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. Part of protein-containing complex. Human ortholog(s) of this gene implicated in chronic obstructive pulmonary disease; multiple myeloma; and rectum cancer. 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; 3-chloropropane-1,2-diol; 4-amino-2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8981,404,507 - 81,493,293 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl981,375,863 - 81,493,293 (+)EnsemblGRCr8
mRatBN7.2973,955,216 - 74,044,020 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl973,955,216 - 74,044,018 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx982,419,375 - 82,508,055 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0987,548,243 - 87,636,932 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0985,935,851 - 86,024,584 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0979,659,275 - 79,748,050 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl979,659,251 - 79,748,078 (+)Ensemblrn6Rnor6.0
Rnor_5.0979,432,205 - 79,520,611 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4971,472,459 - 71,581,936 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera971,352,925 - 71,440,328 (+)NCBICelera
RGSC_v3.1971,619,440 - 71,728,918 (+)NCBI
Cytogenetic Map9q33NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(-)-quinic acid  (ISO)
(1->4)-beta-D-glucan  (ISO)
(S)-naringenin  (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-dimethoxyphenol  (ISO)
2,6-dinitrotoluene  (EXP)
3-chloropropane-1,2-diol  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (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)
6-propyl-2-thiouracil  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
biphenyl-4-amine  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
carbonyl cyanide p-trifluoromethoxyphenylhydrazone  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
curcumin  (ISO)
cyproconazole  (EXP)
D-glucose  (ISO)
DDE  (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)
FR900359  (ISO)
fulvestrant  (ISO)
furan  (EXP)
furfural  (ISO)
glucose  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hydrogen peroxide  (ISO)
hydroxyurea  (ISO)
irinotecan  (ISO)
ivermectin  (ISO)
lipopolysaccharide  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methimazole  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
nitrates  (ISO)
nitrogen mustard  (ISO)
ochratoxin A  (EXP)
ozone  (ISO)
p-anisidine  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (EXP)
picoxystrobin  (ISO)
piperonyl butoxide  (ISO)
pirinixic acid  (EXP)
prochloraz  (EXP)
quercetin  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
selenocystine  (ISO)
sodium arsenite  (ISO)
sodium chloride  (ISO)
sodium fluoride  (ISO)
sulfadimethoxine  (EXP)
sulindac  (EXP)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (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

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. Gamma-linolenic acid alters Ku80, E2F1, and bax expression and induces micronucleus formation in C6 glioma cells in vitro. Benadiba M, etal., IUBMB Life. 2009 Mar;61(3):244-51.
3. 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.
4. 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.
5. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. 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.
7. Variation in DNA repair genes XRCC3, XRCC4, XRCC5 and susceptibility to myeloma. Hayden PJ, etal., Hum Mol Genet. 2007 Dec 15;16(24):3117-27. Epub 2007 Sep 26.
8. Multistudy fine mapping of chromosome 2q identifies XRCC5 as a chronic obstructive pulmonary disease susceptibility gene. Hersh CP, etal., Am J Respir Crit Care Med. 2010 Sep 1;182(5):605-13. doi: 10.1164/rccm.200910-1586OC. Epub 2010 May 12.
9. 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.
10. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
11. Double-strand break repair and colorectal cancer: gene variants within 3' UTRs and microRNAs binding as modulators of cancer risk and clinical outcome. Naccarati A, etal., Oncotarget. 2016 Apr 26;7(17):23156-69. doi: 10.18632/oncotarget.6804.
12. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. Effect of fenofibrate on oxidative DNA damage and on gene expression related to cell proliferation and apoptosis in rats. Nishimura J, etal., Toxicol Sci. 2007 May;97(1):44-54. Epub 2007 Jan 29.
14. 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.
15. 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.
16. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
17. GOA pipeline RGD automated data pipeline
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. 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: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
GRCr8981,404,507 - 81,493,293 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl981,375,863 - 81,493,293 (+)EnsemblGRCr8
mRatBN7.2973,955,216 - 74,044,020 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl973,955,216 - 74,044,018 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx982,419,375 - 82,508,055 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0987,548,243 - 87,636,932 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0985,935,851 - 86,024,584 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0979,659,275 - 79,748,050 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl979,659,251 - 79,748,078 (+)Ensemblrn6Rnor6.0
Rnor_5.0979,432,205 - 79,520,611 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4971,472,459 - 71,581,936 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera971,352,925 - 71,440,328 (+)NCBICelera
RGSC_v3.1971,619,440 - 71,728,918 (+)NCBI
Cytogenetic Map9q33NCBI
XRCC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382216,109,348 - 216,206,293 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2216,107,464 - 216,206,303 (+)Ensemblhg38GRCh38
GRCh372216,974,071 - 217,071,016 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362216,682,378 - 216,779,248 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342216,799,637 - 216,896,509NCBI
Celera2210,743,609 - 210,840,560 (+)NCBICelera
Cytogenetic Map2q35NCBI
HuRef2208,830,614 - 208,927,713 (+)NCBIHuRef
CHM1_12216,979,976 - 217,076,949 (+)NCBICHM1_1
T2T-CHM13v2.02216,592,973 - 216,691,715 (+)NCBIT2T-CHM13v2.0
Xrcc5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39172,346,576 - 72,434,112 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl172,346,586 - 72,434,111 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38172,307,417 - 72,394,953 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl172,307,427 - 72,394,952 (+)Ensemblmm10GRCm38
MGSCv37172,353,995 - 72,441,527 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36172,240,728 - 72,328,156 (+)NCBIMGSCv36mm8
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 (-)Ensembl
ChiLan1.0NW_00495545316,967,453 - 17,054,634 (-)NCBIChiLan1.0ChiLan1.0
XRCC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213118,738,692 - 118,835,746 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B118,753,657 - 118,864,622 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B103,371,459 - 103,468,419 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B221,972,607 - 222,072,318 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B221,972,742 - 222,071,235 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3723,923,245 - 24,015,080 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03723,120,975 - 23,212,731 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3723,120,932 - 23,212,731 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13723,007,952 - 23,098,174 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03722,960,108 - 23,051,031 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03722,977,769 - 23,068,341 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Xrcc5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303171,487,889 - 171,588,600 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365861,055,335 - 1,137,984 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365861,055,478 - 1,137,924 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XRCC5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15118,354,796 - 118,451,960 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.115118,354,943 - 118,451,974 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215131,235,804 - 131,332,992 (+)NCBISscrofa10.2Sscrofa10.2susScr3
XRCC5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110101,952,909 - 102,051,059 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10101,953,067 - 102,049,964 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604097,347,634 - 97,445,372 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xrcc5
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14145,899,531 - 145,986,842 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Xrcc5
400 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)956047863101047863Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)94002992585029925Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)963376862108376862Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)965657365108376720Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94445825699506504Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)94445825685262605Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92956766483835942Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)94172029586720295Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)964220169109220169Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)964220169109220169Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)944458256121768150Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)964220169109220169Rat
1581517Bp284Blood pressure QTL 284arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)93922018684220186Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)968875497121768150Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)948718864108376862Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)94002992585029925Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)964220169109220169Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)95450650499506504Rat

Markers in Region
D9Mco23  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2974,006,592 - 74,007,038 (+)MAPPERmRatBN7.2
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
GRCr8981,492,273 - 81,493,224 (+)Marker Load Pipeline
mRatBN7.2974,042,999 - 74,043,950 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000021656   ⟹   ENSRNOP00000021656
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl981,404,507 - 81,493,293 (+)Ensembl
mRatBN7.2 Ensembl973,955,216 - 74,044,018 (+)Ensembl
Rnor_6.0 Ensembl979,659,251 - 79,748,078 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000129025   ⟹   ENSRNOP00000106308
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl981,404,550 - 81,493,292 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000144374   ⟹   ENSRNOP00000107815
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl981,375,863 - 81,493,293 (+)Ensembl
RefSeq Acc Id: NM_177419   ⟹   NP_803154
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8981,404,507 - 81,493,293 (+)NCBI
mRatBN7.2973,955,216 - 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_063267385   ⟹   XP_063123455
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8981,404,509 - 81,478,194 (+)NCBI
RefSeq Acc Id: NP_803154   ⟸   NM_177419
- UniProtKB: A6KFI3 (UniProtKB/TrEMBL),   G3V817 (UniProtKB/TrEMBL),   Q6P7P8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000021656   ⟸   ENSRNOT00000021656
RefSeq Acc Id: XP_063123455   ⟸   XM_063267385
- Peptide Label: isoform X1
- UniProtKB: Q6P7P8 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000106308   ⟸   ENSRNOT00000129025
Ensembl Acc Id: ENSRNOP00000107815   ⟸   ENSRNOT00000144374
Protein Domains
Ku   Ku70/Ku80 N-terminal alpha/beta

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V817-F1-model_v2 AlphaFold G3V817 1-732 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3976 AgrOrtholog
BioCyc Gene G2FUF-27206 BioCyc
Ensembl Genes ENSRNOG00000016105 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021656 ENTREZGENE
  ENSRNOT00000021656.6 UniProtKB/TrEMBL
  ENSRNOT00000129025.1 UniProtKB/TrEMBL
  ENSRNOT00000144374.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1600.10 UniProtKB/TrEMBL
  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 Xrcc5 ENTREZGENE
PANTHER KU AUTOANTIGEN DNA HELICASE UniProtKB/TrEMBL
  X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 5 UniProtKB/TrEMBL
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
RatGTEx ENSRNOG00000016105 RatGTEx
SMART Ku78 UniProtKB/TrEMBL
Superfamily-SCOP Ku_PK_bind UniProtKB/TrEMBL
  SPOC-like UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
UniProt A0ABK0LB79_RAT UniProtKB/TrEMBL
  A0ABK0LN47_RAT UniProtKB/TrEMBL
  A6KFI3 ENTREZGENE, UniProtKB/TrEMBL
  A6KFI4_RAT UniProtKB/TrEMBL
  G3V817 ENTREZGENE, UniProtKB/TrEMBL
  Q6P7P8 ENTREZGENE, 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