Xrcc6 (X-ray repair cross complementing 6) - Rat Genome Database

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Gene: Xrcc6 (X-ray repair cross complementing 6) Rattus norvegicus
Analyze
Symbol: Xrcc6
Name: X-ray repair cross complementing 6
RGD ID: 2643
Description: Contributes to double-stranded DNA binding activity. Involved in brain development; cellular hyperosmotic salinity response; and cellular response to X-ray. Located in cytoplasm and nucleolus. Part of protein-containing complex. Orthologous to human XRCC6 (X-ray repair cross complementing 6); PARTICIPATES IN non-homologous end joining pathway of double-strand break repair; INTERACTS WITH (R,R,R)-alpha-tocopherol; 2,3,7,8-tetrachlorodibenzodioxine; 7,12-dimethyltetraphene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: G22p1; Ku70; Ku70 DNA-binding component of DNA-dependent proteinkinase complex (thyroid autoantigen 70 kDa); Kup70; thyroid autoantigen; X-ray repair complementing defective repair in Chinese hamster cells 6; X-ray repair cross-complementing protein 6
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
mRatBN7.27113,542,992 - 113,563,762 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7113,543,057 - 113,563,762 (+)Ensembl
Rnor_6.07123,259,881 - 123,280,613 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,259,761 - 123,280,612 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07123,244,581 - 123,265,278 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47120,401,944 - 120,422,923 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17120,436,196 - 120,457,039 (+)NCBI
Celera7109,858,919 - 109,879,605 (+)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-dexrazoxane  (ISO)
(R,R,R)-alpha-tocopherol  (EXP)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2'-dithiodiethanol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3'-diindolylmethane  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (EXP,ISO)
acrolein  (ISO)
acrylonitrile  (EXP)
aldehydo-D-glucose  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
Benzo[ghi]perylene  (ISO)
biphenyl-4-amine  (ISO)
bisphenol A  (EXP,ISO)
bupivacaine  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
cisplatin  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclophosphamide  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
doxorubicin  (EXP,ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
fenthion  (ISO)
folic acid  (ISO)
gentamycin  (EXP)
glucose  (ISO)
idarubicin  (ISO)
ivermectin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
methyl methanesulfonate  (ISO)
N-acetyl-L-cysteine  (EXP)
N-nitrosodiethylamine  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
phosphoramide mustard  (EXP)
potassium bromate  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP)
sodium arsenite  (ISO)
sulindac sulfide  (ISO)
tamoxifen  (EXP)
terbufos  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Autoantigen Ku in the brain. Developmentally regulated expression and subcellular localization. Bakalkin G, etal., Neuroreport. 1998 Jun 22;9(9):2147-51.
2. Hypertonic treatment inhibits radiation-induced nuclear translocation of the Ku proteins G22p1 (Ku70) and Xrcc5 (Ku80) in rat fibroblasts. Endoh D, etal., Radiat Res. 2001 Feb;155(2):320-7.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Transcriptional regulation of P450scc gene expression in the embryonic rodent nervous system. Hammer F, etal., Endocrinology 2004 Feb;145(2):901-12. Epub 2003 Oct 23.
6. Immunolocalization of Ku-proteins (p80/p70): localization of p70 to nucleoli and periphery of both interphase nuclei and metaphase chromosomes. Higashiura M, etal., Exp Cell Res. 1992 Aug;201(2):444-51.
7. Double-strand break repair by Ku70 requires heterodimerization with Ku80 and DNA binding functions. Jin S and Weaver DT, EMBO J. 1997 Nov 17;16(22):6874-85. doi: 10.1093/emboj/16.22.6874.
8. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Lieber MR Annu Rev Biochem. 2010;79:181-211. doi: 10.1146/annurev.biochem.052308.093131.
9. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
10. Deficiency in nuclear accumulation of G22p1 and Xrcc5 proteins in hyper-radiosensitive Long-Evans Cinnamon (LEC) rat cells after X irradiation. Okui T, etal., Radiat Res 2002 May;157(5):553-61.
11. Online Mendelian Inheritance in Man, OMIM (TM). Online Mendelian Inheritance in Man, OMIM (TM).
12. Expression and heterodimer-binding activity of Ku70 and Ku80 in human non-melanoma skin cancer. Parrella P, etal., J Clin Pathol. 2006 Nov;59(11):1181-5. Epub 2006 Feb 23.
13. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
14. GOA pipeline RGD automated data pipeline
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:8621488   PMID:10409678   PMID:10716994   PMID:10783163   PMID:11751629   PMID:12145306   PMID:12377759   PMID:12604618   PMID:15159402   PMID:15979950   PMID:18162465   PMID:18378183  
PMID:18809223   PMID:19121380   PMID:19135898   PMID:19723106   PMID:19946888   PMID:20150414   PMID:20383123   PMID:21568942   PMID:22019940   PMID:22504299   PMID:22658674   PMID:22681889  
PMID:24095731   PMID:25852083   PMID:25941166   PMID:26359349   PMID:27621182   PMID:27829214   PMID:28712728  


Genomics

Comparative Map Data
Xrcc6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27113,542,992 - 113,563,762 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7113,543,057 - 113,563,762 (+)Ensembl
Rnor_6.07123,259,881 - 123,280,613 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,259,761 - 123,280,612 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07123,244,581 - 123,265,278 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47120,401,944 - 120,422,923 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17120,436,196 - 120,457,039 (+)NCBI
Celera7109,858,919 - 109,879,605 (+)NCBICelera
Cytogenetic Map7q34NCBI
XRCC6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382241,621,295 - 41,664,041 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2241,621,163 - 41,664,048 (+)EnsemblGRCh38hg38GRCh38
GRCh372242,017,299 - 42,060,045 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362240,347,241 - 40,389,998 (+)NCBINCBI36hg18NCBI36
Build 342240,341,794 - 40,384,552NCBI
Celera2225,823,724 - 25,866,486 (+)NCBI
Cytogenetic Map22q13.2NCBI
HuRef2224,982,897 - 25,025,516 (+)NCBIHuRef
CHM1_12241,977,343 - 42,020,083 (+)NCBICHM1_1
T2T-CHM13v2.02242,100,225 - 42,143,017 (+)NCBI
Xrcc6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391581,868,805 - 81,924,286 (+)NCBIGRCm39mm39
GRCm39 Ensembl1581,872,036 - 81,924,286 (+)Ensembl
GRCm381581,987,833 - 82,040,085 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1581,987,835 - 82,040,085 (+)EnsemblGRCm38mm10GRCm38
MGSCv371581,846,799 - 81,870,514 (+)NCBIGRCm37mm9NCBIm37
MGSCv361581,843,555 - 81,867,327 (+)NCBImm8
Celera1584,138,425 - 84,161,793 (+)NCBICelera
Cytogenetic Map15E1NCBI
cM Map1538.33NCBI
Xrcc6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541327,135,805 - 27,159,750 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541327,135,785 - 27,158,344 (+)NCBIChiLan1.0ChiLan1.0
XRCC6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12240,626,191 - 40,643,540 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2240,603,038 - 40,643,314 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02222,516,281 - 22,557,379 (+)NCBIMhudiblu_PPA_v0panPan3
XRCC6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11023,637,905 - 23,661,618 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1023,638,237 - 23,661,480 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1023,571,669 - 23,594,987 (-)NCBI
ROS_Cfam_1.01024,383,246 - 24,406,874 (-)NCBI
ROS_Cfam_1.0 Ensembl1024,382,986 - 24,406,763 (-)Ensembl
UMICH_Zoey_3.11024,100,152 - 24,123,487 (-)NCBI
UNSW_CanFamBas_1.01024,421,552 - 24,445,083 (-)NCBI
UU_Cfam_GSD_1.01024,595,424 - 24,619,012 (-)NCBI
Xrcc6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049457,293,429 - 7,315,475 (-)NCBI
SpeTri2.0NW_004936492303,843 - 325,812 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XRCC6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl56,903,495 - 6,929,052 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.156,903,496 - 6,929,162 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.254,274,586 - 4,300,429 (-)NCBISscrofa10.2Sscrofa10.2susScr3
XRCC6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11924,160,459 - 24,204,237 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1924,160,483 - 24,206,320 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666045101,209,345 - 101,253,933 (-)NCBIVero_WHO_p1.0
Xrcc6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247526,979,271 - 7,010,787 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046247526,987,456 - 7,010,834 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH131971  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27113,563,535 - 113,563,743 (+)MAPPERmRatBN7.2
Rnor_6.07123,280,387 - 123,280,594NCBIRnor6.0
Rnor_5.07123,265,052 - 123,265,259UniSTSRnor5.0
RGSC_v3.47120,422,697 - 120,422,904UniSTSRGSC3.4
Celera1617,241,644 - 17,241,851UniSTS
Celera7109,879,379 - 109,879,586UniSTS
RH 3.4 Map7893.1UniSTS
Cytogenetic Map7q34UniSTS
AI230026  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27113,559,122 - 113,559,330 (+)MAPPERmRatBN7.2
Rnor_6.07123,275,974 - 123,276,181NCBIRnor6.0
Rnor_5.07123,260,639 - 123,260,846UniSTSRnor5.0
RGSC_v3.47120,418,284 - 120,418,491UniSTSRGSC3.4
Celera7109,874,966 - 109,875,173UniSTS
RH 3.4 Map7889.2UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)794811085116738842Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)794811326116294265Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7103146217116738842Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:105
Count of miRNA genes:75
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000008819, ENSRNOT00000066849
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 26 56 40 19 40 2 5 74 35 41 11 2
Low 17 1 1 1 6 6 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008819   ⟹   ENSRNOP00000008819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7113,544,966 - 113,563,762 (+)Ensembl
Rnor_6.0 Ensembl7123,259,761 - 123,280,612 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000066849   ⟹   ENSRNOP00000061920
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7113,543,057 - 113,563,607 (+)Ensembl
Rnor_6.0 Ensembl7123,260,607 - 123,280,510 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105863   ⟹   ENSRNOP00000081965
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7113,547,679 - 113,563,762 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108388   ⟹   ENSRNOP00000082673
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7113,543,121 - 113,563,760 (+)Ensembl
RefSeq Acc Id: NM_139080   ⟹   NP_620780
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27113,543,057 - 113,563,762 (+)NCBI
Rnor_6.07123,259,892 - 123,280,613 (+)NCBI
Rnor_5.07123,244,581 - 123,265,278 (+)NCBI
RGSC_v3.47120,401,944 - 120,422,923 (+)RGD
Celera7109,858,919 - 109,879,605 (+)RGD
Sequence:
RefSeq Acc Id: XM_008765671   ⟹   XP_008763893
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27113,542,992 - 113,563,762 (+)NCBI
Rnor_6.07123,259,881 - 123,280,613 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_620780 (Get FASTA)   NCBI Sequence Viewer  
  XP_008763893 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH78718 (Get FASTA)   NCBI Sequence Viewer  
  BAB83858 (Get FASTA)   NCBI Sequence Viewer  
  EDM15680 (Get FASTA)   NCBI Sequence Viewer  
  EDM15681 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_620780   ⟸   NM_139080
- UniProtKB: Q6AZ64 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763893   ⟸   XM_008765671
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000008819   ⟸   ENSRNOT00000008819
RefSeq Acc Id: ENSRNOP00000061920   ⟸   ENSRNOT00000066849
RefSeq Acc Id: ENSRNOP00000081965   ⟸   ENSRNOT00000105863
RefSeq Acc Id: ENSRNOP00000082673   ⟸   ENSRNOT00000108388
Protein Domains
SAP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-E9PT85-F1-model_v2 AlphaFold E9PT85 1-609 view protein structure

Transcriptome

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

Promoters
RGD ID:13695525
Promoter ID:EPDNEW_R6049
Type:multiple initiation site
Name:Xrcc6_1
Description:X-ray repair cross complementing 6
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_6.07123,259,938 - 123,259,998EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
BUF/N (2020)
Visual CSV TAB Printer
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
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
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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
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
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
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/Stm (2019)
Visual CSV TAB Printer
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
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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
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
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
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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
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
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)
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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
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
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
LEW/Crl (2019)
Visual CSV TAB Printer
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
LEXF10A/StmMcwi (2020)
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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
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
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
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
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
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
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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/NRrrcMcwi (2019)
Visual CSV TAB Printer
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
MR/N (2020)
Visual CSV TAB Printer
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
MWF/Hsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
SHR/OlalpcvMcwi (2019)
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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)
Visual CSV TAB Printer
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
SR/JrHsd (2020)
Visual CSV TAB Printer
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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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
WAG/RijCrl (2020)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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/NCrl (2019)
Visual CSV TAB Printer
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
WN/N (2020)
Visual CSV TAB Printer
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 123269458 123269459 C T snv SBH/Ygl (MCW), SBN/Ygl (RGD), SBH/Ygl (RGD), SBN/Ygl (MCW)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 123254123 123254124 C T snv SBH/Ygl (MCW), HTX/Kyo (KyushuU), SDLEF7/Barth (UDEL), SBN/Ygl (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 120411768 120411769 C T snv SBN/Ygl (ICL), SBH/Ygl (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2643 AgrOrtholog
BioCyc Gene G2FUF-32648 BioCyc
Ensembl Genes ENSRNOG00000006392 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008819.5 UniProtKB/TrEMBL
  ENSRNOP00000061920 ENTREZGENE
  ENSRNOP00000061920.1 UniProtKB/TrEMBL
  ENSRNOP00000081965.1 UniProtKB/TrEMBL
  ENSRNOP00000082673 ENTREZGENE
  ENSRNOP00000082673.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008819.8 UniProtKB/TrEMBL
  ENSRNOT00000066849 ENTREZGENE
  ENSRNOT00000066849.2 UniProtKB/TrEMBL
  ENSRNOT00000105863.1 UniProtKB/TrEMBL
  ENSRNOT00000108388 ENTREZGENE
  ENSRNOT00000108388.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.720.30 UniProtKB/TrEMBL
  2.40.290.10 UniProtKB/TrEMBL
  3.40.50.410 UniProtKB/TrEMBL
  4.10.970.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7115290 IMAGE-MGC_LOAD
InterPro DNA_helicase_ATP-dep_Ku UniProtKB/TrEMBL
  DNA_helicase_ATP-dep_Ku70 UniProtKB/TrEMBL
  Ku70_bridge/pillars_dom UniProtKB/TrEMBL
  Ku_C UniProtKB/TrEMBL
  Ku_N UniProtKB/TrEMBL
  SAP_DNA-bd UniProtKB/TrEMBL
  SAP_dom_sf UniProtKB/TrEMBL
  SPOC-like UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report rno:25019 UniProtKB/TrEMBL
MGC_CLONE MGC:93146 IMAGE-MGC_LOAD
NCBI Gene 25019 ENTREZGENE
Pfam Ku_C UniProtKB/TrEMBL
  Ku_N UniProtKB/TrEMBL
  PF02735 UniProtKB/TrEMBL
  SAP UniProtKB/TrEMBL
PhenoGen Xrcc6 PhenoGen
PIRSF Ku70 UniProtKB/TrEMBL
PROSITE SAP UniProtKB/TrEMBL
SMART Ku78 UniProtKB/TrEMBL
  SAP UniProtKB/TrEMBL
Superfamily-SCOP SPOC-like UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
  SSF68906 UniProtKB/TrEMBL
TIGRFAMs ku70 UniProtKB/TrEMBL
UniProt A0A8I5ZSS0_RAT UniProtKB/TrEMBL
  A0A8I5ZXI9_RAT UniProtKB/TrEMBL
  E9PT85_RAT UniProtKB/TrEMBL
  F7EV16_RAT UniProtKB/TrEMBL
  Q6AZ64 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-08 Xrcc6  X-ray repair cross complementing 6  Xrcc6  X-ray repair complementing defective repair in Chinese hamster cells 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Xrcc6  X-ray repair complementing defective repair in Chinese hamster cells 6  G22p1  thyroid autoantigen  Symbol and Name updated 1299863 APPROVED
2002-11-06 G22p1  thyroid autoantigen    Ku70 DNA-binding component of DNA-dependent proteinkinase complex (thyroid autoantigen 70 kDa)  Name updated 625702 APPROVED
2002-06-10 G22p1  Ku70 DNA-binding component of DNA-dependent proteinkinase complex (thyroid autoantigen 70 kDa)      Symbol and Name status set to approved 70586 APPROVED