Xrcc5 (X-ray repair cross complementing 5) - Rat Genome Database

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Gene: Xrcc5 (X-ray repair cross complementing 5) Rattus norvegicus
Analyze
Symbol: Xrcc5
Name: X-ray repair cross complementing 5
RGD ID: 3976
Description: Contributes to double-stranded DNA binding activity. Involved in several processes, including cellular hyperosmotic salinity response; cellular response to X-ray; and cellular response to fatty acid. Localizes to cytoplasm; nucleus; and protein-containing complex. Human ortholog(s) of this gene implicated in chronic obstructive pulmonary disease and multiple myeloma. Orthologous to human XRCC5 (X-ray repair cross complementing 5); PARTICIPATES IN non-homologous end joining pathway of double-strand break repair; INTERACTS WITH 2,6-dinitrotoluene; 4-amino-2,6-dinitrotoluene; 4-hydroperoxycyclophosphamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Ku autoantigen, 80kD); Ku80; Kup80; X-ray repair complementing defective repair in Chinese hamster cells 5; X-ray repair cross complementation (double-strand-break rejoining; X-ray repair cross complementation (double-strand-break rejoining, Ku autoantigen, 80kD); X-ray repair cross-complementing protein 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2973,955,220 - 74,044,020 (+)NCBI
Rnor_6.0 Ensembl979,659,251 - 79,748,078 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0979,659,275 - 79,748,050 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0979,432,205 - 79,520,611 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4971,472,459 - 71,581,936 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1971,619,440 - 71,728,918 (+)NCBI
Celera971,352,925 - 71,440,328 (+)NCBICelera
Cytogenetic Map9q33NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(-)-quinic acid  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2'-dithiodiethanol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-amino-1,8-naphthalimide  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroperoxycyclophosphamide  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
biphenyl-4-amine  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
carbonyl cyanide p-trifluoromethoxyphenylhydrazone  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
curcumin  (ISO)
cyproconazole  (EXP)
D-glucose  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
disodium selenite  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP,ISO)
enzyme inhibitor  (ISO)
epoxiconazole  (EXP)
ethanol  (EXP)
etoposide  (ISO)
fenofibrate  (EXP)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furan  (EXP)
glucose  (ISO)
hydrogen peroxide  (ISO)
hydroxyurea  (ISO)
irinotecan  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
nitrogen mustard  (ISO)
p-anisidine  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenethyl caffeate  (EXP)
piperonyl butoxide  (ISO)
pirinixic acid  (EXP)
prochloraz  (EXP)
quercetin  (ISO)
raloxifene  (ISO)
sodium fluoride  (ISO)
sulindac  (EXP)
tetrachloromethane  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8621488   PMID:10409678   PMID:10535943   PMID:10716994   PMID:10783163   PMID:12377759   PMID:12531011   PMID:12604618   PMID:14704337   PMID:17010969   PMID:17554309   PMID:18809223  
PMID:19135898   PMID:19188702   PMID:19549901   PMID:19581589   PMID:19946888   PMID:20383123   PMID:20439489   PMID:22266820   PMID:22504299   PMID:22658674   PMID:22681889   PMID:24095731  
PMID:25852083   PMID:25941166   PMID:26321753   PMID:26359349   PMID:27248496   PMID:28712728   PMID:32103174  


Genomics

Comparative Map Data
Xrcc5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2973,955,220 - 74,044,020 (+)NCBI
Rnor_6.0 Ensembl979,659,251 - 79,748,078 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0979,659,275 - 79,748,050 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0979,432,205 - 79,520,611 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4971,472,459 - 71,581,936 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1971,619,440 - 71,728,918 (+)NCBI
Celera971,352,925 - 71,440,328 (+)NCBICelera
Cytogenetic Map9q33NCBI
XRCC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2216,107,464 - 216,206,303 (+)EnsemblGRCh38hg38GRCh38
GRCh382216,109,348 - 216,206,293 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372216,974,071 - 217,071,016 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362216,682,378 - 216,779,248 (+)NCBINCBI36hg18NCBI36
Build 342216,799,637 - 216,896,509NCBI
Celera2210,743,609 - 210,840,560 (+)NCBI
Cytogenetic Map2q35NCBI
HuRef2208,830,614 - 208,927,713 (+)NCBIHuRef
CHM1_12216,979,976 - 217,076,949 (+)NCBICHM1_1
Xrcc5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39172,346,576 - 72,434,112 (+)NCBIGRCm39mm39
GRCm39 Ensembl172,346,586 - 72,434,111 (+)Ensembl
GRCm38172,307,417 - 72,394,953 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl172,307,427 - 72,394,952 (+)EnsemblGRCm38mm10GRCm38
MGSCv37172,353,995 - 72,441,527 (+)NCBIGRCm37mm9NCBIm37
MGSCv36172,240,728 - 72,328,156 (+)NCBImm8
Celera172,875,673 - 72,963,703 (+)NCBICelera
Cytogenetic Map1C3NCBI
cM Map136.5NCBI
Xrcc5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545316,967,453 - 17,054,634 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545316,967,453 - 17,054,634 (-)NCBIChiLan1.0ChiLan1.0
XRCC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B221,972,607 - 222,072,318 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B221,972,742 - 222,071,235 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B103,371,459 - 103,468,419 (+)NCBIMhudiblu_PPA_v0panPan3
XRCC5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13723,095,769 - 23,185,680 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3723,095,754 - 23,185,586 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3723,923,245 - 24,015,080 (+)NCBI
ROS_Cfam_1.03723,120,975 - 23,212,731 (+)NCBI
UMICH_Zoey_3.13723,007,952 - 23,098,174 (+)NCBI
UNSW_CanFamBas_1.03722,960,108 - 23,051,031 (+)NCBI
UU_Cfam_GSD_1.03722,977,769 - 23,068,341 (+)NCBI
Xrcc5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303171,487,889 - 171,588,600 (+)NCBI
SpeTri2.0NW_0049365861,055,478 - 1,137,924 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XRCC5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15118,335,925 - 118,452,296 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115118,354,943 - 118,451,974 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215131,235,804 - 131,332,992 (+)NCBISscrofa10.2Sscrofa10.2susScr3
XRCC5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110101,952,909 - 102,051,059 (+)NCBI
ChlSab1.1 Ensembl10101,953,067 - 102,049,964 (+)Ensembl

Position Markers
D9Mco23  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2974,006,592 - 74,007,038 (+)MAPPER
Rnor_6.0979,710,630 - 79,711,077NCBIRnor6.0
Rnor_5.0979,483,369 - 79,483,816UniSTSRnor5.0
RGSC_v3.4971,544,278 - 71,544,725UniSTSRGSC3.4
Celera971,402,636 - 71,403,083UniSTS
Cytogenetic Map9q34UniSTS
RH141867  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2974,042,999 - 74,043,950 (+)MAPPER
Rnor_6.0979,747,031 - 79,747,981NCBIRnor6.0
Rnor_5.0979,519,592 - 79,520,542UniSTSRnor5.0
RGSC_v3.4971,580,917 - 71,581,867UniSTSRGSC3.4
Celera971,439,309 - 71,440,259UniSTS
RH 3.4 Map9674.6UniSTS
Cytogenetic Map9q34UniSTS
RH143010  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2973,987,766 - 73,987,906 (+)MAPPER
Rnor_6.0979,691,804 - 79,691,943NCBIRnor6.0
Rnor_5.0979,464,543 - 79,464,682UniSTSRnor5.0
RGSC_v3.4971,525,452 - 71,525,591UniSTSRGSC3.4
Celera971,383,817 - 71,383,956UniSTS
RH 3.4 Map9675.7UniSTS
Cytogenetic Map9q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94657976991579769Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94657976991579769Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94695242783686153Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96081029882732466Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96173092382890620Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96745166499920892Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96745166499920892Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:150
Count of miRNA genes:120
Interacting mature miRNAs:127
Transcripts:ENSRNOT00000021656
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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 27 46 33 19 33 1 3 74 35 34 11 1
Low 16 11 8 8 7 8 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021656   ⟹   ENSRNOP00000021656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl979,659,251 - 79,748,078 (+)Ensembl
RefSeq Acc Id: NM_177419   ⟹   NP_803154
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2973,955,258 - 74,044,019 (+)NCBI
Rnor_6.0979,659,275 - 79,748,050 (+)NCBI
Rnor_5.0979,432,205 - 79,520,611 (+)NCBI
RGSC_v3.4971,472,459 - 71,581,936 (+)RGD
Celera971,352,925 - 71,440,328 (+)RGD
Sequence:
RefSeq Acc Id: XM_039083873   ⟹   XP_038939801
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2973,955,220 - 74,044,020 (+)NCBI
RefSeq Acc Id: XM_039083874   ⟹   XP_038939802
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2973,982,556 - 74,044,020 (+)NCBI
RefSeq Acc Id: XM_039083875   ⟹   XP_038939803
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2973,983,856 - 74,044,020 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_803154   ⟸   NM_177419
- Sequence:
RefSeq Acc Id: ENSRNOP00000021656   ⟸   ENSRNOT00000021656
RefSeq Acc Id: XP_038939801   ⟸   XM_039083873
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939802   ⟸   XM_039083874
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038939803   ⟸   XM_039083875
- Peptide Label: isoform X3
Protein Domains
Ku

Transcriptome

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

Promoters
RGD ID:13696737
Promoter ID:EPDNEW_R7261
Type:initiation region
Name:Xrcc5_1
Description:X-ray repair cross complementing 5
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_6.0979,659,252 - 79,659,312EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3976 AgrOrtholog
Ensembl Genes ENSRNOG00000016105 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021656 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021656 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.240 UniProtKB/TrEMBL
  2.40.290.10 UniProtKB/TrEMBL
  3.40.50.410 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6887693 IMAGE-MGC_LOAD
InterPro DNA_helicase_ATP-dep_Ku UniProtKB/TrEMBL
  DNA_helicase_ATP-dep_Ku80 UniProtKB/TrEMBL
  Ku_C UniProtKB/TrEMBL
  Ku_C_sf UniProtKB/TrEMBL
  Ku_N UniProtKB/TrEMBL
  Ku_PK_bind UniProtKB/TrEMBL
  SPOC-like UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report rno:363247 UniProtKB/TrEMBL
MGC_CLONE MGC:72979 IMAGE-MGC_LOAD
NCBI Gene 363247 ENTREZGENE
Pfam Ku_C UniProtKB/TrEMBL
  Ku_N UniProtKB/TrEMBL
  Ku_PK_bind UniProtKB/TrEMBL
  PF02735 UniProtKB/TrEMBL
PharmGKB XRCC5 RGD
PhenoGen Xrcc5 PhenoGen
PIRSF Ku80 UniProtKB/TrEMBL
SMART Ku78 UniProtKB/TrEMBL
Superfamily-SCOP Ku_PK_bind UniProtKB/TrEMBL
  SPOC-like UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
UniProt G3V817_RAT UniProtKB/TrEMBL
  Q6P7P8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-08 Xrcc5  X-ray repair cross complementing 5  Xrcc5  X-ray repair complementing defective repair in Chinese hamster cells 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Xrcc5  X-ray repair cross complementation (double-strand-break rejoining; Ku autoantigen, 80kD)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function component of the DNA dependent protein kinase complex 727219