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

Gene ID: 303369, updated on 5-Jan-2022

Summary

Official Symbol
Lig3provided by RGD
Official Full Name
DNA ligase 3provided by RGD
Primary source
RGD:1309875
See related
Ensembl:ENSRNOG00000021815
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, Nov 2021]
Expression
Biased expression in Testes (RPKM 146.4), Thymus (RPKM 143.6) and 9 other tissues See more
Orthologs
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Genomic context

See Lig3 in Genome Data Viewer
Location:
10q26
Exon count:
24
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (67717796..67741141)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (70134734..70158051)

Chromosome 10 - NC_051345.1Genomic Context describing neighboring genes Neighboring gene chaperonin containing TCP1 subunit 6B Neighboring gene zinc finger protein 830 Neighboring gene uncharacterized LOC102547954 Neighboring gene ring finger and FYVE-like domain containing E3 ubiquitin protein ligase Neighboring gene RAD51 paralog D Neighboring gene U6 spliceosomal RNA Neighboring gene fibronectin type III domain containing 8

Genomic regions, transcripts, and products

Expression

  • 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

General gene information

Markers

Homology

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
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
 
involved_in double-strand break repair via alternative nonhomologous end joining IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
involved_in mitochondrial DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in synaptonemal complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
DNA ligase 3
Names
DNA ligase (ATP) 3
ligase III, DNA, ATP-dependent
XP_006247051.1
XP_006247052.1
XP_008766242.1
XP_008766243.1
XP_038941956.1
XP_038941957.1
XP_038941958.1
XP_038941959.1

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)

  1. NM_001394035.1NP_001380964.1  DNA ligase 3 isoform 1

    Status: VALIDATED

    Source sequence(s)
    JACYVU010000220
    Conserved Domains (3) summary
    TIGR00574
    Location:320832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927997
    LIG3_BRCT; DNA ligase 3 BRCT domain
  2. NM_001394036.1NP_001380965.1  DNA ligase 3 isoform 1

    Status: VALIDATED

    Source sequence(s)
    JACYVU010000220
    Conserved Domains (3) summary
    TIGR00574
    Location:320832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927997
    LIG3_BRCT; DNA ligase 3 BRCT domain

RNA

  1. NR_172067.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    JACYVU010000220

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051345.1 Reference mRatBN7.2 Primary Assembly

    Range
    67717796..67741141
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006246989.4XP_006247051.1  DNA ligase 3 isoform X2

    UniProtKB/TrEMBL
    A0A096MKE9
    Conserved Domains (3) summary
    TIGR00574
    Location:320832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927997
    LIG3_BRCT; DNA ligase 3 BRCT domain
  2. XM_006246990.4XP_006247052.1  DNA ligase 3 isoform X2

    UniProtKB/TrEMBL
    A0A096MKE9
    Conserved Domains (3) summary
    TIGR00574
    Location:320832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927997
    LIG3_BRCT; DNA ligase 3 BRCT domain
  3. XM_039086029.1XP_038941957.1  DNA ligase 3 isoform X2

    Conserved Domains (3) summary
    TIGR00574
    Location:320832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927997
    LIG3_BRCT; DNA ligase 3 BRCT domain
  4. XM_039086030.1XP_038941958.1  DNA ligase 3 isoform X2

    Conserved Domains (3) summary
    TIGR00574
    Location:320832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927997
    LIG3_BRCT; DNA ligase 3 BRCT domain
  5. XM_039086028.1XP_038941956.1  DNA ligase 3 isoform X2

    Conserved Domains (3) summary
    TIGR00574
    Location:320832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:927997
    LIG3_BRCT; DNA ligase 3 BRCT domain
  6. XM_008768021.3XP_008766243.1  DNA ligase 3 isoform X3

    Related
    ENSRNOP00000068489.2, ENSRNOT00000076739.3
    Conserved Domains (6) summary
    cd07967
    Location:688826
    OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
    cd07902
    Location:470682
    Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
    TIGR00574
    Location:320832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:98178
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam04675
    Location:266431
    DNA_ligase_A_N; DNA ligase N terminus
    pfam16759
    Location:886956
    LIG3_BRCT; DNA ligase 3 BRCT domain
  7. XM_008768020.3XP_008766242.1  DNA ligase 3 isoform X1

    Conserved Domains (6) summary
    cd07967
    Location:687825
    OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
    cd07902
    Location:469681
    Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
    TIGR00574
    Location:319831
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:98178
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam04675
    Location:265430
    DNA_ligase_A_N; DNA ligase N terminus
    pfam16759
    Location:926996
    LIG3_BRCT; DNA ligase 3 BRCT domain
  8. XM_039086031.1XP_038941959.1  DNA ligase 3 isoform X4

    Conserved Domains (2) summary
    TIGR00574
    Location:320639
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region

RNA

  1. XR_005489836.1 RNA Sequence

  2. XR_005489835.1 RNA Sequence

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