Xrcc1 (X-ray repair cross complementing 1) - Rat Genome Database

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Gene: Xrcc1 (X-ray repair cross complementing 1) Rattus norvegicus
Analyze
Symbol: Xrcc1
Name: X-ray repair cross complementing 1
RGD ID: 619823
Description: Predicted to enable enzyme binding activity and oxidized DNA binding activity. Predicted to contribute to 3' overhang single-stranded DNA endodeoxyribonuclease activity. Involved in several processes, including base-excision repair; response to drug; and response to hypoxia. Located in nucleus. Used to study in situ carcinoma. Biomarker of asphyxia neonatorum; transient cerebral ischemia; and visual epilepsy. Human ortholog(s) of this gene implicated in several diseases, including autosomal recessive spinocerebellar ataxia 26; carcinoma (multiple); hematologic cancer (multiple); hepatitis A; and reproductive organ cancer (multiple). Orthologous to human XRCC1 (X-ray repair cross complementing 1); PARTICIPATES IN base excision repair pathway; nucleotide excision repair pathway; INTERACTS WITH (+)-pilocarpine; (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DNA repair protein XRCC1; X-ray repair complementing defective repair in Chinese hamster cells 1; x-ray repair cross-complementing group 1 protein; X-ray repair cross-complementing protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2180,140,495 - 80,168,705 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl180,141,207 - 80,168,701 (+)Ensembl
Rnor_6.0181,412,635 - 81,441,680 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl181,413,353 - 81,441,678 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0182,673,571 - 82,701,082 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4179,834,167 - 79,860,300 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1179,912,277 - 79,938,411 (+)NCBI
Celera174,594,313 - 74,621,523 (+)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-dexrazoxane  (ISO)
(+)-pilocarpine  (EXP)
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(-)-quinic acid  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methylphenanthrene  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-hydroperoxycyclophosphamide  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
5-formyltetrahydrofolic acid  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (ISO)
acrylamide  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphibole asbestos  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
asbestos  (ISO)
ATP  (ISO)
belinostat  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
Benzo[ghi]perylene  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
buta-1,3-diene  (ISO)
cadmium dichloride  (ISO)
carbamazepine  (ISO)
chloroethene  (EXP,ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclophosphamide  (EXP)
cyproconazole  (EXP)
cytarabine  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
doxorubicin  (ISO)
emodin  (EXP)
epoxiconazole  (EXP)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
fipronil  (EXP)
flavonoids  (ISO)
floxuridine  (ISO)
fluoranthene  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP,ISO)
gefitinib  (ISO)
genistein  (ISO)
glutathione  (ISO)
hydrogen peroxide  (ISO)
idarubicin  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
lead chromate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
levetiracetam  (EXP)
lipopolysaccharide  (ISO)
lupeol  (ISO)
LY294002  (ISO)
malonaldehyde  (ISO)
mancozeb  (ISO)
methamphetamine  (ISO)
methyl methanesulfonate  (ISO)
mithramycin  (ISO)
Monobutylphthalate  (EXP)
N-acetyl-L-cysteine  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
NAD zwitterion  (ISO)
NAD(+)  (ISO)
nicotine  (ISO)
oxaliplatin  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PhIP  (EXP)
piperonyl butoxide  (ISO)
platinum  (ISO)
platinum(0)  (ISO)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
sodium arsenite  (ISO)
styrene  (ISO)
styrene oxide  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP)
theaflavin  (ISO)
trichloroethene  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
ubiquinones  (ISO)
usnic acid  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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2. Almeida Pereira Leite ST, etal., Ann Hepatol. 2013 Sep-Oct;12(5):733-9.
3. Batar B, etal., Leuk Res. 2009 Jun;33(6):759-63. doi: 10.1016/j.leukres.2008.11.005. Epub 2008 Dec 19.
4. Bazgir A, etal., Middle East J Dig Dis. 2018 Jan;10(1):40-44. doi: 10.15171/mejdd.2017.89. Epub 2018 Jan 10.
5. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
6. Bi J, etal., Biomed Res Int. 2013;2013:138785. doi: 10.1155/2013/138785. Epub 2013 Jul 30.
7. Bose S, etal., Gene. 2013 May 1;519(2):231-7. doi: 10.1016/j.gene.2013.02.025. Epub 2013 Feb 27.
8. Bu D, etal., Breast Cancer Res Treat. 2006 Oct;99(3):257-65. Epub 2006 Apr 5.
9. Burri RJ, etal., Radiat Res. 2008 Jul;170(1):49-59.
10. Chen X, etal., Cell Oncol (Dordr). 2018 Oct;41(5):527-539. doi: 10.1007/s13402-018-0390-8. Epub 2018 Aug 7.
11. Chiappe-Gutierrez M, etal., Life Sci. 1998;63(13):1157-67.
12. Deng X, etal., Int J Biol Sci. 2013;9(3):289-94. doi: 10.7150/ijbs.5928. Epub 2013 Mar 7.
13. Dufloth RM, etal., Genet Mol Res. 2008 Jul 1;7(3):574-82.
14. Ganster C, etal., Genes Chromosomes Cancer. 2009 Sep;48(9):760-7. doi: 10.1002/gcc.20680.
15. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
16. GOA data from the GO Consortium
17. Gu M, etal., Virol J. 2018 Mar 20;15(1):47. doi: 10.1186/s12985-018-0962-2.
18. Harrouk W, etal., Mutat Res 2000 Nov 9;461(3):229-41.
19. Hirata H, etal., Biochem Biophys Res Commun. 2006 Apr 21;342(4):1058-62. Epub 2006 Feb 17.
20. Hsu LI, etal., Toxicol Appl Pharmacol. 2008 Apr 15;228(2):144-55. Epub 2007 Dec 14.
21. Hung RJ, etal., Am J Epidemiol. 2005 Nov 15;162(10):925-42. Epub 2005 Oct 12.
22. Jeon YT, etal., Hum Reprod. 2005 Jun;20(6):1586-9. Epub 2005 Mar 10.
23. Jiang T, etal., Med Oncol. 2014 Apr;31(4):887. doi: 10.1007/s12032-014-0887-6. Epub 2014 Feb 26.
24. Joshi D, etal., Ann Hematol. 2016 Jan;95(1):79-85.
25. Kim K, etal., Gynecol Oncol. 2008 Dec;111(3):509-15. Epub 2008 Oct 12.
26. Kiran M, etal., Mol Cell Biochem. 2009 Jul;327(1-2):7-13. doi: 10.1007/s11010-009-0035-3. Epub 2009 Feb 5.
27. Lao T, etal., Mutagenesis. 2008 Nov;23(6):523-32. Epub 2008 Sep 2.
28. Lehmann AR DNA Repair (Amst). 2011 Jul 15;10(7):730-3. doi: 10.1016/j.dnarep.2011.04.023. Epub 2011 May 20.
29. Li D, etal., J Clin Oncol. 2006 Apr 10;24(11):1720-8. Epub 2006 Mar 6.
30. Li N, etal., DNA Repair (Amst). 2007 Sep 1;6(9):1297-306. Epub 2007 Apr 6.
31. Li QW, etal., Asian Pac J Cancer Prev. 2012;13(1):191-4. doi: 10.7314/apjcp.2012.13.1.191.
32. Liu WB, etal., Biochem Biophys Res Commun. 2011 May 20;408(4):595-601. doi: 10.1016/j.bbrc.2011.04.067. Epub 2011 Apr 21.
33. Liu Y, etal., Med Oncol. 2014 Mar;31(3):854. doi: 10.1007/s12032-014-0854-2. Epub 2014 Feb 14.
34. Luo YF, etal., Curr Eye Res. 2011 Jul;36(7):632-6. doi: 10.3109/02713683.2011.571358. Epub 2011 May 20.
35. Majumder M, etal., Int J Cancer. 2007 May 15;120(10):2148-56.
36. Mattar MM, etal., Gene. 2018 Oct 30;675:62-68. doi: 10.1016/j.gene.2018.06.056. Epub 2018 Jun 20.
37. McNeill DR, etal., Nucleic Acids Res. 2011 Oct;39(18):7992-8004. doi: 10.1093/nar/gkr280. Epub 2011 Jul 6.
38. NCBI rat LocusLink and RefSeq merged data July 26, 2002
39. Pipeline to import KEGG annotations from KEGG into RGD
40. Quach N, etal., Brain Res. 2005 May 3;1042(2):236-40.
41. RGD automated data pipeline
42. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
43. RGD automated import pipeline for gene-chemical interactions
44. RGD comprehensive gene curation
45. Sak SC, etal., BMC Genet. 2007 Apr 10;8:13.
46. Salimizand H, etal., Tumour Biol. 2016 Jan;37(1):791-8. doi: 10.1007/s13277-015-3874-4. Epub 2015 Aug 7.
47. Santonocito C, etal., Int J Biol Markers. 2017 May 4;32(2):e190-e194. doi: 10.5301/jbm.5000241.
48. Srivastava A, etal., Ann Surg Oncol. 2009 Jun;16(6):1695-703. Epub 2009 Mar 6.
49. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
50. Syamala VS, etal., Pathol Oncol Res. 2008 Dec 4.
51. Thyagarajan B, etal., Cancer Detect Prev. 2006;30(4):313-21. Epub 2006 Sep 11.
52. Tiseo M, etal., Br J Cancer. 2013 Apr 30;108(8):1695-703. doi: 10.1038/bjc.2013.127. Epub 2013 Apr 2.
53. Tsuchiya N, etal., Int J Oncol. 2006 May;28(5):1217-23.
54. Tumer TB, etal., Arch Toxicol. 2012 Mar;86(3):431-9. doi: 10.1007/s00204-011-0760-8. Epub 2011 Oct 9.
55. Vinson RK and Hales BF, Teratology. 2001 Dec;64(6):283-91.
56. Wang XC, etal., Genet Test Mol Biomarkers. 2016 Apr;20(4):176-84. doi: 10.1089/gtmb.2015.0267. Epub 2016 Feb 26.
57. Wolf N, etal., Mol Vis. 2008 Feb 5;14:274-85.
58. Xu Z, etal., Zhonghua Nan Ke Xue. 2007 Apr;13(4):327-31.
59. Yang Y, etal., J Neurochem. 2010 Jan;112(1):134-49. Epub 2009 Oct 15.
60. Yu MW, etal., J Natl Cancer Inst. 2003 Oct 1;95(19):1485-8. doi: 10.1093/jnci/djg051.
61. Yue AM, etal., Asian Pac J Cancer Prev. 2013;14(1):355-8. doi: 10.7314/apjcp.2013.14.1.355.
62. Zhang L, etal., Hepatology. 2012 Apr;55(4):1008-18. doi: 10.1002/hep.25513.
63. Zhu SM, etal., Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2004 Jun;22(3):173-5.
Additional References at PubMed
PMID:8532526   PMID:14690602   PMID:15489334   PMID:19633665   PMID:28002403  


Genomics

Comparative Map Data
Xrcc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2180,140,495 - 80,168,705 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl180,141,207 - 80,168,701 (+)Ensembl
Rnor_6.0181,412,635 - 81,441,680 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl181,413,353 - 81,441,678 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0182,673,571 - 82,701,082 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4179,834,167 - 79,860,300 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1179,912,277 - 79,938,411 (+)NCBI
Celera174,594,313 - 74,621,523 (+)NCBICelera
Cytogenetic Map1q21NCBI
XRCC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1943,543,311 - 43,580,473 (-)EnsemblGRCh38hg38GRCh38
GRCh381943,543,311 - 43,575,527 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371944,047,463 - 44,079,679 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361948,739,304 - 48,771,555 (-)NCBINCBI36hg18NCBI36
Build 341948,739,303 - 48,771,555NCBI
Celera1940,850,091 - 40,882,209 (-)NCBI
Cytogenetic Map19q13.31NCBI
HuRef1940,478,136 - 40,510,489 (-)NCBIHuRef
CHM1_11944,049,115 - 44,081,452 (-)NCBICHM1_1
Xrcc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39724,246,124 - 24,272,863 (+)NCBIGRCm39mm39
GRCm39 Ensembl724,245,714 - 24,272,865 (+)Ensembl
GRCm38724,546,699 - 24,573,438 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl724,546,289 - 24,573,440 (+)EnsemblGRCm38mm10GRCm38
MGSCv37725,332,169 - 25,358,457 (+)NCBIGRCm37mm9NCBIm37
MGSCv36724,255,049 - 24,282,192 (+)NCBImm8
Celera719,161,255 - 19,187,540 (+)NCBICelera
Cytogenetic Map7A3NCBI
cM Map711.42NCBI
Xrcc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555551,293,416 - 1,315,839 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555551,293,416 - 1,315,839 (-)NCBIChiLan1.0ChiLan1.0
XRCC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11949,093,928 - 49,125,723 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1949,094,014 - 49,125,520 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01940,485,052 - 40,522,188 (-)NCBIMhudiblu_PPA_v0panPan3
XRCC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11111,548,719 - 111,571,816 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1111,548,719 - 111,571,816 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1111,028,445 - 111,051,541 (+)NCBI
ROS_Cfam_1.01112,158,850 - 112,181,954 (+)NCBI
UMICH_Zoey_3.11111,746,938 - 111,770,215 (+)NCBI
UNSW_CanFamBas_1.01111,380,774 - 111,403,889 (+)NCBI
UU_Cfam_GSD_1.01112,265,054 - 112,288,168 (+)NCBI
Xrcc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934916,407,084 - 16,436,413 (-)NCBI
SpeTri2.0NW_004936706752,571 - 783,746 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XRCC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl650,403,686 - 50,425,710 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1650,403,691 - 50,425,730 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2646,158,742 - 46,180,744 (-)NCBISscrofa10.2Sscrofa10.2susScr3
XRCC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1637,062,149 - 37,095,138 (-)NCBI
ChlSab1.1 Ensembl637,060,439 - 37,095,094 (-)Ensembl
Vero_WHO_p1.0NW_02366607316,603,474 - 16,637,686 (-)NCBI
Xrcc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249071,087,611 - 1,113,275 (-)NCBI

Position Markers
Xrcc1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2180,168,335 - 80,168,582 (+)MAPPERmRatBN7.2
Rnor_6.0181,441,311 - 81,441,557NCBIRnor6.0
Rnor_5.0182,700,713 - 82,700,959UniSTSRnor5.0
RGSC_v3.4179,859,931 - 79,860,177UniSTSRGSC3.4
Celera174,621,154 - 74,621,400UniSTS
Cytogenetic Map1q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)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
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15389511782174945Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15389511782174945Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
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
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)17219768090508767Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)177494165122494165Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)177857876122857876Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)177876254106047988Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)178350581123350581Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)178430536123430536Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17843075491209302Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)178479925123479925Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:49
Count of miRNA genes:47
Interacting mature miRNAs:47
Transcripts:ENSRNOT00000027057
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.


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 3 37 49 33 19 33 8 11 74 35 41 11 8
Low 6 8 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027057   ⟹   ENSRNOP00000027057
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl180,141,207 - 80,168,701 (+)Ensembl
Rnor_6.0 Ensembl181,413,353 - 81,441,678 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096411   ⟹   ENSRNOP00000094456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl180,141,207 - 80,159,863 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000100887   ⟹   ENSRNOP00000092376
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl180,141,227 - 80,168,683 (+)Ensembl
RefSeq Acc Id: NM_053435   ⟹   NP_445887
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,141,273 - 80,168,705 (+)NCBI
Rnor_6.0181,413,353 - 81,441,680 (+)NCBI
Rnor_5.0182,673,571 - 82,701,082 (+)NCBI
RGSC_v3.4179,834,167 - 79,860,300 (+)RGD
Celera174,594,313 - 74,621,523 (+)RGD
Sequence:
RefSeq Acc Id: XM_017589796   ⟹   XP_017445285
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,141,171 - 80,168,704 (+)NCBI
Rnor_6.0181,413,237 - 81,441,676 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589797   ⟹   XP_017445286
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,141,169 - 80,168,704 (+)NCBI
Rnor_6.0181,413,236 - 81,441,676 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092830   ⟹   XP_038948758
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,152,951 - 80,168,704 (+)NCBI
RefSeq Acc Id: XM_039092839   ⟹   XP_038948767
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,152,940 - 80,168,704 (+)NCBI
RefSeq Acc Id: XM_039092840   ⟹   XP_038948768
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,152,936 - 80,168,704 (+)NCBI
RefSeq Acc Id: XM_039092851   ⟹   XP_038948779
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,140,495 - 80,168,704 (+)NCBI
RefSeq Acc Id: XM_039092853   ⟹   XP_038948781
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2180,141,445 - 80,168,704 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_445887   ⟸   NM_053435
- Sequence:
RefSeq Acc Id: XP_017445286   ⟸   XM_017589797
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017445285   ⟸   XM_017589796
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000027057   ⟸   ENSRNOT00000027057
RefSeq Acc Id: XP_038948779   ⟸   XM_039092851
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038948781   ⟸   XM_039092853
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038948768   ⟸   XM_039092840
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038948767   ⟸   XM_039092839
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038948758   ⟸   XM_039092830
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000092376   ⟸   ENSRNOT00000100887
RefSeq Acc Id: ENSRNOP00000094456   ⟸   ENSRNOT00000096411
Protein Domains
BRCT

Transcriptome

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

Promoters
RGD ID:13689799
Promoter ID:EPDNEW_R323
Type:multiple initiation site
Name:Xrcc1_1
Description:X-ray repair cross complementing 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_6.0181,413,321 - 81,413,381EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (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
MNS/Gib (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
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (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: 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)
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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: 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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NHsd (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
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619823 AgrOrtholog
Ensembl Genes ENSRNOG00000019915 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000027057 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027057 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.260 UniProtKB/Swiss-Prot
  3.40.50.10190 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7099372 IMAGE-MGC_LOAD
InterPro BRCT_dom UniProtKB/Swiss-Prot
  BRCT_dom_sf UniProtKB/Swiss-Prot
  Galactose-bd-like_sf UniProtKB/Swiss-Prot
  Xrcc1_N UniProtKB/Swiss-Prot
KEGG Report rno:84495 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91581 IMAGE-MGC_LOAD
NCBI Gene 84495 ENTREZGENE
Pfam BRCT UniProtKB/Swiss-Prot
  BRCT_2 UniProtKB/Swiss-Prot
  XRCC1_N UniProtKB/Swiss-Prot
PharmGKB XRCC1 RGD
PhenoGen Xrcc1 PhenoGen
PROSITE BRCT UniProtKB/Swiss-Prot
SMART BRCT UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49785 UniProtKB/Swiss-Prot
  SSF52113 UniProtKB/Swiss-Prot
UniProt Q9ESZ0 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q6IRJ9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-08 Xrcc1  X-ray repair cross complementing 1  Xrcc1  X-ray repair complementing defective repair in Chinese hamster cells 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Xrcc1  X-ray repair complementing defective repair in Chinese hamster cells 1    x-ray repair cross-complementing group 1 protein  Name updated 1299863 APPROVED
2002-08-07 Xrcc1  x-ray repair cross-complementing group 1 protein      Symbol and Name status set to provisional 70820 PROVISIONAL