LIG1 DNA ligase 1 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Association of DNA Ligase 1 Rs20579 Polymorphism With Lung Cancer Risk Among Taiwanese.
Title: The Association of DNA Ligase 1 Rs20579 Polymorphism With Lung Cancer Risk Among Taiwanese.
Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1.
Title: Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1.
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.
Ligase 1 is a predictor of platinum resistance and its blockade is synthetically lethal in XRCC1 deficient epithelial ovarian cancers.
Title: Ligase 1 is a predictor of platinum resistance and its blockade is synthetically lethal in XRCC1 deficient epithelial ovarian cancers.
DNA ligase I fidelity mediates the mutagenic ligation of pol beta oxidized and mismatch nucleotide insertion products in base excision repair.
Title: DNA ligase I fidelity mediates the mutagenic ligation of pol β oxidized and mismatch nucleotide insertion products in base excision repair.
DNA ligase I variants fail in the ligation of mutagenic repair intermediates with mismatches and oxidative DNA damage.
Title: DNA ligase I variants fail in the ligation of mutagenic repair intermediates with mismatches and oxidative DNA damage.
Human DNA ligases in replication and repair.
Title: Human DNA ligases in replication and repair.
LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency.
Title: LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency.
Dynamic DNA-bound PCNA complexes co-ordinate Okazaki fragment synthesis, processing and ligation.
Title: Dynamic DNA-bound PCNA complexes co-ordinate Okazaki fragment synthesis, processing and ligation.
Altered DNA ligase activity in human disease.
Title: Altered DNA ligase activity in human disease.

Submit: New GeneRIF Correction See all GeneRIFs (55)

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
Immunodeficiency 96 MedGen: C5676930 OMIM: 619774 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-12449 (e-PCR)
- UniSTS:66841

NoName (e-PCR)
- UniSTS:486685

SHGC-132086 (e-PCR)
- UniSTS:183198

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

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Preferred Names: DNA ligase 1

Names: ligase I, DNA, ATP-dependent; polydeoxyribonucleotide synthase [ATP] 1

NP_000225.1

EC 6.5.1.1

NP_001275992.1

EC 6.5.1.1

NP_001275993.1

EC 6.5.1.1

NP_001307899.1

EC 6.5.1.1

NP_001307900.1

EC 6.5.1.1

XP_047294789.1

EC 6.5.1.1

XP_047294790.1

EC 6.5.1.1

XP_054176994.1

EC 6.5.1.1

XP_054176995.1

EC 6.5.1.1

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

NG_007395.1 RefSeqGene

Range

4701..59859

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_78

mRNA and Protein(s)

NM_000234.3 → NP_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:164 → 914

CDC9; ATP-dependent DNA ligase [Replication, recombination and repair]

cl25751
Location:10 → 275

DUF4045; Domain of unknown function (DUF4045)
NM_001289063.2 → NP_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:723 → 868

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:500 → 718

Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I

PLN03113
Location:133 → 883

PLN03113; DNA ligase 1; Provisional

pfam04675
Location:257 → 428

DNA_ligase_A_N; DNA ligase N terminus
NM_001289064.2 → NP_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:686 → 831

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:463 → 681

Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I

PLN03113
Location:103 → 846

PLN03113; DNA ligase 1; Provisional

pfam04675
Location:220 → 391

DNA_ligase_A_N; DNA ligase N terminus
NM_001320970.2 → NP_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:753 → 898

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:530 → 748

Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I

PLN03113
Location:163 → 913

PLN03113; DNA ligase 1; Provisional

pfam04675
Location:287 → 458

DNA_ligase_A_N; DNA ligase N terminus
NM_001320971.2 → NP_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:724 → 869

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:501 → 719

Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I

PLN03113
Location:134 → 884

PLN03113; DNA ligase 1; Provisional

pfam04675
Location:258 → 429

DNA_ligase_A_N; DNA ligase N terminus