Lig3 DNA ligase 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lig3provided by RGD
Official Full Name: DNA ligase 3provided by RGD
Primary source: RGD:1309875
See related: Ensembl:ENSRNOG00000021815 AllianceGenome:RGD:1309875
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 base-excision repair, DNA ligation. Located in nucleus. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human LIG3 (DNA ligase 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Testes (RPKM 146.4), Thymus (RPKM 143.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q26

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (68215371..68238705)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (67717808..67741141)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (70134734..70158051)

Chromosome 10 - NC_086028.1 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?

CircRNA Galntl6 sponges miR-335 to ameliorate stress-induced hypertension through upregulating Lig3 in rostral ventrolateral medulla.
Title: CircRNA Galntl6 sponges miR-335 to ameliorate stress-induced hypertension through upregulating Lig3 in rostral ventrolateral medulla.

Submit: New GeneRIF Correction

General gene information

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Markers

RH134877 (e-PCR)
- UniSTS:218155

BE109015 (e-PCR)
- UniSTS:248180

Lig3 (e-PCR), detects polymorphism
- UniSTS:525691

RH141104 (e-PCR)
- UniSTS:223101

D10Chm170 (e-PCR)
- UniSTS:518070

MARC_3929-3930:996679185:1 (e-PCR)
- UniSTS:269288

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	ISO Inferred from Sequence Orthology 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 zinc 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	ISO Inferred from Sequence Orthology more info
NOT involved_in V(D)J recombination	ISO Inferred from Sequence Orthology more info
involved_in base-excision repair, DNA ligation	IBA Inferred from Biological aspect of Ancestor more info
involved_in base-excision repair, DNA ligation	IDA Inferred from Direct Assay more info	PubMed
involved_in base-excision repair, DNA ligation	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in double-strand break repair	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair via alternative nonhomologous end joining	ISO Inferred from Sequence Orthology 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 mitochondrial DNA repair	ISO Inferred from Sequence Orthology more info
involved_in mitochondrial DNA repair	ISO Inferred from Sequence Orthology more info
involved_in mitochondrion organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of DNA recombination	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of mitochondrial DNA replication	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of DNA ligase III-XRCC1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of DNA ligase III-XRCC1 complex	ISO Inferred from Sequence Orthology more info
located_in condensed nuclear chromosome	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	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	ISO Inferred from Sequence Orthology more info
located_in synaptonemal complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA ligase 3

Names: DNA ligase (ATP) 3; ligase III, DNA, ATP-dependent

NP_001380964.1

EC 6.5.1.1

NP_001380965.1

EC 6.5.1.1

XP_008766242.2

EC 6.5.1.1

XP_008766243.2

EC 6.5.1.1

XP_038941956.1

EC 6.5.1.1

XP_038941957.1

EC 6.5.1.1

XP_038941958.1

EC 6.5.1.1

XP_038941959.2

EC 6.5.1.1

XP_063125149.1

EC 6.5.1.1

XP_063125150.1

EC 6.5.1.1

XP_063125151.1

EC 6.5.1.1

XP_063125152.1

EC 6.5.1.1

XP_063125153.1

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_001394035.1 → NP_001380964.1 DNA ligase 3 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A0A0G2JV76, A6HHE1

Conserved Domains (3) summary

TIGR00574
Location:320 → 832

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

pfam00645
Location:97 → 182

zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region

pfam16759
Location:927 → 997

LIG3_BRCT; DNA ligase 3 BRCT domain
NM_001394036.1 → NP_001380965.1 DNA ligase 3 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A0A0G2JV76, A6HHE1

Related

ENSRNOP00000069379.2, ENSRNOT00000084076.2

Conserved Domains (3) summary

TIGR00574
Location:320 → 832

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

pfam00645
Location:97 → 182

zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region

pfam16759
Location:927 → 997

LIG3_BRCT; DNA ligase 3 BRCT domain

RNA

NR_172067.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

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_086028.1 Reference GRCr8

Range

68215371..68238705

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039086031.2 → XP_038941959.2 DNA ligase 3 isoform X8
XM_008768020.4 → XP_008766242.2 DNA ligase 3 isoform X2
XM_063269083.1 → XP_063125153.1 DNA ligase 3 isoform X7
XM_063269081.1 → XP_063125151.1 DNA ligase 3 isoform X5
XM_008768021.4 → XP_008766243.2 DNA ligase 3 isoform X4
XM_063269079.1 → XP_063125149.1 DNA ligase 3 isoform X1
XM_039086029.2 → XP_038941957.1 DNA ligase 3 isoform X3

UniProtKB/TrEMBL

A0A0G2JV76, A6HHE1

Conserved Domains (3) summary

TIGR00574
Location:320 → 832

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

pfam00645
Location:97 → 182

zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region

pfam16759
Location:927 → 997

LIG3_BRCT; DNA ligase 3 BRCT domain
XM_039086030.2 → XP_038941958.1 DNA ligase 3 isoform X3

UniProtKB/TrEMBL

A0A0G2JV76, A6HHE1

Conserved Domains (3) summary

TIGR00574
Location:320 → 832

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

pfam00645
Location:97 → 182

zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region

pfam16759
Location:927 → 997

LIG3_BRCT; DNA ligase 3 BRCT domain
XM_063269080.1 → XP_063125150.1 DNA ligase 3 isoform X3
XM_039086028.2 → XP_038941956.1 DNA ligase 3 isoform X3

UniProtKB/TrEMBL

A0A0G2JV76, A6HHE1

Conserved Domains (3) summary

TIGR00574
Location:320 → 832

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

pfam00645
Location:97 → 182

zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region

pfam16759
Location:927 → 997

LIG3_BRCT; DNA ligase 3 BRCT domain
XM_063269082.1 → XP_063125152.1 DNA ligase 3 isoform X6