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 several processes, including positive regulation of protein import into nucleus; response to estradiol; and response to genistein. Located in mitochondrial matrix. Biomarker of ductal carcinoma in situ. Human ortholog(s) of this gene implicated in several diseases, including Fanconi anemia complementation group S; breast cancer (multiple); cervix uteri carcinoma in situ; gastrointestinal system cancer (multiple); 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
Black Rat
Alliance Orthologs
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: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81086,917,693 - 86,978,012 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1086,917,693 - 86,977,763 (-)EnsemblGRCr8
mRatBN7.21086,417,441 - 86,477,762 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1086,418,000 - 86,477,304 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1091,454,623 - 91,513,795 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01090,930,035 - 90,990,102 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01086,323,338 - 86,383,395 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01089,394,821 - 89,455,093 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1089,394,803 - 89,454,681 (-)Ensemblrn6Rnor6.0
Rnor_5.01089,192,653 - 89,252,760 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41090,513,630 - 90,572,676 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1085,140,052 - 85,200,670 (-)NCBICelera
RGSC_v3.11090,527,999 - 90,587,046 (-)NCBI
Cytogenetic Map10q31NCBI
JBrowse:




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 Pancreatic Carcinoma  (ISO)
Familial Prostate Cancer  (ISO)
Fanconi anemia complementation group A  (ISO)
Fanconi anemia complementation group S  (ISO)
hereditary breast ovarian cancer syndrome  (ISO)
hereditary mixed polyposis syndrome 1  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
hereditary spastic paraplegia 11  (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)
periventricular nodular heterotopia  (ISO)
Premature Aging  (ISO)
prostate cancer  (ISO)
Prostatic Neoplasms  (ISO)
punctate palmoplantar keratoderma type II  (ISO)
rhabdomyosarcoma  (ISO)
stomach cancer  (ISO)
stomach carcinoma  (ISO)
Triple Negative Breast Neoplasms  (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)
2,2'-Methylenebis(4-methyl-6-tert-butylphenol)  (ISO)
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)
Bufotalin  (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)
dinaciclib  (ISO)
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)
GSK-J4  (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)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (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)
okadaic acid  (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-alpha hydrobromide  (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)
talazoparib  (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)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

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

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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1086,917,693 - 86,977,763 (-)EnsemblGRCr8
mRatBN7.21086,417,441 - 86,477,762 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1086,418,000 - 86,477,304 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1091,454,623 - 91,513,795 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01090,930,035 - 90,990,102 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01086,323,338 - 86,383,395 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01089,394,821 - 89,455,093 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1089,394,803 - 89,454,681 (-)Ensemblrn6Rnor6.0
Rnor_5.01089,192,653 - 89,252,760 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41090,513,630 - 90,572,676 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1085,140,052 - 85,200,670 (-)NCBICelera
RGSC_v3.11090,527,999 - 90,587,046 (-)NCBI
Cytogenetic Map10q31NCBI
BRCA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381743,044,295 - 43,170,327 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1743,044,292 - 43,170,245 (-)Ensemblhg38GRCh38
GRCh371741,196,312 - 41,322,344 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361738,449,840 - 38,530,994 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm3811101,488,761 - 101,551,955 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11101,488,764 - 101,551,955 (-)Ensemblmm10GRCm38
MGSCv3711101,350,078 - 101,413,269 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
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 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha919,422,566 - 19,486,083 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0920,677,057 - 20,743,989 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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
SpeTri2.0 EnsemblNW_00493649017,735,516 - 17,801,454 (-)EnsemblSpeTri2.0 Ensembl
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 (+)EnsemblsusScr11Sscrofa11.1
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247951,186,043 - 1,238,986 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Brca1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1960,775,195 - 60,835,480 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Brca1
324 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105107189796071897Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102702353598502431Rat
8657410Bp374Blood pressure QTL 374heart left ventricle size trait (VT:0002753)heart left ventricle end-diastolic diameter (CMO:0000982)1067476608107713808Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103550938391417879Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063719161107713808Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108101207791729860Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042546145107713808Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1058073360103073360Rat
12903252Cm113Cardiac mass QTL 1130.047heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105429633699451733Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108306123692869129Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105046480295464802Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1064939013107713808Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076951790107713808Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1079272424102982300Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104493935989939359Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104552916496099749Rat
70168Eae12Experimental allergic encephalomyelitis QTL 120.0009nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1073599825107713808Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1054296227107713808Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107674313395464802Rat
12903269Am15Aortic mass QTL 150.042aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105086028895860288Rat
12903266Cm114Cardiac mass QTL 1140.02heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1066817119107713808Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107395035396620293Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062556066107556066Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14282327487823274Rat
12880372Am12Aortic mass QTL 120.003aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062556066107556066Rat
12880375Kidm66Kidney mass QTL 660.009kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104493935989939359Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106724133498502431Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
12880370Cm105Cardiac mass QTL 1050.008heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104282327487823274Rat
12880371Cm106Cardiac mass QTL 1060.007heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106184349698710773Rat
11565453Kidm58Kidney mass QTL 580.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)107369533997272278Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1065390777107713808Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1081012077101828297Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102293137391127454Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107304965694495280Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)104949549294495492Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1052269185107713808Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068920187107713808Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)1065307813107713808Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1061843496106843496Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)102980091091417879Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070698731107713808Rat
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)102758722696099902Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105530797293608131Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1061843496100198886Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104360879388608793Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
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)1040535708107713808Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104994371094943710Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104493935989939359Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1066108888107555881Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1061843496100198886Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104786912992869129Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108450348796432422Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107674313395604677Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108450348796432422Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105060467795604677Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103550938388177745Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107395035396620293Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1076128947107713808Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)1061997479106997479Rat
2301405Cm69Cardiac mass QTL 690.031heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102702353599451848Rat

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
Celera1085,180,493 - 85,180,621UniSTS
RGSC_v3.11090,566,863 - 90,566,992RGD
Cytogenetic Map10q32.1UniSTS
D10Chm56  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81086,921,047 - 86,921,278 (+)Marker Load Pipeline
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

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 90 59 6 350 190 11 144 77 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000028109   ⟹   ENSRNOP00000028109
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1086,924,793 - 86,977,763 (-)Ensembl
mRatBN7.2 Ensembl1086,418,468 - 86,477,304 (-)Ensembl
Rnor_6.0 Ensembl1089,395,848 - 89,454,681 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000083111   ⟹   ENSRNOP00000072366
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1086,917,693 - 86,975,057 (-)Ensembl
mRatBN7.2 Ensembl1086,418,000 - 86,477,304 (-)Ensembl
Rnor_6.0 Ensembl1089,394,803 - 89,452,200 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000140859   ⟹   ENSRNOP00000108202
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1086,917,693 - 86,975,672 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000161138   ⟹   ENSRNOP00000099541
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1086,917,693 - 86,977,763 (-)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
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:
Ensembl Acc Id: ENSRNOP00000028109   ⟸   ENSRNOT00000028109
Ensembl 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
- UniProtKB: P97951 (UniProtKB/Swiss-Prot),   O54952 (UniProtKB/Swiss-Prot)
Ensembl Acc Id: ENSRNOP00000108202   ⟸   ENSRNOT00000140859
Ensembl Acc Id: ENSRNOP00000099541   ⟸   ENSRNOT00000161138
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
Ensembl Transcript ENSRNOT00000028109 ENTREZGENE
  ENSRNOT00000161138 ENTREZGENE
Gene3D-CATH 3.30.40.10 UniProtKB/Swiss-Prot
  3.40.50.10190 UniProtKB/Swiss-Prot
InterPro BRCA1 UniProtKB/Swiss-Prot
  BRCA1-associated UniProtKB/Swiss-Prot
  BRCA1_serine_dom UniProtKB/Swiss-Prot
  BRCT_dom UniProtKB/Swiss-Prot
  BRCT_dom_sf UniProtKB/Swiss-Prot
  Znf_C3HC4_RING-type UniProtKB/Swiss-Prot
  Znf_RING UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot
  Znf_RING_CS UniProtKB/Swiss-Prot
KEGG Report rno:497672 UniProtKB/Swiss-Prot
NCBI Gene Brca1 ENTREZGENE
PANTHER BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN UniProtKB/Swiss-Prot
  PTHR13763 UniProtKB/Swiss-Prot
Pfam BRCT UniProtKB/Swiss-Prot
  BRCT_assoc UniProtKB/Swiss-Prot
  zf-C3HC4 UniProtKB/Swiss-Prot
PharmGKB BRCA1 RGD
PhenoGen Brca1 PhenoGen
PIRSF BRCA1 UniProtKB/Swiss-Prot
PRINTS BRSTCANCERI UniProtKB/Swiss-Prot
PROSITE BRCT UniProtKB/Swiss-Prot
  ZF_RING_1 UniProtKB/Swiss-Prot
  ZF_RING_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000020701 RatGTEx
SMART BRCT UniProtKB/Swiss-Prot
  RING UniProtKB/Swiss-Prot
Superfamily-SCOP RING/U-box UniProtKB/Swiss-Prot
  SSF52113 UniProtKB/Swiss-Prot
UniProt A0A0G2K2T3 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0KXN9_RAT UniProtKB/TrEMBL
  A0ABK0LV95_RAT 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