Nbn (nibrin) - Rat Genome Database

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Gene: Nbn (nibrin) Rattus norvegicus
Analyze
Symbol: Nbn
Name: nibrin
RGD ID: 621420
Description: Predicted to enable several functions, including histone binding activity; phosphorylation-dependent protein binding activity; and protein serine/threonine kinase activator activity. Involved in several processes, including host-mediated suppression of symbiont invasion; negative regulation of neuron differentiation; and regulation of fibroblast proliferation. Predicted to be located in nucleus and replication fork. Predicted to be part of BRCA1-C complex and Mre11 complex. Predicted to be active in chromosome, telomeric region and site of double-strand break. Human ortholog(s) of this gene implicated in several diseases, including Nijmegen breakage syndrome; acute lymphoblastic leukemia; aplastic anemia; rectum cancer; and reproductive organ cancer (multiple). Orthologous to human NBN (nibrin); PARTICIPATES IN ataxia telangiectasia-mutated (ATM) signaling pathway; homologous recombination pathway of double-strand break repair; INTERACTS WITH (S)-colchicine; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC93174; Nbs1; nijmegen breakage syndrome protein 1 homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8534,256,678 - 34,291,163 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl534,256,627 - 34,291,162 (+)EnsemblGRCr8
mRatBN7.2529,459,574 - 29,494,152 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl529,459,457 - 29,494,150 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx531,615,796 - 31,650,590 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0533,208,466 - 33,243,256 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0533,168,642 - 33,203,436 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0529,622,347 - 29,656,877 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl529,622,281 - 29,656,864 (+)Ensemblrn6Rnor6.0
Rnor_5.0534,300,932 - 34,335,393 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4530,541,610 - 30,576,168 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera528,665,088 - 28,699,404 (+)NCBICelera
RGSC_v3.1530,541,609 - 30,576,168 (+)NCBI
Cytogenetic Map5q13NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(S)-colchicine  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-methoxyethanol  (EXP)
2-palmitoylglycerol  (ISO)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
acrolein  (ISO)
aflatoxin M1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
aristolochic acid A  (EXP,ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP,ISO)
atrazine  (ISO)
benzene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
celastrol  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
cholesterol  (ISO)
cisplatin  (ISO)
copper(II) sulfate  (ISO)
delphinidin  (ISO)
diarsenic trioxide  (EXP,ISO)
Dibutyl phosphate  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
entinostat  (ISO)
enzyme inhibitor  (ISO)
fenofibrate  (EXP)
finasteride  (EXP)
folic acid  (ISO)
FR900359  (ISO)
gedunin  (ISO)
genistein  (ISO)
glafenine  (EXP)
hexadecanoic acid  (ISO)
isoprenaline  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
methylmercury chloride  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
myristicin  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
Nonidet P-40  (ISO)
oxaliplatin  (EXP)
oxybenzone  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
parathion  (ISO)
pentamidine  (ISO)
perfluorohexanesulfonic acid  (ISO)
pirinixic acid  (EXP,ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
Ptaquiloside  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
riddelliine  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vincaleukoblastine  (EXP)
vinclozolin  (EXP)
vincristine  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
blastocyst growth  (IEA,ISO,ISS)
cell population proliferation  (ISO)
DNA damage checkpoint signaling  (ISO)
DNA damage response  (IEA)
DNA double-strand break processing  (IEA,ISO,ISS)
DNA repair  (IEA)
DNA strand resection involved in replication fork processing  (IEA,ISO)
double-strand break repair  (IEA,ISO,ISS)
double-strand break repair via alternative nonhomologous end joining  (IEA,ISO)
double-strand break repair via homologous recombination  (IBA,IEA,ISO)
host-mediated suppression of symbiont invasion  (IMP)
immune response  (IEA)
in utero embryonic development  (IEA,ISO,ISS)
intrinsic apoptotic signaling pathway  (ISO)
isotype switching  (IEA,ISO,ISS)
meiotic cell cycle  (IEA)
mitotic G2 DNA damage checkpoint signaling  (IBA,IEA,ISO,ISS)
negative regulation of neuron differentiation  (IMP)
negative regulation of telomere capping  (IEA,ISO)
neuromuscular process controlling balance  (ISO)
positive regulation of cell population proliferation  (IMP)
positive regulation of double-strand break repair  (IEA,ISO)
positive regulation of telomere maintenance  (IEA,ISO)
protection from non-homologous end joining at telomere  (IEA,ISO,ISS)
protein localization to site of double-strand break  (IEA,ISO,ISS)
R-loop processing  (IEA,ISO,ISS)
regulation of fibroblast proliferation  (IDA)
response to xenobiotic stimulus  (IEP)
t-circle formation  (IEA,ISO)
telomere maintenance  (IEA,ISO,ISS)
telomere maintenance in response to DNA damage  (IEA,ISO,ISS)
telomere maintenance via telomere trimming  (IEA,ISO)
telomeric 3' overhang formation  (IEA,ISO)

Cellular Component
BRCA1-C complex  (IEA,ISO)
chromosome  (IEA)
chromosome, telomeric region  (IEA,ISO,ISS)
Mre11 complex  (IBA,IEA,ISO,ISS)
nuclear inclusion body  (IEA,ISO,ISS)
nucleolus  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IEA,ISO)
PML body  (IEA,ISO)
replication fork  (IEA,ISO)
site of double-strand break  (IEA,ISO,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. ATM protein kinase: the linchpin of cellular defenses to stress. Bhatti S, etal., Cell Mol Life Sci. 2011 Sep;68(18):2977-3006. doi: 10.1007/s00018-011-0683-9. Epub 2011 May 2.
2. Diagnostic markers of ovarian cancer by high-throughput antigen cloning and detection on arrays. Chatterjee M, etal., Cancer Res. 2006 Jan 15;66(2):1181-90.
3. c-Myc directly regulates the transcription of the NBS1 gene involved in DNA double-strand break repair. Chiang YC, etal., J Biol Chem. 2003 May 23;278(21):19286-91. Epub 2003 Mar 13.
4. NBS1 is a prostate cancer susceptibility gene. Cybulski C, etal., Cancer Res. 2004 Feb 15;64(4):1215-9.
5. A Rad50-dependent pathway of DNA repair is deficient in Fanconi anemia fibroblasts. Donahue SL and Campbell C, Nucleic Acids Res 2004 Jun 15;32(10):3248-57. Print 2004.
6. 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.
7. Regulation of homologous recombination in eukaryotes. Heyer WD, etal., Annu Rev Genet. 2010;44:113-39. doi: 10.1146/annurev-genet-051710-150955.
8. Breast cancer risk is associated with the genes encoding the DNA double-strand break repair Mre11/Rad50/Nbs1 complex. Hsu HM, etal., Cancer Epidemiol Biomarkers Prev. 2007 Oct;16(10):2024-32.
9. Deficiency of the Mre11 DNA repair complex in Alzheimer's disease brains. Jacobsen E, etal., Brain Res Mol Brain Res. 2004 Sep 10;128(1):1-7.
10. The MRE11-NBS1-RAD50 pathway is perturbed in SV40 large T antigen-immortalized AT-1, AT-2 and HL-1 cardiomyocytes. Lanson NA Jr, etal., Nucleic Acids Res 2000 Aug 1;28(15):2882-92.
11. NBS1, the Nijmegen breakage syndrome gene product, regulates neuronal proliferation and differentiation. Lee WT, etal., J Neurochem. 2007 Jul;102(1):141-52. Epub 2007 Apr 17.
12. Terminal differentiation of cardiac and skeletal myocytes induces permissivity to AAV transduction by relieving inhibition imposed by DNA damage response proteins. Lovric J, etal., Mol Ther. 2012 Nov;20(11):2087-97. doi: 10.1038/mt.2012.144. Epub 2012 Jul 31.
13. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
14. 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.
15. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. Possible involvement of oxidative stress in fenofibrate-induced hepatocarcinogenesis in rats. Nishimura J, etal., Arch Toxicol. 2008 Feb 6.
17. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
18. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
19. GOA pipeline RGD automated data pipeline
20. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
22. Comprehensive gene review and curation RGD comprehensive gene curation
23. I171V germline mutation in the NBS1 gene significantly increases risk of breast cancer. Roznowski K, etal., Breast Cancer Res Treat. 2008 Jul;110(2):343-8. Epub 2007 Sep 26.
24. Intact Mre11/Rad50/Nbs1 complex predicts good response to radiotherapy in early breast cancer. Soderlund K, etal., Int J Radiat Oncol Biol Phys. 2007 May 1;68(1):50-8. Epub 2007 Mar 6.
25. Nibrin, a novel DNA double-strand break repair protein, is mutated in Nijmegen breakage syndrome. Varon R, etal., Cell. 1998 May 1;93(3):467-76.
26. DNA damage: a trigger of innate immunity but a requirement for adaptive immune homeostasis. Xu Y Nat Rev Immunol. 2006 Apr;6(4):261-70.
Additional References at PubMed
PMID:9590181   PMID:10766245   PMID:10811102   PMID:10888888   PMID:11438675   PMID:11448772   PMID:11486038   PMID:11555636   PMID:11934988   PMID:12447371   PMID:12470659   PMID:12477932  
PMID:12529385   PMID:14612522   PMID:15489334   PMID:15668383   PMID:15790808   PMID:15821748   PMID:15916964   PMID:16374507   PMID:17694070   PMID:18614044   PMID:19135898   PMID:19151086  
PMID:23444137   PMID:27918544   PMID:38372104  


Genomics

Comparative Map Data
Nbn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8534,256,678 - 34,291,163 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl534,256,627 - 34,291,162 (+)EnsemblGRCr8
mRatBN7.2529,459,574 - 29,494,152 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl529,459,457 - 29,494,150 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx531,615,796 - 31,650,590 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0533,208,466 - 33,243,256 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0533,168,642 - 33,203,436 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0529,622,347 - 29,656,877 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl529,622,281 - 29,656,864 (+)Ensemblrn6Rnor6.0
Rnor_5.0534,300,932 - 34,335,393 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4530,541,610 - 30,576,168 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera528,665,088 - 28,699,404 (+)NCBICelera
RGSC_v3.1530,541,609 - 30,576,168 (+)NCBI
Cytogenetic Map5q13NCBI
NBN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38889,933,331 - 89,984,667 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl889,924,515 - 90,003,228 (-)Ensemblhg38GRCh38
GRCh37890,945,559 - 90,996,895 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36891,014,740 - 91,066,075 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34891,014,888 - 91,066,072NCBI
Celera887,140,375 - 87,191,710 (-)NCBICelera
Cytogenetic Map8q21.3NCBI
HuRef886,155,741 - 86,207,078 (-)NCBIHuRef
CHM1_1890,986,489 - 91,037,825 (-)NCBICHM1_1
T2T-CHM13v2.0891,056,512 - 91,107,848 (-)NCBIT2T-CHM13v2.0
Nbn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39415,955,388 - 15,992,589 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl415,957,925 - 15,992,589 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38415,957,587 - 15,992,589 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl415,957,925 - 15,992,589 (+)Ensemblmm10GRCm38
MGSCv37415,885,114 - 15,919,736 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36415,885,115 - 15,919,736 (+)NCBIMGSCv36mm8
Celera415,761,229 - 15,795,887 (+)NCBICelera
Cytogenetic Map4A2NCBI
cM Map46.66NCBI
Nbn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554176,839,312 - 6,880,133 (-)Ensembl
ChiLan1.0NW_0049554176,840,916 - 6,880,479 (-)NCBIChiLan1.0ChiLan1.0
NBN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v27107,329,160 - 107,380,523 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1882,868,830 - 82,938,522 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0886,622,797 - 86,674,202 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1888,575,198 - 88,626,200 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl888,575,198 - 88,626,307 (-)EnsemblpanPan2panpan1.1
NBN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12935,416,093 - 35,477,569 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2935,416,093 - 35,477,563 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2935,567,773 - 35,628,935 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02935,612,774 - 35,674,851 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2935,612,774 - 35,692,878 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12935,604,159 - 35,665,432 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02935,624,597 - 35,685,889 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02936,059,084 - 36,120,657 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nbn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530343,980,776 - 44,018,864 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365443,775,220 - 3,808,837 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365443,773,828 - 3,812,673 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NBN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl446,787,691 - 46,874,603 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1446,787,664 - 46,854,331 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2451,264,106 - 51,288,533 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NBN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1885,017,807 - 85,069,219 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl885,015,752 - 85,069,028 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603955,810,092 - 55,861,864 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nbn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247442,013,922 - 2,061,708 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247442,013,936 - 2,061,726 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Nbn
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11127,791,546 - 127,827,688 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nbn
339 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:196
Count of miRNA genes:148
Interacting mature miRNAs:159
Transcripts:ENSRNOT00000012377
Prediction methods:Microtar, Miranda, 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
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)51373115343590997Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)53275164977751649Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5692228281330203Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53331167378311673Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)52367149379046465Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5862723052665523Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51757663362576633Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51460607859606078Rat
1578774Tcas8Tongue tumor susceptibility QTL 83.47tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)51570745160707451Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906491770353Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5692228237468560Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5706553574335773Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)53331167378311673Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51748608062486080Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)53275164977751649Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906487027358Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52602321171023211Rat
2303577Gluco47Glucose level QTL 473blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51652001961520019Rat
1549901Neudeg2Neurodegradation QTL 240nervous system integrity trait (VT:0010566)mononuclear cell count (CMO:0002119)53113042148841739Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)51748608062486080Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)52367149368671493Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5862723053627230Rat

Markers in Region
AW530937  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2529,486,006 - 29,486,190 (+)MAPPERmRatBN7.2
Rnor_6.0529,648,732 - 29,648,915NCBIRnor6.0
Rnor_5.0534,327,248 - 34,327,431UniSTSRnor5.0
RGSC_v3.4530,568,048 - 30,568,231UniSTSRGSC3.4
Celera528,691,328 - 28,691,511UniSTS
RH 3.4 Map5162.33UniSTS
Cytogenetic Map5q13UniSTS


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 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000012377   ⟹   ENSRNOP00000012377
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl534,256,627 - 34,291,162 (+)Ensembl
mRatBN7.2 Ensembl529,459,457 - 29,494,150 (+)Ensembl
Rnor_6.0 Ensembl529,622,281 - 29,656,864 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000111074   ⟹   ENSRNOP00000091774
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl534,261,018 - 34,288,616 (+)Ensembl
mRatBN7.2 Ensembl529,464,003 - 29,491,605 (+)Ensembl
RefSeq Acc Id: NM_138873   ⟹   NP_620228
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8534,256,678 - 34,291,138 (+)NCBI
mRatBN7.2529,459,663 - 29,494,127 (+)NCBI
Rnor_6.0529,622,347 - 29,656,852 (+)NCBI
Rnor_5.0534,300,932 - 34,335,393 (+)NCBI
RGSC_v3.4530,541,610 - 30,576,168 (+)RGD
Celera528,665,088 - 28,699,404 (+)RGD
Sequence:
RefSeq Acc Id: XM_006237916   ⟹   XP_006237978
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8534,256,835 - 34,291,163 (+)NCBI
mRatBN7.2529,459,796 - 29,494,152 (+)NCBI
Rnor_6.0529,622,515 - 29,656,877 (+)NCBI
Rnor_5.0534,300,932 - 34,335,393 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039110890   ⟹   XP_038966818
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8534,262,722 - 34,291,163 (+)NCBI
mRatBN7.2529,459,574 - 29,493,983 (+)NCBI
Protein Sequences
Protein RefSeqs NP_620228 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237978 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966818 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF91228 (Get FASTA)   NCBI Sequence Viewer  
  AAH85700 (Get FASTA)   NCBI Sequence Viewer  
  EDL98480 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000012377
  ENSRNOP00000091774
GenBank Protein Q9JIL9 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_620228   ⟸   NM_138873
- UniProtKB: Q5RKL2 (UniProtKB/Swiss-Prot),   Q9JIL9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006237978   ⟸   XM_006237916
- Peptide Label: isoform X1
- UniProtKB: A6IIB0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012377   ⟸   ENSRNOT00000012377
RefSeq Acc Id: XP_038966818   ⟸   XM_039110890
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000091774   ⟸   ENSRNOT00000111074
Protein Domains
BRCT   FHA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JIL9-F1-model_v2 AlphaFold Q9JIL9 1-750 view protein structure

Transcriptome

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

Promoters
RGD ID:13693580
Promoter ID:EPDNEW_R4105
Type:initiation region
Name:Nbn_1
Description:nibrin
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_6.0529,622,259 - 29,622,319EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621420 AgrOrtholog
BioCyc Gene G2FUF-41861 BioCyc
Ensembl Genes ENSRNOG00000008580 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000012377 ENTREZGENE
  ENSRNOT00000111074 ENTREZGENE
Gene3D-CATH 2.60.200.20 UniProtKB/Swiss-Prot
  3.40.50.10190 UniProtKB/Swiss-Prot
  3.40.50.10980 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7130978 IMAGE-MGC_LOAD
InterPro BRCT_dom UniProtKB/Swiss-Prot
  BRCT_dom_sf UniProtKB/Swiss-Prot
  DNA-repair_Nbs1_C UniProtKB/Swiss-Prot
  FHA_dom UniProtKB/Swiss-Prot
  Nibrin-rel UniProtKB/Swiss-Prot
  Nibrin_BRCT2 UniProtKB/Swiss-Prot
  Nibrin_BRCT2_sf UniProtKB/Swiss-Prot
  Nibrin_met UniProtKB/Swiss-Prot
  SMAD_FHA_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:85482 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93174 IMAGE-MGC_LOAD
NCBI Gene 85482 ENTREZGENE
PANTHER NIBRIN UniProtKB/Swiss-Prot
  PTHR12162 UniProtKB/Swiss-Prot
Pfam BRCT UniProtKB/Swiss-Prot
  FHA UniProtKB/Swiss-Prot
  Nbs1_C UniProtKB/Swiss-Prot
  NIBRIN_BRCT_II UniProtKB/Swiss-Prot
PhenoGen Nbn PhenoGen
PIRSF Nibrin_animal UniProtKB/Swiss-Prot
PROSITE FHA_DOMAIN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000008580 RatGTEx
SMART FHA UniProtKB/Swiss-Prot
  Nbs1_C UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49879 UniProtKB/Swiss-Prot
  SSF52113 UniProtKB/Swiss-Prot
UniProt A0A8I6AGS6_RAT UniProtKB/TrEMBL
  A6IIB0 ENTREZGENE, UniProtKB/TrEMBL
  G3V766_RAT UniProtKB/TrEMBL
  NBN_RAT UniProtKB/Swiss-Prot
  Q5RKL2 ENTREZGENE
  Q9JIL9 ENTREZGENE
UniProt Secondary Q5RKL2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Nbn  nibrin      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Nbn  nibrin      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in heart, peak expression at postnatal day 10 68816