Lig1 DNA ligase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Lig1provided by RGD
Full Name: DNA ligase 1provided by RGD
Primary source: RGD:621424
See related: EnsemblRapid:ENSRNOG00000014193 AllianceGenome:RGD:621424
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables DNA ligase activity. Involved in DNA repair. Predicted to be located in nucleoplasm. Predicted to be active in mitochondrion and nucleus. Used to study epilepsy with generalized tonic-clonic seizures. Human ortholog(s) of this gene implicated in inherited metabolic disorder and primary immunodeficiency disease. Orthologous to human LIG1 (DNA ligase 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 163.8), Spleen (RPKM 108.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q21

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (83243043..83281707)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (74165688..74204400)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (75356212..75394757)

Chromosome 1 - NC_086019.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Role and Mechanism of Spinal NF-kappaB-CXCL1/CXCR2 in Rats with Nucleus Pulposus-induced Radicular Pain.
Title: The Role and Mechanism of Spinal NF-κB-CXCL1/CXCR2 in Rats with Nucleus Pulposus-induced Radicular Pain.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

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 (ATP) activity	IEA Inferred from Electronic Annotation more info
enables DNA ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA ligase activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

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 recombination	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
NOT acts_upstream_of_or_within DNA repair	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA replication	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in base-excision repair	IEA Inferred from Electronic Annotation more info
involved_in base-excision repair	ISO Inferred from Sequence Orthology more info
involved_in cell division	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
involved_in lagging strand elongation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within response to hydrogen peroxide	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA ligase 1

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

NP_001019439.1

EC 6.5.1.1

XP_038947878.1

EC 6.5.1.1

XP_038947883.1

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.

mRNA and Protein(s)

NM_001024268.3 → NP_001019439.1 DNA ligase 1

See identical proteins and their annotated locations for NP_001019439.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

Q9JHY8

UniProtKB/TrEMBL

F1M624, Q566D8

Related

ENSRNOP00000106715.1, ENSRNOT00000144210.1

Conserved Domains (4) summary

cd07969
Location:749 → 894

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:526 → 744

Adenylation_DNA_ligase_I_Euk; Adenylation domain of eukaryotic DNA Ligase I

PLN03113
Location:159 → 909

PLN03113; DNA ligase 1; Provisional

pfam04675
Location:283 → 454

DNA_ligase_A_N; DNA ligase N terminus

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

83243043..83281707

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039091950.2 → XP_038947878.1 DNA ligase 1 isoform X1

UniProtKB/Swiss-Prot

Q9JHY8

UniProtKB/TrEMBL

A0A8J8XFV7, A6KSM0

Related

ENSRNOP00000089677.1, ENSRNOT00000109652.2

Conserved Domains (2) summary

PTZ00121
Location:2 → 270

PTZ00121; MAEBL; Provisional

PLN03113
Location:174 → 924

PLN03113; DNA ligase 1; Provisional
XM_039091955.2 → XP_038947883.1 DNA ligase 1 isoform X1

UniProtKB/Swiss-Prot

Q9JHY8

UniProtKB/TrEMBL

A0A8J8XFV7, A6KSM0

Conserved Domains (2) summary

PTZ00121
Location:2 → 270

PTZ00121; MAEBL; Provisional

PLN03113
Location:174 → 924

PLN03113; DNA ligase 1; Provisional