Lig4 (DNA ligase 4) - Rat Genome Database
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Gene: Lig4 (DNA ligase 4) Rattus norvegicus
Analyze
Symbol: Lig4
Name: DNA ligase 4
RGD ID: 1304639
Description: Exhibits ATP binding activity; DNA binding activity; and DNA ligase (ATP) activity. Involved in DNA ligation and cellular response to lithium ion. Localizes to nucleus. Human ortholog(s) of this gene implicated in several diseases, including DNA ligase IV deficiency; colorectal cancer; high grade glioma; multiple myeloma; and prostate cancer. Orthologous to human LIG4 (DNA ligase 4); PARTICIPATES IN non-homologous end joining pathway of double-strand break repair; INTERACTS WITH 17beta-estradiol; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DNA ligase (ATP) 4; ligase IV, DNA, ATP-dependent; LOC290907
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21679,518,393 - 79,526,956 (+)NCBI
Rnor_6.0 Ensembl1685,331,866 - 85,337,769 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01685,331,771 - 85,339,496 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01684,770,824 - 84,778,539 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41684,881,880 - 84,888,448 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11684,871,561 - 84,874,322 (+)NCBI
Celera1677,305,627 - 77,312,388 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Damaraju S, etal., Clin Cancer Res. 2006 Apr 15;12(8):2545-54.
2. Felgentreff K, etal., J Clin Immunol. 2016 May;36(4):341-53. doi: 10.1007/s10875-016-0266-5. Epub 2016 Apr 11.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Kuhmann C, etal., Hum Mol Genet. 2014 Apr 15;23(8):2043-54. doi: 10.1093/hmg/ddt599. Epub 2013 Nov 26.
6. Li D, etal., Clin Cancer Res. 2009 Jan 15;15(2):740-6.
7. Lieber MR Annu Rev Biochem. 2010;79:181-211. doi: 10.1146/annurev.biochem.052308.093131.
8. MGD data from the GO Consortium
9. Nagaki S, etal., Biochem Biophys Res Commun. 1998 May 8;246(1):137-41.
10. Nijnik A, etal., J Clin Invest. 2009 Jun;119(6):1696-705. doi: 10.1172/JCI32743. Epub 2009 May 18.
11. OMIM Disease Annotation Pipeline
12. Pipeline to import KEGG annotations from KEGG into RGD
13. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. RGD automated import pipeline for gene-chemical interactions
15. RGD comprehensive gene curation
16. Roddam PL, etal., J Med Genet. 2002 Dec;39(12):900-5.
17. Rucci F, etal., Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):3024-9. doi: 10.1073/pnas.0914865107. Epub 2010 Feb 1.
18. Zhao P, etal., BMC Cancer. 2013 May 10;13:234. doi: 10.1186/1471-2407-13-234.
19. Zhuang J, etal., Biochem Biophys Res Commun. 2009 Mar 13;380(3):650-4. Epub 2009 Jan 31.
Additional References at PubMed
PMID:8798671   PMID:9242410   PMID:9809069   PMID:9823897   PMID:9875844   PMID:9889105   PMID:10716994   PMID:10823907   PMID:10911993   PMID:11248063   PMID:11779495   PMID:12361565  
PMID:12517771   PMID:12531011   PMID:12589063   PMID:15175260   PMID:15194694   PMID:15968270   PMID:16777961   PMID:17554302   PMID:17713479   PMID:19589734   PMID:20383123   PMID:21390131  
PMID:22192310   PMID:23275564   PMID:24837021   PMID:25941166   PMID:29463814  


Genomics

Comparative Map Data
Lig4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21679,518,393 - 79,526,956 (+)NCBI
Rnor_6.0 Ensembl1685,331,866 - 85,337,769 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01685,331,771 - 85,339,496 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01684,770,824 - 84,778,539 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41684,881,880 - 84,888,448 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11684,871,561 - 84,874,322 (+)NCBI
Celera1677,305,627 - 77,312,388 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
LIG4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl13108,207,439 - 108,218,368 (-)EnsemblGRCh38hg38GRCh38
GRCh3813108,207,442 - 108,218,349 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3713108,859,790 - 108,870,697 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3613107,657,791 - 107,668,717 (-)NCBINCBI36hg18NCBI36
Build 3413107,657,791 - 107,665,883NCBI
Celera1389,704,529 - 89,715,460 (-)NCBI
Cytogenetic Map13q33.3NCBI
HuRef1389,450,570 - 89,461,621 (-)NCBIHuRef
CHM1_113108,828,932 - 108,839,838 (-)NCBICHM1_1
Lig4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39810,020,020 - 10,027,680 (-)NCBIGRCm39mm39
GRCm39 Ensembl810,019,049 - 10,027,686 (-)Ensembl
GRCm3889,970,020 - 9,977,680 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl89,969,049 - 9,977,686 (-)EnsemblGRCm38mm10GRCm38
MGSCv3789,970,020 - 9,976,323 (-)NCBIGRCm37mm9NCBIm37
MGSCv3689,969,992 - 9,976,295 (-)NCBImm8
Celera810,145,430 - 10,151,733 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
Lig4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554043,606,077 - 3,615,193 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554043,606,077 - 3,615,193 (+)NCBIChiLan1.0ChiLan1.0
LIG4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113108,474,718 - 108,485,421 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13108,475,820 - 108,478,555 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01389,336,434 - 89,347,418 (-)NCBIMhudiblu_PPA_v0panPan3
LIG4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12256,980,333 - 56,987,636 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2256,980,622 - 56,983,357 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2256,752,066 - 56,759,380 (-)NCBI
ROS_Cfam_1.02257,500,830 - 57,508,151 (-)NCBI
UMICH_Zoey_3.12257,101,978 - 57,109,289 (-)NCBI
UNSW_CanFamBas_1.02257,090,156 - 57,097,580 (-)NCBI
UU_Cfam_GSD_1.02257,127,280 - 57,134,599 (-)NCBI
Lig4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_ltri_2NW_024404945192,083,762 - 192,090,382 (-)NCBI
SpeTri2.0NW_0049364723,861,833 - 3,867,943 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIG4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1175,537,032 - 75,547,691 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11175,537,027 - 75,547,711 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21182,953,056 - 82,962,185 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LIG4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1386,576,200 - 86,587,097 (-)NCBI
ChlSab1.1 Ensembl386,577,304 - 86,580,039 (-)Ensembl
Lig4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247933,699,394 - 3,706,591 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164151271086512710Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164151271086512710Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164655818890668790Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165781635790668790Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165781635790668790Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165781635790668790Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165928577589248943Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:26
Count of miRNA genes:25
Interacting mature miRNAs:26
Transcripts:ENSRNOT00000019615
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 30 28 16 19 16 73 30 35 11
Low 1 13 29 25 25 8 11 1 5 6 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019615   ⟹   ENSRNOP00000019615
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1685,331,866 - 85,337,769 (+)Ensembl
RefSeq Acc Id: NM_001106095   ⟹   NP_001099565
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21679,518,468 - 79,525,229 (+)NCBI
Rnor_6.01685,331,866 - 85,337,769 (+)NCBI
Rnor_5.01684,770,824 - 84,778,539 (+)NCBI
RGSC_v3.41684,881,880 - 84,888,448 (+)RGD
Celera1677,305,627 - 77,312,388 (+)RGD
Sequence:
RefSeq Acc Id: XM_006253477   ⟹   XP_006253539
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21679,518,393 - 79,526,956 (+)NCBI
Rnor_6.01685,331,771 - 85,339,496 (+)NCBI
Rnor_5.01684,770,824 - 84,778,539 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600050   ⟹   XP_017455539
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01685,331,771 - 85,339,496 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099565 (Get FASTA)   NCBI Sequence Viewer  
  XP_006253539 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM08799 (Get FASTA)   NCBI Sequence Viewer  
  EDM08800 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099565   ⟸   NM_001106095
- UniProtKB: D4A0U6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253539   ⟸   XM_006253477
- Peptide Label: isoform X1
- UniProtKB: D4A0U6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455539   ⟸   XM_017600050
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000019615   ⟸   ENSRNOT00000019615
Protein Domains
BRCT   DNA_LIGASE_A3

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13700249
Promoter ID:EPDNEW_R10772
Type:initiation region
Name:Lig4_1
Description:DNA ligase 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01685,331,847 - 85,331,907EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304639 AgrOrtholog
Ensembl Genes ENSRNOG00000014605 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019615 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019615 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.3260.10 UniProtKB/TrEMBL
  3.40.50.10190 UniProtKB/TrEMBL
InterPro Adenylation_DNA_ligase_IV UniProtKB/TrEMBL
  BRCT UniProtKB/TrEMBL
  BRCT_dom_sf UniProtKB/TrEMBL
  DNA_ligase UniProtKB/TrEMBL
  DNA_ligase_A_C UniProtKB/TrEMBL
  DNA_ligase_A_M UniProtKB/TrEMBL
  DNA_ligase_A_N UniProtKB/TrEMBL
  DNA_ligase_CS UniProtKB/TrEMBL
  DNA_ligase_IV UniProtKB/TrEMBL
  DNA_ligase_N_sf UniProtKB/TrEMBL
  LIG4 UniProtKB/TrEMBL
  NA-bd_OB-fold UniProtKB/TrEMBL
KEGG Report rno:290907 UniProtKB/TrEMBL
NCBI Gene 290907 ENTREZGENE
PANTHER PTHR45997 UniProtKB/TrEMBL
Pfam BRCT UniProtKB/TrEMBL
  DNA_ligase_A_C UniProtKB/TrEMBL
  DNA_ligase_A_M UniProtKB/TrEMBL
  DNA_ligase_A_N UniProtKB/TrEMBL
  DNA_ligase_IV UniProtKB/TrEMBL
PhenoGen Lig4 PhenoGen
PROSITE BRCT UniProtKB/TrEMBL
  DNA_LIGASE_A1 UniProtKB/TrEMBL
  DNA_LIGASE_A2 UniProtKB/TrEMBL
  DNA_LIGASE_A3 UniProtKB/TrEMBL
SMART BRCT UniProtKB/TrEMBL
Superfamily-SCOP BRCT UniProtKB/TrEMBL
  Nucleic_acid_OB UniProtKB/TrEMBL
  SSF117018 UniProtKB/TrEMBL
TIGRFAMs dnl1 UniProtKB/TrEMBL
UniProt D4A0U6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-04 Lig4  DNA ligase 4  Lig4  ligase IV, DNA, ATP-dependent  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Lig4  ligase IV, DNA, ATP-dependent   Lig4_predicted  ligase IV, DNA, ATP-dependent (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Lig4_predicted  ligase IV, DNA, ATP-dependent (predicted)      Symbol and Name status set to approved 70820 APPROVED