Lig1 (DNA ligase 1) - Rat Genome Database

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Gene: Lig1 (DNA ligase 1) Rattus norvegicus
Analyze
Symbol: Lig1
Name: DNA ligase 1
RGD ID: 621424
Description: 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); PARTICIPATES IN mismatch repair pathway; nucleotide excision repair pathway; base excision repair pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DNA ligase (ATP) 1; DNA ligase 1-like; DNA ligase I; ligase I, DNA, ATP-dependent; LOC100911727; LOC360304; MGC105416; polydeoxyribonucleotide synthase [ATP] 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8183,243,043 - 83,281,707 (+)NCBIGRCr8
mRatBN7.2174,165,688 - 74,204,400 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl174,165,842 - 74,204,413 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx179,486,858 - 79,525,331 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0188,051,204 - 88,089,678 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0181,241,935 - 81,280,405 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0175,356,212 - 75,394,757 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl175,356,220 - 75,394,758 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0176,723,841 - 76,762,378 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4173,728,892 - 73,767,429 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera169,539,708 - 69,578,250 (+)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(1->4)-beta-D-glucan  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
acetamide  (EXP)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
aurintricarboxylic acid  (ISO)
benzo[a]pyrene  (ISO)
biphenyl-4-amine  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
Brevetoxin B  (ISO)
bromoacetate  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carmustine  (EXP)
cefaloridine  (EXP)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
CU-O LINKAGE  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
DDE  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
dichloroacetic acid  (ISO)
dicrotophos  (ISO)
diuron  (ISO)
doxorubicin  (EXP,ISO)
Enterolactone  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
FR900359  (ISO)
furan  (EXP,ISO)
hexadecanoic acid  (ISO)
imiquimod  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
methotrexate  (EXP)
methyl methanesulfonate  (ISO)
miconazole  (EXP)
mitomycin C  (ISO)
N(4)-hydroxycytidine  (ISO)
N(6),N(6)-dimethyladenine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (ISO)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenethyl isothiocyanate  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
progesterone  (EXP,ISO)
resveratrol  (EXP,ISO)
rotenone  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP,ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tebufenpyrad  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (EXP)
thioacetamide  (EXP)
tioguanine  (EXP)
titanium dioxide  (ISO)
toluene 2,4-diisocyanate  (ISO)
topotecan  (EXP)
Tributyltin oxide  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
trovafloxacin  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Rat liver DNA ligases. Catalytic properties of a novel form of DNA ligase. Elder RH, etal., Eur J Biochem 1992 Jan 15;203(1-2):53-8.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Down-Regulation of Astrocytic Kir4.1 Channels during the Audiogenic Epileptogenesis in Leucine-Rich Glioma-Inactivated 1 (Lgi1) Mutant Rats. Kinboshi M, etal., Int J Mol Sci. 2019 Feb 26;20(5). pii: ijms20051013. doi: 10.3390/ijms20051013.
5. DNA polymerases and repair synthesis in NER in human cells. Lehmann AR DNA Repair (Amst). 2011 Jul 15;10(7):730-3. doi: 10.1016/j.dnarep.2011.04.023. Epub 2011 May 20.
6. Mechanisms and functions of DNA mismatch repair. Li GM Cell Res. 2008 Jan;18(1):85-98.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
11. Reactome: A Knowledgebase of Biological Processes Reactome
12. GOA pipeline RGD automated data pipeline
13. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
15. Comprehensive gene review and curation RGD comprehensive gene curation
16. Proteomics profiling of nuclear proteins for kidney fibroblasts suggests hypoxia, meiosis, and cancer may meet in the nucleus. Shakib K, etal., Proteomics. 2005 Jul;5(11):2819-38.
17. Growth retardation and immunodeficiency in a patient with mutations in the DNA ligase I gene. Webster AD, etal., Lancet. 1992 Jun 20;339(8808):1508-9.
Additional References at PubMed
PMID:8889548   PMID:9001252   PMID:9809069   PMID:11896201   PMID:12477932   PMID:15871698   PMID:19589734   PMID:21390131   PMID:21655080   PMID:22082260   PMID:38098294  


Genomics

Comparative Map Data
Lig1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8183,243,043 - 83,281,707 (+)NCBIGRCr8
mRatBN7.2174,165,688 - 74,204,400 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl174,165,842 - 74,204,413 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx179,486,858 - 79,525,331 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0188,051,204 - 88,089,678 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0181,241,935 - 81,280,405 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0175,356,212 - 75,394,757 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl175,356,220 - 75,394,758 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0176,723,841 - 76,762,378 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4173,728,892 - 73,767,429 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera169,539,708 - 69,578,250 (+)NCBICelera
Cytogenetic Map1q21NCBI
LIG1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381948,115,445 - 48,170,344 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1948,115,445 - 48,170,603 (-)EnsemblGRCh38hg38GRCh38
GRCh371948,618,702 - 48,673,601 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361953,310,515 - 53,365,372 (-)NCBINCBI36Build 36hg18NCBI36
Build 341953,310,514 - 53,365,372NCBI
Celera1945,483,843 - 45,538,716 (-)NCBICelera
Cytogenetic Map19q13.33NCBI
HuRef1945,000,496 - 45,055,385 (-)NCBIHuRef
CHM1_11948,620,871 - 48,675,746 (-)NCBICHM1_1
T2T-CHM13v2.01951,109,368 - 51,164,335 (-)NCBIT2T-CHM13v2.0
Lig1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39713,011,101 - 13,045,351 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl713,011,239 - 13,045,350 (+)EnsemblGRCm39 Ensembl
GRCm38713,277,175 - 13,311,426 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl713,277,283 - 13,311,433 (+)EnsemblGRCm38mm10GRCm38
MGSCv37713,864,175 - 13,896,776 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36712,177,462 - 12,211,570 (+)NCBIMGSCv36mm8
Celera710,895,505 - 10,928,085 (+)NCBICelera
Cytogenetic Map7A1NCBI
cM Map77.82NCBI
Lig1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955609126,278 - 160,063 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955609118,442 - 160,009 (+)NCBIChiLan1.0ChiLan1.0
LIG1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22054,216,752 - 54,270,751 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11956,086,671 - 56,140,577 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01945,056,737 - 45,110,867 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11953,706,778 - 53,761,088 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1953,706,778 - 53,761,088 (-)Ensemblpanpan1.1panPan2
LIG1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11108,105,523 - 108,143,954 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1108,105,987 - 108,143,953 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1107,588,229 - 107,626,678 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01108,631,409 - 108,669,892 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1108,631,442 - 108,669,892 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11108,276,098 - 108,314,538 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01107,944,424 - 107,982,875 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01108,812,276 - 108,850,757 (+)NCBIUU_Cfam_GSD_1.0
Lig1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934920,624,726 - 20,658,139 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366642,242,897 - 2,276,715 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366642,242,916 - 2,276,286 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LIG1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl653,620,483 - 53,686,562 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1653,620,483 - 53,660,020 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2649,204,975 - 49,270,718 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LIG1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1641,354,701 - 41,405,417 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl641,351,389 - 41,403,421 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607321,141,181 - 21,192,034 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lig1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248325,665,493 - 5,712,258 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248325,665,855 - 5,708,824 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lig1
156 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:159
Count of miRNA genes:127
Interacting mature miRNAs:136
Transcripts:ENSRNOT00000019799
Prediction methods:Microtar, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13523959878430678Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15389511782174945Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13523959878430678Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)11148131282174945Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13344984878449848Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)166023617118608521Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)17219768090508767Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14580314078430678Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13483685879836858Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13344984878449848Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15389511782174945Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat

Markers in Region
AI137243  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2174,172,375 - 74,173,720 (+)MAPPERmRatBN7.2
Rnor_6.0175,362,738 - 75,364,081NCBIRnor6.0
Rnor_5.0176,730,359 - 76,731,702UniSTSRnor5.0
RGSC_v3.4173,735,410 - 73,736,753UniSTSRGSC3.4
Celera169,546,226 - 69,547,569UniSTS
Cytogenetic Map1q21UniSTS


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 24 24 18 9 18 43 20 27 1
Low 1 19 33 23 10 23 8 11 31 15 14 10 8
Below cutoff

Sequence


Ensembl Acc Id: ENSRNOT00000019799   ⟹   ENSRNOP00000019799
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl174,165,851 - 74,204,397 (+)Ensembl
Rnor_6.0 Ensembl175,356,220 - 75,394,758 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000064178   ⟹   ENSRNOP00000061228
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl174,169,657 - 74,204,401 (+)Ensembl
Rnor_6.0 Ensembl175,233,703 - 75,264,293 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000109652   ⟹   ENSRNOP00000089677
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl174,165,842 - 74,204,413 (+)Ensembl
RefSeq Acc Id: NM_001024268   ⟹   NP_001019439
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8183,243,170 - 83,281,707 (+)NCBI
mRatBN7.2174,165,858 - 74,204,400 (+)NCBI
Rnor_6.0175,356,220 - 75,394,757 (+)NCBI
Rnor_5.0176,723,841 - 76,762,378 (+)NCBI
RGSC_v3.4173,728,892 - 73,767,429 (+)RGD
Celera169,539,708 - 69,578,250 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039091950   ⟹   XP_038947878
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8183,243,043 - 83,281,704 (+)NCBI
mRatBN7.2174,165,992 - 74,204,400 (+)NCBI
RefSeq Acc Id: XM_039091955   ⟹   XP_038947883
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8183,243,608 - 83,281,704 (+)NCBI
mRatBN7.2174,166,425 - 74,204,400 (+)NCBI
RefSeq Acc Id: NP_001019439   ⟸   NM_001024268
- UniProtKB: Q9JHY8 (UniProtKB/Swiss-Prot),   Q566D8 (UniProtKB/TrEMBL),   F1M624 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000019799   ⟸   ENSRNOT00000019799
RefSeq Acc Id: XP_038947878   ⟸   XM_039091950
- Peptide Label: isoform X1
- UniProtKB: Q9JHY8 (UniProtKB/Swiss-Prot),   A0A8J8XFV7 (UniProtKB/TrEMBL),   A6KSM0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038947883   ⟸   XM_039091955
- Peptide Label: isoform X1
- UniProtKB: Q9JHY8 (UniProtKB/Swiss-Prot),   A0A8J8XFV7 (UniProtKB/TrEMBL),   A6KSM0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000061228   ⟸   ENSRNOT00000064178
Ensembl Acc Id: ENSRNOP00000089677   ⟸   ENSRNOT00000109652
Protein Domains
ATP-dependent DNA ligase family profile

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M8E6-F1-model_v2 AlphaFold F1M8E6 1-832 view protein structure
AF-Q9JHY8-F1-model_v2 AlphaFold Q9JHY8 1-918 view protein structure

Transcriptome

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

Promoters
RGD ID:13689715
Promoter ID:EPDNEW_R240
Type:multiple initiation site
Name:Lig1_1
Description:DNA ligase 1
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_6.0175,356,211 - 75,356,271EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621424 AgrOrtholog
BioCyc Gene G2FUF-60673 BioCyc
Ensembl Genes ENSRNOG00000014193 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000047206 Ensembl
Ensembl Transcript ENSRNOT00000019799.7 UniProtKB/TrEMBL
  ENSRNOT00000064178.3 UniProtKB/TrEMBL
  ENSRNOT00000109652.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.3260.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.40.50.140 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.1490.70 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA ligase/mRNA capping enzyme UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7317599 IMAGE-MGC_LOAD
InterPro DNA_ligase_ATP-dep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_ligase_ATP-dep_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_ligase_ATP-dep_cent UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_ligase_ATP-dep_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_ligase_ATP-dep_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_ligase_N_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA-bd_OB-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:81513 UniProtKB/TrEMBL
MGC_CLONE MGC:105416 IMAGE-MGC_LOAD
NCBI Gene 81513 ENTREZGENE
PANTHER DNA LIGASE 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA LIGASE 1/3 FAMILY MEMBER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DNA_ligase_A_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_ligase_A_M UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_ligase_A_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB LIG1 RGD
PhenoGen Lig1 PhenoGen
PROSITE DNA_LIGASE_A1 UniProtKB/TrEMBL
  DNA_LIGASE_A2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_LIGASE_A3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000014193 RatGTEx
  ENSRNOG00000047206 RatGTEx
Superfamily-SCOP DNA ligase/mRNA capping enzyme, catalytic domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF117018 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50249 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6A998_RAT UniProtKB/TrEMBL
  A0A8J8XFV7 ENTREZGENE, UniProtKB/TrEMBL
  A6KSM0 ENTREZGENE, UniProtKB/TrEMBL
  A6KSM2_RAT UniProtKB/TrEMBL
  DNLI1_RAT UniProtKB/Swiss-Prot
  F1M624 ENTREZGENE
  F1M8E6_RAT UniProtKB/TrEMBL
  Q566D8 ENTREZGENE, UniProtKB/TrEMBL
  Q9JHY8 ENTREZGENE
UniProt Secondary F1M624 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Lig1  DNA ligase 1  LOC100911727  DNA ligase 1-like  Data merged from RGD:6491367 737654 PROVISIONAL
2016-05-11 Lig1  DNA ligase 1  Lig1  ligase I, DNA, ATP-dependent  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100911727  DNA ligase 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-04-05 Lig1  ligase I, DNA, ATP-dependent  Lig1_predicted  ligase I, DNA, ATP-dependent (predicted)  Data merged from RGD:1307019 737654 APPROVED
2005-01-20 Lig1  ligase I, DNA, ATP-dependent    DNA ligase I  Name updated 1299863 APPROVED
2005-01-12 Lig1_predicted  ligase I, DNA, ATP-dependent (predicted)      Symbol and Name status set to approved 70820 APPROVED
2002-08-07 Lig1  DNA ligase I      Symbol and Name status set to provisional 70820 PROVISIONAL