Brca1 (BRCA1, DNA repair associated) - Rat Genome Database

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Gene: Brca1 (BRCA1, DNA repair associated) Rattus norvegicus
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Symbol: Brca1
Name: BRCA1, DNA repair associated
RGD ID: 2218
Description: Enables chromatin binding activity. Involved in positive regulation of protein import into nucleus; response to estradiol; and response to nutrient. Located in mitochondrial matrix. Biomarker of ductal carcinoma in situ. Human ortholog(s) of this gene implicated in several diseases, including breast cancer (multiple); cervix uteri carcinoma in situ; gastrointestinal system cancer (multiple); hereditary breast ovarian cancer syndrome; and reproductive organ cancer (multiple). Orthologous to human BRCA1 (BRCA1 DNA repair associated); PARTICIPATES IN ataxia telangiectasia-mutated (ATM) signaling pathway; forkhead class A signaling pathway; homologous recombination pathway of double-strand break repair; INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BRCA-1; breast cancer 1; breast cancer 1, early onset; breast cancer type 1 susceptibility protein homolog; RING-type E3 ubiquitin transferase BRCA1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Brca1m1Uwm   Brca1em1Kyo  
Genetic Models: SD-Brca1m1Uwm SD-Brca1em1Kyo
Is Marker For: Strains:   SD   SD-Brca1m1Uwm  
Candidate Gene For: Mcs15
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81086,917,693 - 86,978,012 (-)NCBIGRCr8
mRatBN7.21086,417,441 - 86,477,762 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1086,418,000 - 86,477,304 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1091,454,623 - 91,513,795 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01090,930,035 - 90,990,102 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01086,323,338 - 86,383,395 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01089,394,821 - 89,455,093 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1089,394,803 - 89,454,681 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01089,192,653 - 89,252,760 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41090,513,630 - 90,572,676 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11090,527,999 - 90,587,046 (-)NCBI
Celera1085,140,052 - 85,200,670 (-)NCBICelera
Cytogenetic Map10q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
adenoid cystic carcinoma  (ISO)
Animal Mammary Neoplasms  (ISO)
bilateral breast cancer  (ISO)
breast adenocarcinoma  (ISO)
breast cancer  (ISO,ISS)
Breast Cancer, Familial  (ISO)
breast carcinoma  (ISO)
breast ductal carcinoma  (ISO)
Breast Neoplasms  (ISO)
Burkitt lymphoma  (ISO)
carcinoma  (ISO)
cervical cancer  (ISO)
cervix uteri carcinoma in situ  (ISO)
Chromosome Breakage  (ISO)
colon cancer  (ISO)
colon carcinoma  (ISO)
colorectal cancer  (ISO)
colorectal carcinoma  (ISO)
disease of cellular proliferation  (ISO)
ductal carcinoma in situ  (IEP)
dysgerminoma  (ISO)
endometrial carcinoma  (ISO)
esophagus squamous cell carcinoma  (ISO)
Experimental Mammary Neoplasms  (IEP,ISO)
Familial Prostate Cancer  (ISO)
Fanconi anemia complementation group A  (ISO)
Fanconi Anemia Complementation Group S  (ISO)
genetic disease  (ISO)
hereditary breast ovarian cancer syndrome  (ISO)
hereditary mixed polyposis syndrome 1  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
Hyperplasia  (ISO)
hypertension  (ISO)
infant-type hemispheric glioma  (ISO)
invasive ductal carcinoma  (ISO)
lung cancer  (ISO)
lung non-small cell carcinoma  (ISO)
mouth disease  (ISO)
nasopharynx carcinoma  (ISO)
Neoplastic Cell Transformation  (ISO)
ovarian cancer  (ISO)
ovarian carcinoma  (ISO)
Ovarian Neoplasms  (ISO)
ovary serous adenocarcinoma  (ISO)
pancreatic cancer  (ISO)
pancreatic carcinoma  (ISO)
peritoneum cancer  (ISO)
Premature Aging  (ISO)
prostate cancer  (ISO)
Prostatic Neoplasms  (ISO)
punctate palmoplantar keratoderma type II  (ISO)
rhabdomyosarcoma  (ISO)
stomach cancer  (ISO)
stomach carcinoma  (ISO)
urinary bladder cancer  (ISO)
Urinary Bladder Neoplasm  (ISO)
uterine corpus cancer  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-alpha-phellandrene  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-naringenin  (ISO)
(S)-nicotine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,1-dichloroethene  (ISO)
1-naphthyl isothiocyanate  (EXP)
1-nitropyrene  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-acetamidofluorene  (EXP)
2-butoxyethanol  (ISO)
2-methylcholine  (ISO)
2-naphthylamine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (EXP,ISO)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (ISO)
8-hydroxy-2'-deoxyguanosine  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
acrylamide  (EXP)
Aflatoxin G1  (ISO)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
alpha-naphthoflavone  (ISO)
alpha-phellandrene  (ISO)
alpha-pinene  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
arecoline  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzophenanthridine  (ISO)
beta-hexachlorocyclohexane  (ISO)
bifenthrin  (ISO)
biphenyl-4-amine  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
bromoacetate  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
Calcium propionate  (ISO)
camptothecin  (ISO)
cannabidiol  (ISO)
carboplatin  (ISO)
carfilzomib  (ISO)
casticin  (ISO)
ceric oxide  (EXP)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP,ISO)
daidzein  (ISO)
DDE  (ISO)
Decamethylcyclopentasiloxane  (ISO)
deguelin  (ISO)
diamminedichloroplatinum  (ISO)
diarsenic trioxide  (ISO)
dibenzofuran  (EXP)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
dieldrin  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
doxorubicin  (ISO)
emetine  (ISO)
endosulfan  (ISO)
Enterolactone  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (ISO)
etoposide  (ISO)
fenthion  (ISO)
fenvalerate  (EXP,ISO)
flavonoids  (EXP)
folic acid  (ISO)
FR900359  (ISO)
fulvestrant  (ISO)
furan  (EXP)
furazolidone  (ISO)
gemcitabine  (ISO)
genistein  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
glyphosate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hexamethylcyclotrisiloxane  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
indole-3-methanol  (ISO)
L-methionine  (ISO)
Lasiocarpine  (ISO)
lead diacetate  (ISO)
leptomycin B  (ISO)
lipopolysaccharide  (ISO)
lucanthone  (ISO)
methotrexate  (ISO)
methoxsalen  (ISO)
methyl methanesulfonate  (ISO)
mitomycin C  (ISO)
Monobutylphthalate  (EXP)
myristicin  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (ISO)
nickel dichloride  (ISO)
nicotine  (ISO)
nitrogen mustard  (ISO)
O-methyleugenol  (EXP)
ochratoxin A  (EXP)
octamethylcyclotetrasiloxane  (ISO)
olaparib  (ISO)
ouabain  (ISO)
oxaliplatin  (EXP,ISO)
oxybenzone  (ISO)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
PCB138  (ISO)
phenobarbital  (ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
phosphoramide mustard  (EXP)
pifithrin-?  (ISO)
pirinixic acid  (ISO)
potassium bromate  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
procyanidin B2  (ISO)
promethazine  (EXP)
propanal  (ISO)
pyrethrins  (EXP)
quercetin  (ISO)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
riddelliine  (ISO)
rotenone  (ISO)
rucaparib  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
succimer  (ISO)
sulindac  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
terbufos  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tetramethrin  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
topotecan  (EXP)
toxaphene  (ISO)
transplatin  (ISO)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
trovafloxacin  (ISO)
tungsten  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
veliparib  (ISO)
vorinostat  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular response to indole-3-methanol  (IEA,ISO)
cellular response to ionizing radiation  (IEA,ISO)
cellular response to tumor necrosis factor  (IEA,ISO)
centrosome cycle  (IEA,ISO)
chordate embryonic development  (IBA,IEA,ISO)
chromosome segregation  (IEA,ISO)
DNA damage response  (ISO)
dosage compensation by inactivation of X chromosome  (IEA)
double-strand break repair  (ISO)
double-strand break repair via homologous recombination  (IBA,IEA,ISO)
fatty acid biosynthetic process  (IEA)
intrinsic apoptotic signaling pathway in response to DNA damage  (IEA,ISO)
mitotic G2 DNA damage checkpoint signaling  (IBA,IEA,ISO)
mitotic G2/M transition checkpoint  (ISO)
negative regulation of cell growth  (IEA,ISO)
negative regulation of DNA-templated transcription  (IEA,ISO)
negative regulation of extrinsic apoptotic signaling pathway via death domain receptors  (IEA,ISO)
negative regulation of fatty acid biosynthetic process  (IEA,ISO,ISS)
negative regulation of gene expression via chromosomal CpG island methylation  (IEA,ISO)
negative regulation of intracellular estrogen receptor signaling pathway  (IEA,ISO)
negative regulation of reactive oxygen species metabolic process  (IEA,ISO)
positive regulation of angiogenesis  (IEA,ISO)
positive regulation of DNA repair  (IEA,ISO)
positive regulation of DNA-templated transcription  (ISO,ISS)
positive regulation of gene expression  (ISO)
positive regulation of protein import into nucleus  (IMP)
positive regulation of transcription by RNA polymerase II  (IBA,IEA,ISO)
positive regulation of vascular endothelial growth factor production  (IEA,ISO)
postreplication repair  (IEA,ISO)
protein autoubiquitination  (IEA,ISO,ISS)
protein K6-linked ubiquitination  (IEA,ISO,ISS)
protein ubiquitination  (ISO)
random inactivation of X chromosome  (IEA,ISO)
regulation of cell cycle  (ISO)
regulation of transcription by RNA polymerase II  (ISO,ISS)
response to estradiol  (IEP)
response to genistein  (IEP)
response to ionizing radiation  (ISO)
response to lipid  (IEP)
response to nutrient  (IEP)
sex-chromosome dosage compensation  (IBA)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Retroviral transduction of splice variant Brca1-Delta11 or mutant Brca1-W1777Stop causes mouse epithelial mammary atypical duct hyperplasia. Bachelier R, etal., Virchows Arch. 2002 Mar;440(3):261-6. Epub 2001 Sep 22.
2. Transcriptional regulation by p53. Beckerman R and Prives C, Cold Spring Harb Perspect Biol. 2010 Aug;2(8):a000935. doi: 10.1101/cshperspect.a000935. Epub 2010 Apr 28.
3. Sequence analysis of the rat Brca1 homolog and its promoter region. Bennett LM, etal., Mamm Genome 1999 Jan;10(1):19-25.
4. Localization of human BRCA1 and BRCA2 in non-inherited colorectal carcinomas and matched normal mucosas. Bernard-Gallon DJ, etal., Anticancer Res. 2001 May-Jun;21(3B):2011-20.
5. Prepubertal estradiol and genistein exposures up-regulate BRCA1 mRNA and reduce mammary tumorigenesis. Cabanes A, etal., Carcinogenesis. 2004 May;25(5):741-8. Epub 2004 Jan 16.
6. Senescence, aging, and malignant transformation mediated by p53 in mice lacking the Brca1 full-length isoform. Cao L, etal., Genes Dev. 2003 Jan 15;17(2):201-13.
7. Allelic imbalance in BRCA1 and BRCA2 gene expression is associated with an increased breast cancer risk. Chen X, etal., Hum Mol Genet. 2008 May 1;17(9):1336-48. Epub 2008 Jan 19.
8. Phosphorylated BRCA1 is predominantly located in the nucleus and mitochondria. Coene ED, etal., Mol Biol Cell. 2005 Feb;16(2):997-1010. Epub 2004 Dec 9.
9. Prolactin blocks nuclear translocation of VDR by regulating its interaction with BRCA1 in osteosarcoma cells. Deng C, etal., Mol Endocrinol. 2009 Feb;23(2):226-36. doi: 10.1210/me.2008-0075. Epub 2008 Dec 12.
10. Low levels of BRCA1 protein expression predict a worse prognosis in stage I-II colon cancer. Du C, etal., Int J Biol Markers. 2021 Mar;36(1):47-53. doi: 10.1177/1724600820986572. Epub 2021 Feb 14.
11. Tumor-protective and tumor-promoting actions of dietary whey proteins in an N-methyl-N-nitrosourea model of rat mammary carcinogenesis. Eason RR, etal., Nutr Cancer. 2006;55(2):171-7.
12. Risks of cancer in BRCA1-mutation carriers. Breast Cancer Linkage Consortium. Ford D, etal., Lancet. 1994 Mar 19;343(8899):692-5.
13. Prevalent somatic BRCA1 mutations shape clinically relevant genomic patterns of nasopharyngeal carcinoma in Southeast Europe. Fountzilas G, etal., Int J Cancer. 2018 Jan 1;142(1):66-80. doi: 10.1002/ijc.31023. Epub 2017 Sep 30.
14. Correlation between BRCA1 expression and clinicopathological factors including brain metastases in patients with non-small-cell lung cancer. Gachechiladze M, etal., Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2013 Sep;157(3):227-32. doi: 10.5507/bp.2012.099. Epub 2012 Nov 1.
15. 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.
16. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
17. Expression of DNA double-strand break repair proteins ATM and BRCA1 predicts survival in colorectal cancer. Grabsch H, etal., Clin Cancer Res. 2006 Mar 1;12(5):1494-500. doi: 10.1158/1078-0432.CCR-05-2105.
18. Methylation of breast cancer susceptibility gene 1 (BRCA1) predicts recurrence in patients with curatively resected stage I non-small cell lung cancer. Harada H, etal., Cancer. 2013 Feb 15;119(4):792-8. doi: 10.1002/cncr.27754. Epub 2013 Jan 18.
19. The Nrf2 regulatory network provides an interface between redox and intermediary metabolism. Hayes JD and Dinkova-Kostova AT, Trends Biochem Sci. 2014 Apr;39(4):199-218. doi: 10.1016/j.tibs.2014.02.002. Epub 2014 Mar 16.
20. Growth retardation and tumour inhibition by BRCA1. Holt JT, etal., Nat Genet. 1996 Mar;12(3):298-302. doi: 10.1038/ng0396-298.
21. Effects of BRCA1 transgene expression on murine mammary gland development and mutagen-induced mammary neoplasia. Hoshino A, etal., Int J Biol Sci. 2007 Apr 25;3(5):281-91.
22. Evidence for purifying selection acting on silent sites in BRCA1. Hurst LD and Pal C, Trends Genet 2001 Feb;17(2):62-5.
23. Gene Data File Integration of LocusLink data, October 12, 2001
24. Structure of the 53BP1 BRCT region bound to p53 and its comparison to the Brca1 BRCT structure. Joo WS, etal., Genes Dev 2002 Mar 1;16(5):583-93.
25. Increased BRCA1 protein in mammary tumours of rats fed marine omega-3 fatty acids. Jourdan ML, etal., Oncol Rep. 2007 Apr;17(4):713-9.
26. Differing effects of adjuvant chemotherapy according to BRCA1 nuclear expression in gastric cancer. Kim JW, etal., Cancer Chemother Pharmacol. 2013 Jun;71(6):1435-43. doi: 10.1007/s00280-013-2141-x. Epub 2013 Apr 30.
27. Chromatin remodeling and histone modification in the conversion of oligodendrocyte precursors to neural stem cells. Kondo T and Raff M, Genes Dev. 2004 Dec 1;18(23):2963-72.
28. Tumor suppressor gene BRCA-1 is expressed by embryonic and adult neural stem cells and involved in cell proliferation. Korhonen L, etal., J Neurosci Res 2003 Mar 15;71(6):769-76.
29. Genetic loci controlling breast cancer susceptibility in the Wistar-Kyoto rat. Lan H, etal., Genetics 2001 Jan;157(1):331-9.
30. Evaluation of the protective effect of Nigella sativa extract and its primary active component thymoquinone against DMBA-induced breast cancer in female rats. Linjawi SA, etal., Arch Med Sci. 2015 Mar 16;11(1):220-9. doi: 10.5114/aoms.2013.33329. Epub 2013 Feb 28.
31. BRCA1 shields vascular smooth muscle cells from oxidative stress. Lovren F, etal., J Thorac Cardiovasc Surg. 2014 Jun;147(6):1946-55, 1955.e1. doi: 10.1016/j.jtcvs.2013.09.060. Epub 2013 Nov 13.
32. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
33. Prostate cancer in male BRCA1 and BRCA2 mutation carriers has a more aggressive phenotype. Mitra A, etal., Br J Cancer. 2008 Jan 29;98(2):502-7. Epub 2008 Jan 8.
34. Prostate cancer in male BRCA1 and BRCA2 mutation carriers has a more aggressive phenotype. Mitra A, etal., Br J Cancer. 2008 Jan 8;.
35. Frequent promoter methylation of CDH1, DAPK, RARB, and HIC1 genes in carcinoma of cervix uteri: its relationship to clinical outcome. Narayan G, etal., Mol Cancer. 2003 May 13;2:24.
36. Oral contraceptives and the risk of hereditary ovarian cancer. Hereditary Ovarian Cancer Clinical Study Group. Narod SA, etal., N Engl J Med 1998 Aug 13;339(7):424-8.
37. Common mutations in BRCA1 and BRCA2 do not contribute to early prostate cancer in Jewish men. Nastiuk KL, etal., Prostate 1999 Aug 1;40(3):172-7.
38. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
39. Pathology of familial breast cancer: differences between breast cancers in carriers of BRCA1 or BRCA2 mutations and sporadic cases. Breast Cancer Linkage Consortium. NO_AUTHOR Lancet 1997 May 24;349(9064):1505-10.
40. Reduced Brca1 protein expression in 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine-induced rat mammary carcinomas. Okochi E, etal., Mol Carcinog. 2002 Aug;34(4):211-8.
41. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
42. Double-strand break repair: 53BP1 comes into focus. Panier S and Boulton SJ, Nat Rev Mol Cell Biol. 2014 Jan;15(1):7-18. doi: 10.1038/nrm3719. Epub 2013 Dec 11.
43. Denaturing gradient gel electrophoresis screening of the BRCA1 gene in cells from precancerous cervical lesions. Park SJ, etal., J Reprod Med. 1999 Jul;44(7):575-80.
44. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
45. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
46. ERCC1 and BRCA1 mRNA expressions are associated with clinical outcome of non-small cell lung cancer treated with platinum-based chemotherapy. Qin X, etal., Tumour Biol. 2014 May;35(5):4697-704. doi: 10.1007/s13277-014-1615-8. Epub 2014 Jan 18.
47. Expression of BRCA1 protein in breast cancer and its prognostic significance. Rakha EA, etal., Hum Pathol. 2008 Apr 7;.
48. GOA pipeline RGD automated data pipeline
49. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
50. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
51. Molecular characterization, homology modeling and docking studies of the R2787H missense variation in BRCA2 gene: Association with breast cancer. Riahi A, etal., J Theor Biol. 2016 Aug 21;403:188-196. doi: 10.1016/j.jtbi.2016.05.013. Epub 2016 May 19.
52. BRCA1-Associated Protein 1 (BAP1) Immunohistochemical Expression as a Diagnostic Tool in Malignant Pleural Mesothelioma Classification: A Large Retrospective Study. Righi L, etal., J Thorac Oncol. 2016 Nov;11(11):2006-2017. doi: 10.1016/j.jtho.2016.06.020. Epub 2016 Jul 13.
53. The basal-like mammary carcinomas induced by Brca1 or Bard1 inactivation implicate the BRCA1/BARD1 heterodimer in tumor suppression. Shakya R, etal., Proc Natl Acad Sci U S A. 2008 May 13;105(19):7040-5. Epub 2008 Apr 28.
54. High incidence of mutations in BRCA1 and BRCA2 genes in ovarian cancer. Smirnova TY, etal., Bull Exp Biol Med. 2007 Jul;144(1):83-5.
55. BRCA1 promoter methylation in peripheral blood DNA of mutation negative familial breast cancer patients with a BRCA1 tumour phenotype. Snell C, etal., Breast Cancer Res. 2008;10(1):R12. Epub 2008 Feb 12.
56. BRCA1 mutations and colorectal cancer in Poland. Suchy J, etal., Fam Cancer. 2010 Dec;9(4):541-4. doi: 10.1007/s10689-010-9378-x.
57. Association study of candidate genes for the prevalence and progression of knee osteoarthritis. Valdes AM, etal., Arthritis Rheum. 2004 Aug;50(8):2497-507.
58. The functional BRCA1 rs799917 genetic polymorphism is associated with gastric cancer risk in a Chinese Han population. Wang K, etal., Tumour Biol. 2015 Jan;36(1):393-7. doi: 10.1007/s13277-014-2655-9. Epub 2014 Sep 30.
59. 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.
60. A novel set of DNA methylation markers in urine sediments for sensitive/specific detection of bladder cancer. Yu J, etal., Clin Cancer Res. 2007 Dec 15;13(24):7296-304.
61. BRCA1a has antitumor activity in TN breast, ovarian and prostate cancers. Yuli C, etal., Oncogene. 2007 Sep 6;26(41):6031-7. doi: 10.1038/sj.onc.1210420. Epub 2007 Mar 26.
62. Production of knockout rats using ENU mutagenesis and a yeast-based screening assay. Zan Y, etal., Nat Biotechnol 2003 Jun;21(6):645-51.
63. [Relationship between the protein expression of ERCC1, BRCA, β-tubulin and K-ras and the efficacy and prognosis in advanced non-small cell lung cancer]. Zhang L, etal., Zhonghua Zhong Liu Za Zhi. 2011 Mar;33(3):212-6.
64. A functional BRCA1 coding sequence genetic variant contributes to risk of esophageal squamous cell carcinoma. Zhang X, etal., Carcinogenesis. 2013 Oct;34(10):2309-13. doi: 10.1093/carcin/bgt213. Epub 2013 Jun 8.
65. Loss of BRCA1 expression leads to worse survival in patients with gastric carcinoma. Zhang ZZ, etal., World J Gastroenterol. 2013 Mar 28;19(12):1968-74. doi: 10.3748/wjg.v19.i12.1968.
Additional References at PubMed
PMID:8895509   PMID:8944023   PMID:9171368   PMID:9662397   PMID:9774970   PMID:10868478   PMID:11172592   PMID:11934988   PMID:12419249   PMID:12890688   PMID:12913077   PMID:14654789  
PMID:15123655   PMID:15254237   PMID:15265711   PMID:15965487   PMID:16288014   PMID:16326698   PMID:16331276   PMID:17349954   PMID:17505062   PMID:17525340   PMID:17525341   PMID:17525342  
PMID:17643121   PMID:17873885   PMID:18516675   PMID:18809582   PMID:19117993   PMID:19261748   PMID:19261749   PMID:20160719   PMID:20351172   PMID:20495005   PMID:20551173   PMID:20668305  
PMID:20820192   PMID:21102443   PMID:21282464   PMID:22186889   PMID:22549958   PMID:23039116   PMID:23271346   PMID:23415688   PMID:23855721   PMID:26490168   PMID:27494651   PMID:28585187  
PMID:29498408   PMID:29656893  


Genomics

Comparative Map Data
Brca1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81086,917,693 - 86,978,012 (-)NCBIGRCr8
mRatBN7.21086,417,441 - 86,477,762 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1086,418,000 - 86,477,304 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1091,454,623 - 91,513,795 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01090,930,035 - 90,990,102 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01086,323,338 - 86,383,395 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01089,394,821 - 89,455,093 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1089,394,803 - 89,454,681 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01089,192,653 - 89,252,760 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41090,513,630 - 90,572,676 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11090,527,999 - 90,587,046 (-)NCBI
Celera1085,140,052 - 85,200,670 (-)NCBICelera
Cytogenetic Map10q31NCBI
BRCA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381743,044,295 - 43,170,327 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1743,044,295 - 43,170,245 (-)EnsemblGRCh38hg38GRCh38
GRCh371741,196,312 - 41,277,381 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361738,449,840 - 38,530,994 (-)NCBINCBI36Build 36hg18NCBI36
Build 341738,449,843 - 38,530,934NCBI
Celera1737,853,171 - 37,934,354 (-)NCBICelera
Cytogenetic Map17q21.31NCBI
HuRef1736,962,663 - 37,043,809 (-)NCBIHuRef
CHM1_11741,431,851 - 41,513,018 (-)NCBICHM1_1
T2T-CHM13v2.01743,902,857 - 44,029,084 (-)NCBIT2T-CHM13v2.0
Brca1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911101,379,587 - 101,442,808 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11101,379,590 - 101,442,781 (-)EnsemblGRCm39 Ensembl
GRCm3811101,488,761 - 101,551,955 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11101,488,764 - 101,551,955 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711101,350,078 - 101,413,269 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611101,304,854 - 101,365,210 (-)NCBIMGSCv36mm8
Celera11113,175,987 - 113,239,169 (-)NCBICelera
Cytogenetic Map11DNCBI
cM Map1165.18NCBI
Brca1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545116,819,023 - 16,855,528 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545116,819,463 - 16,870,780 (-)NCBIChiLan1.0ChiLan1.0
BRCA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21921,865,798 - 21,957,438 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11723,755,123 - 23,836,219 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01714,197,946 - 14,279,064 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11714,429,601 - 14,506,815 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1714,428,526 - 14,506,815 (+)Ensemblpanpan1.1panPan2
BRCA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1919,958,941 - 20,025,494 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl919,958,391 - 20,025,494 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha919,422,566 - 19,486,083 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0920,677,057 - 20,743,989 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl920,677,128 - 20,743,989 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1919,464,421 - 19,527,988 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0919,730,981 - 19,794,752 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0919,833,116 - 19,896,786 (+)NCBIUU_Cfam_GSD_1.0
Brca1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560219,272,096 - 19,340,929 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493649017,735,444 - 17,801,456 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BRCA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1219,786,020 - 19,854,668 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11219,788,087 - 19,854,515 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21220,028,878 - 20,093,800 (-)NCBISscrofa10.2Sscrofa10.2susScr3
BRCA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11663,162,827 - 63,243,928 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607733,932,799 - 34,042,352 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Brca1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247951,188,136 - 1,241,964 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247951,186,043 - 1,238,986 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Brca1
491 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:126
Count of miRNA genes:93
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000028109
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108256485692369470Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)107563188787055282Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108051528791230079Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)107877551698279596Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)107889965587307728Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107437208494965338Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)108402232193995963Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107255241693995749Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108400727295933025Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608594965338Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108400727295933025Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat

Markers in Region
D10Arb30  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21086,457,117 - 86,457,246 (+)MAPPERmRatBN7.2
Rnor_6.01089,434,505 - 89,434,633NCBIRnor6.0
Rnor_5.01089,232,320 - 89,232,448UniSTSRnor5.0
RGSC_v3.41090,552,493 - 90,552,622RGDRGSC3.4
RGSC_v3.41090,552,494 - 90,552,622UniSTSRGSC3.4
RGSC_v3.11090,566,863 - 90,566,992RGD
Celera1085,180,493 - 85,180,621UniSTS
Cytogenetic Map10q32.1UniSTS
D10Chm56  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21086,420,805 - 86,421,038 (+)MAPPERmRatBN7.2
Rnor_6.01089,398,186 - 89,398,416NCBIRnor6.0
Rnor_5.01089,196,018 - 89,196,248UniSTSRnor5.0
RGSC_v3.41090,515,968 - 90,516,198UniSTSRGSC3.4
Celera1085,143,640 - 85,143,870UniSTS
Cytogenetic Map10q32.1UniSTS


Related Rat Strains
The following Strains have been annotated to Brca1
SD     SD-Brca1m1Uwm    


Genetic Models
This gene Brca1 is modified in the following models/strains:
SD-Brca1m1Uwm     SD-Brca1em1Kyo    


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 14 24 18 12 18 28 16 29
Low 3 25 33 23 7 23 4 4 46 19 12 11 4
Below cutoff 4 4 7 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000028109   ⟹   ENSRNOP00000028109
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1086,418,468 - 86,477,304 (-)Ensembl
Rnor_6.0 Ensembl1089,395,848 - 89,454,681 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083111   ⟹   ENSRNOP00000072366
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1086,418,000 - 86,477,304 (-)Ensembl
Rnor_6.0 Ensembl1089,394,803 - 89,452,200 (-)Ensembl
RefSeq Acc Id: NM_012514   ⟹   NP_036646
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81086,917,693 - 86,977,581 (-)NCBI
mRatBN7.21086,417,451 - 86,477,331 (-)NCBI
Rnor_6.01089,395,848 - 89,454,681 (-)NCBI
Rnor_5.01089,192,653 - 89,252,760 (-)NCBI
RGSC_v3.41090,513,630 - 90,572,676 (-)RGD
Celera1085,140,052 - 85,200,670 (-)RGD
Sequence:
RefSeq Acc Id: XM_008768092   ⟹   XP_008766314
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81086,917,693 - 86,978,012 (-)NCBI
mRatBN7.21086,417,441 - 86,477,762 (-)NCBI
Rnor_6.01089,394,821 - 89,455,093 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039086541   ⟹   XP_038942469
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81086,917,693 - 86,978,012 (-)NCBI
mRatBN7.21086,417,441 - 86,477,762 (-)NCBI
RefSeq Acc Id: XM_039086542   ⟹   XP_038942470
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81086,924,977 - 86,978,012 (-)NCBI
mRatBN7.21086,424,640 - 86,477,762 (-)NCBI
RefSeq Acc Id: XM_063269583   ⟹   XP_063125653
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81086,917,693 - 86,978,012 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_036646   ⟸   NM_012514
- UniProtKB: P97951 (UniProtKB/Swiss-Prot),   O54952 (UniProtKB/Swiss-Prot),   A6HJD2 (UniProtKB/TrEMBL),   G3V8S5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766314   ⟸   XM_008768092
- Peptide Label: isoform X1
- UniProtKB: P97951 (UniProtKB/Swiss-Prot),   O54952 (UniProtKB/Swiss-Prot),   A6HJD2 (UniProtKB/TrEMBL),   G3V8S5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000028109   ⟸   ENSRNOT00000028109
RefSeq Acc Id: ENSRNOP00000072366   ⟸   ENSRNOT00000083111
RefSeq Acc Id: XP_038942469   ⟸   XM_039086541
- Peptide Label: isoform X1
- UniProtKB: P97951 (UniProtKB/Swiss-Prot),   O54952 (UniProtKB/Swiss-Prot),   A6HJD2 (UniProtKB/TrEMBL),   G3V8S5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038942470   ⟸   XM_039086542
- Peptide Label: isoform X3
- UniProtKB: A0A0G2K2T3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063125653   ⟸   XM_063269583
- Peptide Label: isoform X2
Protein Domains
BRCA1 serine-rich   BRCT   RING-type

Transcriptome

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

Promoters
RGD ID:13697764
Promoter ID:EPDNEW_R8289
Type:initiation region
Name:Brca1_1
Description:BRCA1, DNA repair associated
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_6.01089,454,684 - 89,454,744EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2218 AgrOrtholog
BioCyc Gene G2FUF-23168 BioCyc
Ensembl Genes ENSRNOG00000020701 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028109 ENTREZGENE
  ENSRNOT00000028109.4 UniProtKB/TrEMBL
  ENSRNOT00000083111.2 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.10190 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro BRCA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BRCA1-associated UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BRCA1_serine_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BRCT_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BRCT_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C3HC4_RING-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:497672 UniProtKB/Swiss-Prot
NCBI Gene Brca1 ENTREZGENE
PANTHER BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR13763 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam BRCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BRCT_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C3HC4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB BRCA1 RGD
PhenoGen Brca1 PhenoGen
PIRSF BRCA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS BRSTCANCERI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE BRCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_RING_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020701 RatGTEx
SMART BRCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP RING/U-box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K2T3 ENTREZGENE, UniProtKB/TrEMBL
  A6HJD2 ENTREZGENE, UniProtKB/TrEMBL
  B0FT14_RAT UniProtKB/TrEMBL
  BRCA1_RAT UniProtKB/Swiss-Prot
  G3V8S5 ENTREZGENE, UniProtKB/TrEMBL
  O54952 ENTREZGENE
  P97951 ENTREZGENE
UniProt Secondary P97951 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Brca1  BRCA1, DNA repair associated  Brca1  breast cancer 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Brca1  breast cancer 1  Brca1  breast cancer 1, early onset  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-01-14 Brca1  breast cancer 1, early onset  Brca1  breast cancer 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Brca1  breast cancer 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains amino terminal RING-finger domain with high homology in rat mouse and human suggesting a conserved biological function 62417
gene_domains contains an amino terminal RING finger domain, two nuclear localization signals, two BRCT domains at the carboxy terminus and a highly acidic region 67955
gene_mutations_overexpression intron 6 contains a polymorphism of a pentanucleotide TTTTG repeat between the WKY and WF strains 67955
gene_other a pronounced peak in the ratio of nonsynonymous to synonymous substitutions between codon 200-300, suggests that purifying (negative) selection is acting on silent sites 68720