Lig4 DNA ligase 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lig4provided by RGD
Official Full Name: DNA ligase 4provided by RGD
Primary source: RGD:1304639
See related: EnsemblRapid:ENSRNOG00000014605 AllianceGenome:RGD:1304639
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 ATP binding activity; DNA binding activity; and DNA ligase (ATP) activity. Involved in DNA ligation and cellular response to lithium ion. Predicted to be located in condensed chromosome and nucleoplasm. Predicted to be part of DNA ligase IV complex and DNA-dependent protein kinase-DNA ligase 4 complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in several diseases, including DNA ligase IV deficiency; colorectal cancer; multiple myeloma; pancreatic cancer; and prostate cancer. Orthologous to human LIG4 (DNA ligase 4). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 213.2), Spleen (RPKM 69.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16q12.5

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (86220345..86228930)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (79518393..79526956)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (85331771..85339496)

Chromosome 16 - NC_086034.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IBA Inferred from Biological aspect of Ancestor more info
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA ligase (ATP) activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA ligase (ATP) activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA ligase (ATP) activity	ISO Inferred from Sequence Orthology more info
enables DNA ligase activity	ISO Inferred from Sequence Orthology more info
enables ligase activity	ISO Inferred from Sequence Orthology more info
enables magnesium ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DN2 thymocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in DNA biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in DNA ligation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within DNA ligation	ISO Inferred from Sequence Orthology more info
involved_in DNA ligation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA ligation involved in DNA recombination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA ligation involved in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA ligation involved in DNA repair	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA repair	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within T cell receptor V(D)J recombination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within V(D)J recombination	ISO Inferred from Sequence Orthology more info
involved_in V(D)J recombination	ISO Inferred from Sequence Orthology more info
involved_in cellular response to ionizing radiation	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lithium ion	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within central nervous system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromosome organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within double-strand break repair	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair via classical nonhomologous end joining	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair via nonhomologous end joining	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
acts_upstream_of fibroblast proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within fibroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in immunoglobulin V(D)J recombination	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within immunoglobulin V(D)J recombination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within isotype switching	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of neurogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in nucleotide-excision repair, DNA gap filling	IBA Inferred from Biological aspect of Ancestor more info
involved_in nucleotide-excision repair, DNA gap filling	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of chromosome organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of fibroblast proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of neurogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pro-B cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in response to X-ray	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to gamma radiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to ionizing radiation	ISO Inferred from Sequence Orthology more info
involved_in single strand break repair	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within somatic stem cell population maintenance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within stem cell proliferation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of DNA ligase IV complex	IBA Inferred from Biological aspect of Ancestor more info
part_of DNA ligase IV complex	ISO Inferred from Sequence Orthology more info
part_of DNA-dependent protein kinase-DNA ligase 4 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of DNA-dependent protein kinase-DNA ligase 4 complex	ISO Inferred from Sequence Orthology more info
located_in condensed chromosome	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
part_of nonhomologous end joining complex	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	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA ligase 4

Names: DNA ligase (ATP) 4; ligase IV, DNA, ATP-dependent

NP_001099565.1

EC 6.5.1.1

XP_006253539.1

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_001106095.2 → NP_001099565.1 DNA ligase 4

See identical proteins and their annotated locations for NP_001099565.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000016

UniProtKB/TrEMBL

A6IWS2, D4A0U6

Conserved Domains (7) summary

cd07968
Location:459 → 596

OBF_DNA_ligase_IV; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit

cd07903
Location:235 → 455

Adenylation_DNA_ligase_IV; Adenylation domain of DNA Ligase IV

cd00027
Location:845 → 899

BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...

TIGR00574
Location:81 → 602

dnl1; DNA ligase I, ATP-dependent (dnl1)

pfam00533
Location:654 → 730

BRCT; BRCA1 C Terminus (BRCT) domain

pfam04675
Location:15 → 203

DNA_ligase_A_N; DNA ligase N terminus

pfam11411
Location:750 → 782

DNA_ligase_IV; DNA ligase IV
NM_001434434.1 → NP_001421363.1 DNA ligase 4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000016

UniProtKB/TrEMBL

A6IWS2, D4A0U6

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_086034.1 Reference GRCr8

Range

86220345..86228930

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006253477.5 → XP_006253539.1 DNA ligase 4 isoform X1

Related

ENSRNOP00000077244.1, ENSRNOT00000112670.2

Conserved Domains (7) summary

cd07968
Location:459 → 596

OBF_DNA_ligase_IV; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit

cd07903
Location:235 → 455

Adenylation_DNA_ligase_IV; Adenylation domain of DNA Ligase IV

cd00027
Location:845 → 899

BRCT; Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo ...

TIGR00574
Location:81 → 602

dnl1; DNA ligase I, ATP-dependent (dnl1)

pfam00533
Location:654 → 730

BRCT; BRCA1 C Terminus (BRCT) domain

pfam04675
Location:15 → 203

DNA_ligase_A_N; DNA ligase N terminus

pfam11411
Location:750 → 782

DNA_ligase_IV; DNA ligase IV