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 chromatin-protein adaptor activity; phosphorylation-dependent protein binding activity; and protein serine/threonine kinase activator activity. Involved in several processes, including negative regulation of neuron differentiation; negative regulation of viral entry into host cell; and regulation of fibroblast proliferation. Predicted to be located in Golgi apparatus; 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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8534,256,678 - 34,291,163 (+)NCBIGRCr8
mRatBN7.2529,459,574 - 29,494,152 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl529,459,457 - 29,494,150 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx531,615,796 - 31,650,590 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0533,208,466 - 33,243,256 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0533,168,642 - 33,203,436 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0529,622,347 - 29,656,877 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl529,622,281 - 29,656,864 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0534,300,932 - 34,335,393 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4530,541,610 - 30,576,168 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1530,541,609 - 30,576,168 (+)NCBI
Celera528,665,088 - 28,699,404 (+)NCBICelera
Cytogenetic Map5q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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)
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)
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)
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)
DNA damage checkpoint signaling  (ISO)
DNA double-strand break processing  (IEA,ISO,ISS)
DNA duplex unwinding  (IBA,IEA,ISO)
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)
in utero embryonic development  (ISO,ISS)
intrinsic apoptotic signaling pathway  (IEA,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)
negative regulation of viral entry into host cell  (IMP)
neuroblast proliferation  (IEA,ISO)
neuromuscular process controlling balance  (IEA,ISO)
positive regulation of cell population proliferation  (IMP)
positive regulation of protein autophosphorylation  (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  (ISO,ISS)
telomere maintenance via telomere trimming  (ISO)
telomeric 3' overhang formation  (IEA,ISO)

Cellular Component
BRCA1-C complex  (IEA,ISO)
chromosome, telomeric region  (IEA,ISO,ISS)
Golgi apparatus  (IEA,ISO)
Mre11 complex  (IBA,IEA,ISO,ISS)
nuclear inclusion body  (IEA,ISO,ISS)
nucleolus  (IEA,ISO)
nucleoplasm  (ISO)
nucleus  (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 (+)NCBIGRCr8
mRatBN7.2529,459,574 - 29,494,152 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl529,459,457 - 29,494,150 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx531,615,796 - 31,650,590 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0533,208,466 - 33,243,256 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0533,168,642 - 33,203,436 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0529,622,347 - 29,656,877 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl529,622,281 - 29,656,864 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0534,300,932 - 34,335,393 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4530,541,610 - 30,576,168 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1530,541,609 - 30,576,168 (+)NCBI
Celera528,665,088 - 28,699,404 (+)NCBICelera
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 (-)EnsemblGRCh38hg38GRCh38
GRCh37890,945,559 - 90,996,895 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36891,014,740 - 91,066,075 (-)NCBINCBI36Build 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 Ensembl
GRCm38415,957,587 - 15,992,589 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl415,957,925 - 15,992,589 (+)EnsemblGRCm38mm10GRCm38
MGSCv37415,885,114 - 15,919,736 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2935,567,773 - 35,628,935 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02935,612,774 - 35,674,851 (-)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247442,013,936 - 2,061,726 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nbn
442 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
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)5228222669540447Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
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)52122674466226744Rat
1549901Neudeg2Neurodegradation QTL 240nervous system integrity trait (VT:0010566)mononuclear cell count (CMO:0002119)52483871044045280Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52851548973515489Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52851548973515489Rat

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
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 43 57 41 19 41 8 10 74 35 41 11 8
Low 1
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000012377   ⟹   ENSRNOP00000012377
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl529,459,457 - 29,494,150 (+)Ensembl
Rnor_6.0 Ensembl529,622,281 - 29,656,864 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000111074   ⟹   ENSRNOP00000091774
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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:
RefSeq Acc Id: ENSRNOP00000012377   ⟸   ENSRNOT00000012377
RefSeq Acc Id: XP_038966818   ⟸   XM_039110890
- Peptide Label: isoform X2
RefSeq 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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012377.5 UniProtKB/TrEMBL
  ENSRNOT00000111074 ENTREZGENE
  ENSRNOT00000111074.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.200.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.10190 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.10980 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7130978 IMAGE-MGC_LOAD
InterPro BRCT_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BRCT_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA-repair_Nbs1_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FHA_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nibrin-rel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nibrin_BRCT2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nibrin_BRCT2_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nibrin_met UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMAD_FHA_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:85482 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93174 IMAGE-MGC_LOAD
NCBI Gene 85482 ENTREZGENE
PANTHER NIBRIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12162 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam BRCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nbs1_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NIBRIN_BRCT_II UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nbn PhenoGen
PIRSF Nibrin_animal UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE FHA_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000008580 RatGTEx
SMART FHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nbs1_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49879 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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