Xrcc3 (X-ray repair cross complementing 3) - Rat Genome Database

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Gene: Xrcc3 (X-ray repair cross complementing 3) Rattus norvegicus
Analyze
Symbol: Xrcc3
Name: X-ray repair cross complementing 3
RGD ID: 1306849
Description: Predicted to enable ATP binding activity and ATP-dependent DNA damage sensor activity. Predicted to contribute to crossover junction DNA endonuclease activity and four-way junction DNA binding activity. Involved in response to organic substance. Predicted to be located in several cellular components, including mitochondrion; nucleoplasm; and perinuclear region of cytoplasm. Predicted to be part of Rad51C-XRCC3 complex. Predicted to be active in replication fork. Human ortholog(s) of this gene implicated in breast cancer; familial melanoma; and pancreatic cancer. Orthologous to human XRCC3 (X-ray repair cross complementing 3); PARTICIPATES IN homologous recombination pathway of double-strand break repair; INTERACTS WITH (+)-pilocarpine; 2,3,7,8-tetrachlorodibenzodioxine; amphetamine.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: DNA repair protein XRCC3; DNA repair protein XRCC3-like; LOC100359601; LOC102551085; LOC314463; rCG27697-like; X-ray repair complementing defective repair in Chinese hamster cells 3
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
mRatBN7.26130,863,405 - 130,873,765 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6130,863,959 - 130,872,444 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.06136,366,917 - 136,380,751 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6136,371,555 - 136,379,348 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06145,372,463 - 145,388,673 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46136,594,276 - 136,602,069 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera6128,413,783 - 128,427,617 (-)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. The genetic association database. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
2. Detecting pathway-based gene-gene and gene-environment interactions in pancreatic cancer. Duell EJ, etal., Cancer Epidemiol Biomarkers Prev. 2008 Jun;17(6):1470-9.
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. Regulation of homologous recombination in eukaryotes. Heyer WD, etal., Annu Rev Genet. 2010;44:113-39. doi: 10.1146/annurev-genet-051710-150955.
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
10. Zhonghua lao dong wei sheng zhi ye bing za zhi = Zhonghua laodong weisheng zhiyebing zazhi = Chinese journal of industrial hygiene and occupational diseases Zhu SM, etal., Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2004 Jun;22(3):173-5.
Additional References at PubMed
PMID:10422536   PMID:11751635   PMID:14716019   PMID:15507207   PMID:15632090   PMID:16215984   PMID:20207730   PMID:20413593   PMID:21903669   PMID:23108668   PMID:23149936   PMID:26323318  
PMID:27918544  


Genomics

Comparative Map Data
Xrcc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26130,863,405 - 130,873,765 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6130,863,959 - 130,872,444 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.06136,366,917 - 136,380,751 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6136,371,555 - 136,379,348 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06145,372,463 - 145,388,673 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46136,594,276 - 136,602,069 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera6128,413,783 - 128,427,617 (-)NCBICelera
Cytogenetic Map6q32NCBI
XRCC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3814103,697,617 - 103,715,451 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl14103,697,609 - 103,715,504 (-)EnsemblGRCh38hg38GRCh38
GRCh3714104,163,954 - 104,181,788 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3614103,233,707 - 103,251,576 (-)NCBINCBI36Build 36hg18NCBI36
Build 3414103,233,707 - 103,251,549NCBI
Celera1484,218,198 - 84,236,079 (-)NCBICelera
Cytogenetic Map14q32.33NCBI
HuRef1484,342,246 - 84,360,133 (-)NCBIHuRef
CHM1_114104,102,095 - 104,119,977 (-)NCBICHM1_1
T2T-CHM13v2.01497,933,664 - 97,951,508 (-)NCBIT2T-CHM13v2.0
Xrcc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912111,769,626 - 111,780,326 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl12111,769,626 - 111,780,307 (-)EnsemblGRCm39 Ensembl
GRCm3812111,803,192 - 111,813,893 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12111,803,192 - 111,813,873 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712113,041,404 - 113,052,052 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3612112,251,001 - 112,261,649 (-)NCBIMGSCv36mm8
MGSCv3612106,079,489 - 106,090,338 (-)NCBIMGSCv36mm8
Celera12113,007,859 - 113,018,415 (-)NCBICelera
Cytogenetic Map12F1NCBI
Xrcc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555382,501,607 - 2,509,778 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555382,499,297 - 2,511,898 (-)NCBIChiLan1.0ChiLan1.0
XRCC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan114104,072,380 - 104,091,265 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01484,323,644 - 84,341,763 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.114104,131,908 - 104,146,133 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl14104,131,903 - 104,149,037 (-)Ensemblpanpan1.1panPan2
XRCC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1871,441,732 - 71,452,922 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl871,442,429 - 71,449,408 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha870,954,852 - 70,966,020 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0871,720,493 - 71,731,659 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl871,720,507 - 71,728,101 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1871,409,125 - 71,420,318 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0871,449,552 - 71,460,747 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0871,848,235 - 71,859,401 (-)NCBIUU_Cfam_GSD_1.0
Xrcc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244086402,633,405 - 2,645,985 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366211,462,428 - 1,473,868 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049366211,462,441 - 1,474,937 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XRCC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.27130,828,033 - 130,841,152 (+)NCBISscrofa10.2Sscrofa10.2susScr3
XRCC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12481,627,911 - 81,641,598 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2481,630,099 - 81,641,218 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605368,942,543 - 68,955,259 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xrcc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247341,217,549 - 1,223,280 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247341,216,641 - 1,223,860 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Xrcc3
36 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:50
Count of miRNA genes:46
Interacting mature miRNAs:50
Transcripts:ENSRNOT00000016208
Prediction methods: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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6105156861140994061Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6106752656132339866Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6112636280140994061Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6122549046137801795Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6122549046140286318Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6122549046140994061Rat
2312560Pur20Proteinuria QTL 202.10.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)6125628133137801795Rat

Markers in Region
AI874768  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26130,866,521 - 130,866,648 (+)MAPPERmRatBN7.2
Rnor_6.06136,373,501 - 136,373,627NCBIRnor6.0
Rnor_5.06145,381,478 - 145,381,604UniSTSRnor5.0
RGSC_v3.46136,596,222 - 136,596,348UniSTSRGSC3.4
Celera6128,420,367 - 128,420,493UniSTS
Cytogenetic Map6q32UniSTS
RH129416  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26130,866,514 - 130,866,734 (+)MAPPERmRatBN7.2
Rnor_6.06136,373,494 - 136,373,713NCBIRnor6.0
Rnor_5.06145,381,471 - 145,381,690UniSTSRnor5.0
RGSC_v3.46136,596,215 - 136,596,434UniSTSRGSC3.4
Celera6128,420,360 - 128,420,579UniSTS
RH 3.4 Map6781.0UniSTS
Cytogenetic Map6q32UniSTS
BE101314  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26130,865,769 - 130,865,925 (+)MAPPERmRatBN7.2
Rnor_6.06136,372,749 - 136,372,904NCBIRnor6.0
Rnor_5.06145,380,726 - 145,380,881UniSTSRnor5.0
RGSC_v3.46136,595,470 - 136,595,625UniSTSRGSC3.4
Celera6128,419,615 - 128,419,770UniSTS
RH 3.4 Map6781.1UniSTS
Cytogenetic Map6q32UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 2 2 2 2 8 2 4 3
Low 1 39 55 39 17 39 8 11 54 33 37 8 8
Below cutoff 4 12

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016208   ⟹   ENSRNOP00000016208
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6130,863,959 - 130,872,444 (-)Ensembl
Rnor_6.0 Ensembl6136,371,555 - 136,379,348 (-)Ensembl
RefSeq Acc Id: XM_006240649   ⟹   XP_006240711
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,863,405 - 130,873,633 (-)NCBI
Rnor_6.06136,366,917 - 136,380,616 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240650   ⟹   XP_006240712
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,863,405 - 130,873,764 (-)NCBI
Rnor_6.06136,366,917 - 136,380,751 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039113385   ⟹   XP_038969313
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,863,405 - 130,873,765 (-)NCBI
Protein Sequences
Protein RefSeqs XP_006240711 (Get FASTA)   NCBI Sequence Viewer  
  XP_006240712 (Get FASTA)   NCBI Sequence Viewer  
  XP_038969313 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97445 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006240712   ⟸   XM_006240650
- Peptide Label: isoform X1
- UniProtKB: D4A5N4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240711   ⟸   XM_006240649
- Peptide Label: isoform X1
- UniProtKB: D4A5N4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016208   ⟸   ENSRNOT00000016208
RefSeq Acc Id: XP_038969313   ⟸   XM_039113385
- Peptide Label: isoform X2
Protein Domains
RecA family profile

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A5N4-F1-model_v2 AlphaFold D4A5N4 1-349 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306849 AgrOrtholog
BioCyc Gene G2FUF-35826 BioCyc
Ensembl Genes ENSRNOG00000012141 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016208 ENTREZGENE
  ENSRNOP00000016208.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016208 ENTREZGENE
  ENSRNOT00000016208.4 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro DNA_recomb/repair_Rad51_C UniProtKB/TrEMBL
  DNA_recomb/repair_RecA-like UniProtKB/TrEMBL
  DNA_recomb_RecA/RadB_ATP-bd UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  XRCC3-like_C UniProtKB/TrEMBL
KEGG Report rno:102551085 UniProtKB/TrEMBL
NCBI Gene Xrcc3 ENTREZGENE
PANTHER DNA REPAIR PROTEIN XRCC3 UniProtKB/TrEMBL
  DNA REPAIR PROTEIN XRCC3 UniProtKB/TrEMBL
Pfam Rad51 UniProtKB/TrEMBL
PhenoGen Xrcc3 PhenoGen
PIRSF Rad51 UniProtKB/TrEMBL
PROSITE RECA_2 UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt D4A5N4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-08 Xrcc3  X-ray repair cross complementing 3  Xrcc3  X-ray repair complementing defective repair in Chinese hamster cells 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-20 Xrcc3  X-ray repair complementing defective repair in Chinese hamster cells 3  LOC102551085  DNA repair protein XRCC3-like  Data Merged 737654 APPROVED
2013-12-17 LOC102551085  DNA repair protein XRCC3-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-07-24 Xrcc3  X-ray repair complementing defective repair in Chinese hamster cells 3  LOC100359601  rCG27697-like  Name updated 737654 APPROVED
2010-05-20 LOC100359601  rCG27697-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Xrcc3  X-ray repair complementing defective repair in Chinese hamster cells 3   Xrcc3_predicted  X-ray repair complementing defective repair in Chinese hamster cells 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Xrcc3_predicted  X-ray repair complementing defective repair in Chinese hamster cells 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED