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LIG1 DNA ligase 1 [ Homo sapiens (human) ]

Gene ID: 3978, updated on 20-Dec-2019

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
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
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

Genomic context

See LIG1 in Genome Data Viewer
Location:
19q13.33
Exon count:
29
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (48115445..48170603, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (48618702..48673852, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene calcium binding protein 5 Neighboring gene phospholipase A2 group IVC Neighboring gene PLA2G4C antisense RNA 1 Neighboring gene uncharacterized LOC107985293 Neighboring gene zinc finger SWIM-type containing 9 Neighboring gene caspase recruitment domain family member 8 Neighboring gene vomeronasal 1 receptor 97 pseudogene

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

Homology

Clone Names

  • MGC117397, MGC130025

Gene Ontology Provided by GOA

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

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_024307281.1

NCBI Reference Sequences (RefSeq)

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
    P18858
    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/Swiss-Prot
    P18858
    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_001289064.1NP_001275993.1  DNA ligase 1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AK297296, BC108318
    Consensus CDS
    CCDS74410.1
    UniProtKB/Swiss-Prot
    P18858
    UniProtKB/TrEMBL
    B4DM52, F5GZ28
    Related
    ENSP00000441531.1, ENST00000536218.5
    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
    UniProtKB/Swiss-Prot
    P18858
    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
    UniProtKB/Swiss-Prot
    P18858
    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
  4. NR_135499.2 RNA Sequence

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

    Source sequence(s)
    AC011466, BC108318, KC877741

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    48115445..48170603 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024451513.1XP_024307281.1  DNA ligase 1 isoform X1

    Conserved Domains (2) summary
    cl25417
    Location:119878
    CDC9; ATP-dependent DNA ligase [Replication, recombination and repair]
    cl25574
    Location:10211
    TOP2c; TopoisomeraseII

RNA

  1. XR_002958316.1 RNA Sequence

  2. XR_002958315.1 RNA Sequence

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