
    pfam04675
    Location:257428
    DNA_ligase_A_N; DNA ligase N terminus
  3. NM_001289064.2NP_001275993.1  DNA ligase 1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AK297296, BC108318
    Consensus CDS
    CCDS74410.1
    UniProtKB/TrEMBL
    B4DM52, F5GZ28, M0R1G7
    Related
    ENSP00000471861.2, ENST00000596549.6
    Conserved Domains (4) summary
    cd07969
    Location:686831
    OBF_DNA_ligase_I; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit
    cd07900
    Location:463681
    Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I
    PLN03113
    Location:103846
    PLN03113; DNA ligase 1; Provisional
    pfam04675
    Location:220391
    DNA_ligase_A_N; DNA ligase N terminus
  4. NM_001320970.2NP_001307899.1  DNA ligase 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, KC877741
    Consensus CDS
    CCDS92658.1
    UniProtKB/TrEMBL
    A0A8V8TQC4, A0A8V8TQQ7
    Related
    ENSP00000514663.1, ENST00000699866.1
    Conserved Domains (4) summary
    cd07969
    Location:753898
    OBF_DNA_ligase_I; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit
    cd07900
    Location:530748
    Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I
    PLN03113
    Location:163913
    PLN03113; DNA ligase 1; Provisional
    pfam04675
    Location:287458
    DNA_ligase_A_N; DNA ligase N terminus
  5. NM_001320971.2NP_001307900.1  DNA ligase 1 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, KC877741
    Consensus CDS
    CCDS92657.1
    UniProtKB/TrEMBL
    A0A8V8TPH8, A0A8V8TQQ7
    Related
    ENSP00000514670.1, ENST00000699874.1
    Conserved Domains (4) summary
    cd07969
    Location:724869
    OBF_DNA_ligase_I; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit
    cd07900
    Location:501719
    Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I
    PLN03113
    Location:134884
    PLN03113; DNA ligase 1; Provisional
    pfam04675
    Location:258429
    DNA_ligase_A_N; DNA ligase N terminus

RNA

  1. NR_110296.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AB208791, BC108318, BC110622
    Related
    ENST00000594759.5
  2. NR_135497.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, BC110622
    Related
    ENST00000601091.5
  3. NR_135498.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, KC877741
    Related
    ENST00000596672.6
  4. NR_135499.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, KC877741
    Related
    ENST00000699873.1
  5. NR_135500.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, KC877741
    Related
    ENST00000699872.1
  6. NR_135501.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, KC877741
    Related
    ENST00000699869.1

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    48115445..48170344 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047438833.1XP_047294789.1  DNA ligase 1 isoform X1

    UniProtKB/TrEMBL
    B4DUE1
    Related
    ENST00000594067.5
  2. XM_047438834.1XP_047294790.1  DNA ligase 1 isoform X2

    UniProtKB/TrEMBL
    A0A8V8TPH4
    Related
    ENSP00000514666.1, ENST00000699870.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    51109368..51164335 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321019.1XP_054176994.1  DNA ligase 1 isoform X1

    UniProtKB/TrEMBL
    B4DUE1
  2. XM_054321020.1XP_054176995.1  DNA ligase 1 isoform X2

    UniProtKB/TrEMBL
    A0A8V8TPH4