Human Gene BRCA1 (uc010whm.2)
  Description: Homo sapiens breast cancer 1, early onset (BRCA1), transcript variant 6, non-coding RNA.
RefSeq Summary (NR_027676): This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020].
Transcript (Including UTRs)
   Position: hg19 chr17:41,196,312-41,277,340 Size: 81,029 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr17:41,197,695-41,277,202 Size: 79,508 Coding Exon Count: 8 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:41,196,312-41,277,340)mRNA (may differ from genome)Protein (173 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsHGNC
LynxMalacardsMGIPubMedTreefamUniProtKB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): BRCA1
CDC HuGE Published Literature: BRCA1
Positive Disease Associations: breast cancer , breast cancer, male , breast cancer; ovarian cancer , endometrial carcinoma , germline BRCA1 mutation , ovarian cancer , tumor progression
Related Studies:
  1. breast cancer
    Bau, D. T. et al. 2004, Breast cancer risk and the DNA double-strand break end-joining capacity of nonhomologous end-joining genes are affected by BRCA1., Cancer research. 2004 Jul;64(14):5013-9. [PubMed 15256476]
    Because BRCA1 is a well-documented breast cancer susceptibility gene, this association between NHEJ and BRCA1 not only suggests a role of BRCA1 in NHEJ but also provides essential support for the tumorigenic contribution of NHEJ in breast cancer development..
  2. breast cancer
    Robson, M. E. et al. 2004, A combined analysis of outcome following breast cancer: differences in survival based onBRCA1/BRCA2 mutation status and administration of adjuvant treatment., Breast cancer research. 2004 ;6(1):R8-R17. [PubMed 14680495]
    BRCA1 mutations, but not BRCA2 mutations, are associated with reduced survival in Ashkenazi women undergoing breast-conserving treatment for invasive breast cancer, but the poor prognosis associated with germline BRCA1 mutations is mitigated by adjuvant chemotherapy. The risk for metachronous ipsilateral disease does not appear to be increased for either BRCA1 or BRCA2 mutation carriers, at least up to 10 years of follow up.
  3. breast cancer
    Zhou, Y. Z. et al. 2004, [Germline mutations in the BRCA1 and BRCA2 genes from breast cancer families in China Han people], Zhonghua yi xue za zhi. 2004 Feb;84(4):294-8. [PubMed 15059511]
    Two pathogenic SNPs have been found in BRCA1 and may be related to early-onset breast cancer. One of them may be a novel mutation characterized of familial breast cancer in China.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: BRCA1
Diseases sorted by gene-association score: breast-ovarian cancer, familial, 1* (1280), pancreatic cancer 4* (969), hereditary breast ovarian cancer* (777), brca1 hereditary breast and ovarian cancer syndrome* (500), punctate porokeratosis* (400), ovarian cancer, somatic* (337), rhabdomyosarcoma* (283), breast cancer* (240), tumor predisposition syndrome* (200), pancreatic cancer* (181), bap1 tumor predisposition syndrome* (179), fanconi anemia, complementation group a* (142), brca2 hereditary breast and ovarian cancer syndrome* (121), pancreatic cancer susceptibility 4* (100), fallopian tube carcinoma (49), primary peritoneal carcinoma* (43), sporadic breast cancer (38), bilateral breast cancer (37), ovarian cystadenoma (25), premature menopause (25), female reproductive organ cancer (20), hereditary site-specific ovarian cancer syndrome* (18), breast reconstruction (18), breast carcinoma in situ (17), li-fraumeni syndrome (15), peritoneum cancer (13), nijmegen breakage syndrome (13), mutagen sensitivity (13), riddle syndrome (13), radiation induced cancer (13), ovary epithelial cancer (12), malignant ovarian surface epithelial-stromal neoplasm (12), reproductive organ cancer (11), lynch syndrome (11), nosophobia (11), cancerophobia (11), fallopian tube adenocarcinoma (10), prostate cancer* (9), ataxia-telangiectasia (9), ductal carcinoma in situ (9), uterine corpus serous adenocarcinoma (9), tuberculous salpingitis (8), breast ductal carcinoma (7), papillary serous adenocarcinoma (7), colorectal cancer, hereditary nonpolyposis, type 1 (7), endometrial cancer (7), breast medullary carcinoma (7), synchronous bilateral breast carcinoma (7), hypertrophy of breast (6), cowden disease (6), canavan disease (6), glycogen-rich clear cell breast carcinoma (5), dysgerminoma of ovary (5), pre-malignant neoplasm (5), adamantinoma of long bones (5), uterine corpus cancer (5), clear cell adenofibroma (4), in situ carcinoma (4), triple-receptor negative breast cancer (4), cystadenofibroma (4), warsaw breakage syndrome (4), miles-carpenter syndrome (3), colorectal cancer (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.31 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 51.80 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -54.40138-0.394 Picture PostScript Text
3' UTR -427.221383-0.309 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011364 - BRCA1
IPR001357 - BRCT_dom

Pfam Domains:
PF00533 - BRCA1 C Terminus (BRCT) domain

SCOP Domains:
52113 - BRCT domain

ModBase Predicted Comparative 3D Structure on C6YB45
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0004842 ubiquitin-protein transferase activity
GO:0008270 zinc ion binding

Biological Process:
GO:0006281 DNA repair
GO:0006974 cellular response to DNA damage stimulus
GO:0016567 protein ubiquitination

Cellular Component:
GO:0005634 nucleus
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK293762 - Homo sapiens cDNA FLJ58524 complete cds, highly similar to Homo sapiens breast cancer 1, early onset (BRCA1), transcript variant BRCA1-delta 11b, mRNA.
LF384806 - JP 2014500723-A/192309: Polycomb-Associated Non-Coding RNAs.
Y08864 - H.sapiens mRNA for breast and ovarian cancer susceptibility protein (BRCA1), 3'UTR.
JD503196 - Sequence 484220 from Patent EP1572962.
LF327934 - JP 2014500723-A/135437: Polycomb-Associated Non-Coding RNAs.
MS839225 - Sequence 338 from Patent WO2017013436.
JD372542 - Sequence 353566 from Patent EP1572962.
JD093954 - Sequence 74978 from Patent EP1572962.
JD349851 - Sequence 330875 from Patent EP1572962.
BC072418 - Homo sapiens breast cancer 1, early onset, mRNA (cDNA clone IMAGE:6181860), complete cds.
JD518021 - Sequence 499045 from Patent EP1572962.
JD366726 - Sequence 347750 from Patent EP1572962.
JD474101 - Sequence 455125 from Patent EP1572962.
JD141995 - Sequence 123019 from Patent EP1572962.
JD318791 - Sequence 299815 from Patent EP1572962.
JD239477 - Sequence 220501 from Patent EP1572962.
JD083661 - Sequence 64685 from Patent EP1572962.
JD110198 - Sequence 91222 from Patent EP1572962.
JD516185 - Sequence 497209 from Patent EP1572962.
JD084878 - Sequence 65902 from Patent EP1572962.
JD182820 - Sequence 163844 from Patent EP1572962.
JD331968 - Sequence 312992 from Patent EP1572962.
JD308815 - Sequence 289839 from Patent EP1572962.
JD096357 - Sequence 77381 from Patent EP1572962.
JD334170 - Sequence 315194 from Patent EP1572962.
U68041 - Human breast and ovarian cancer susceptibility protein (BRCA1) mRNA, partial cds.
JD177455 - Sequence 158479 from Patent EP1572962.
JD162926 - Sequence 143950 from Patent EP1572962.
JD063051 - Sequence 44075 from Patent EP1572962.
JD515572 - Sequence 496596 from Patent EP1572962.
JD047611 - Sequence 28635 from Patent EP1572962.
JD135794 - Sequence 116818 from Patent EP1572962.
JD222496 - Sequence 203520 from Patent EP1572962.
JD112498 - Sequence 93522 from Patent EP1572962.
JD396242 - Sequence 377266 from Patent EP1572962.
JD083487 - Sequence 64511 from Patent EP1572962.
JD313313 - Sequence 294337 from Patent EP1572962.
JD411991 - Sequence 393015 from Patent EP1572962.
JD258470 - Sequence 239494 from Patent EP1572962.
JD417717 - Sequence 398741 from Patent EP1572962.
JD340802 - Sequence 321826 from Patent EP1572962.
JD340800 - Sequence 321824 from Patent EP1572962.
JD340801 - Sequence 321825 from Patent EP1572962.
JD056839 - Sequence 37863 from Patent EP1572962.
JD541064 - Sequence 522088 from Patent EP1572962.
JD446374 - Sequence 427398 from Patent EP1572962.
JD344152 - Sequence 325176 from Patent EP1572962.
JD347091 - Sequence 328115 from Patent EP1572962.
JD519965 - Sequence 500989 from Patent EP1572962.
DQ333386 - Homo sapiens BRCA1 isoform E1aA-delta2-17 mRNA, complete cds, alternatively spliced.
DQ333387 - Homo sapiens BRCA1 isoform PI21-delta2-21 mRNA, complete cds, alternatively spliced.
DQ363751 - Homo sapiens breast and ovarian cancer sususceptibility protein (BRCA1) mRNA, complete cds, alternatively spliced.
JD320588 - Sequence 301612 from Patent EP1572962.
JD123048 - Sequence 104072 from Patent EP1572962.
BC115037 - Homo sapiens breast cancer 1, early onset, mRNA (cDNA clone MGC:131629 IMAGE:7961446), complete cds.
JD104066 - Sequence 85090 from Patent EP1572962.
JD187021 - Sequence 168045 from Patent EP1572962.
JD156151 - Sequence 137175 from Patent EP1572962.
LF327935 - JP 2014500723-A/135438: Polycomb-Associated Non-Coding RNAs.
JD156150 - Sequence 137174 from Patent EP1572962.
JD156149 - Sequence 137173 from Patent EP1572962.
KP272106 - Homo sapiens isolate TWH94001 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, partial cds.
JN686490 - Homo sapiens breast and ovarian cancer sususceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494347 - Homo sapiens isolate TWH-1562-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494348 - Homo sapiens isolate TWH-1326-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494352 - Homo sapiens isolate HKSH-0090-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494353 - Homo sapiens isolate TWH-1519-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494354 - Homo sapiens isolate HKSH-0246-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494355 - Homo sapiens isolate HKSH-0181-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494356 - Homo sapiens isolate QMH-0112-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494357 - Homo sapiens isolate TWH-1558-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494358 - Homo sapiens isolate FP-0148-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494359 - Homo sapiens isolate FP-0163-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494360 - Homo sapiens isolate QMH-0260-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494361 - Homo sapiens isolate OV-0102-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494362 - Homo sapiens isolate TWH-1330-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494363 - Homo sapiens isolate OV-0167-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494364 - Homo sapiens isolate OV-0215-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494365 - Homo sapiens isolate HKSH-0177-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494366 - Homo sapiens isolate OV-0104-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494367 - Homo sapiens isolate FP-0157-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494368 - Homo sapiens isolate HKSH-0229-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494369 - Homo sapiens isolate TWH-0468-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494370 - Homo sapiens isolate OV-0205-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494371 - Homo sapiens isolate OV-0051-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494372 - Homo sapiens isolate TWH-1552-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494373 - Homo sapiens isolate HKSH-0186-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
MG494374 - Homo sapiens isolate TWH-1304-0-1 truncated breast and ovarian cancer susceptibility protein 1 (BRCA1) mRNA, complete cds.
U64805 - Homo sapiens Brca1-delta11b (Brca1) mRNA, complete cds.
AF005068 - Homo sapiens breast and ovarian cancer susceptibility protein splice variant (BRCA1) mRNA, complete cds.
U14680 - Homo sapiens breast and ovarian cancer susceptibility (BRCA1) mRNA, complete cds.
KJ901305 - Synthetic construct Homo sapiens clone ccsbBroadEn_10699 BRCA1 gene, encodes complete protein.
AB385129 - Synthetic construct DNA, clone: pF1KB5593, Homo sapiens BRCA1 gene for breast cancer type 1 susceptibility protein, complete cds, without stop codon, in Flexi system.
AY751490 - Homo sapiens breast and ovarian cancer susceptibility protein (BRCA1) mRNA, BRCA1-2201T/2430C/2731T/3232G/3667G/4427C/4956G allele, partial cds.
KJ890779 - Synthetic construct Homo sapiens clone ccsbBroadEn_00173 BRCA1 gene, encodes complete protein.
KR711442 - Synthetic construct Homo sapiens clone CCSBHm_00023562 BRCA1 (BRCA1) mRNA, encodes complete protein.
KR711443 - Synthetic construct Homo sapiens clone CCSBHm_00023622 BRCA1 (BRCA1) mRNA, encodes complete protein.
KR711444 - Synthetic construct Homo sapiens clone CCSBHm_00023651 BRCA1 (BRCA1) mRNA, encodes complete protein.
KR711445 - Synthetic construct Homo sapiens clone CCSBHm_00023739 BRCA1 (BRCA1) mRNA, encodes complete protein.
JD296335 - Sequence 277359 from Patent EP1572962.
JD207374 - Sequence 188398 from Patent EP1572962.
JD493142 - Sequence 474166 from Patent EP1572962.
JD491739 - Sequence 472763 from Patent EP1572962.
BC046142 - Homo sapiens breast cancer 1, early onset, mRNA (cDNA clone IMAGE:4342873).
BC085615 - Homo sapiens breast cancer 1, early onset, mRNA (cDNA clone IMAGE:6042052), partial cds.
JD219355 - Sequence 200379 from Patent EP1572962.
AK316200 - Homo sapiens cDNA, FLJ79099 partial cds, highly similar to Homo sapiens breast cancer 1, early onset (BRCA1), transcript variant BRCA1-delta 11b, mRNA.
JD309089 - Sequence 290113 from Patent EP1572962.
BC012577 - Homo sapiens breast cancer 1, early onset, mRNA (cDNA clone IMAGE:3996658), with apparent retained intron.
AK308084 - Homo sapiens cDNA, FLJ98032.
AK307553 - Homo sapiens cDNA, FLJ97501.
BC030969 - Homo sapiens breast cancer 1, early onset, mRNA (cDNA clone IMAGE:4804551), partial cds.
BC106745 - Homo sapiens breast cancer 1, early onset, mRNA (cDNA clone IMAGE:40017569), partial cds.
BC106746 - Homo sapiens breast cancer 1, early onset, mRNA (cDNA clone IMAGE:40017570), partial cds.
BC114511 - Homo sapiens breast cancer 1, early onset, mRNA (cDNA clone IMAGE:40017573).
BC114562 - Homo sapiens cDNA clone IMAGE:40017575, containing frame-shift errors.
AB621825 - Homo sapiens BRCA1 mRNA for breast cancer type 1 susceptibility protein, partial cds, clone: HP08575-RBd67C11.
MA790387 - JP 2018524990-A/338: Molecular Diagnostic Test for Cancer.
MA620383 - JP 2018138019-A/192309: Polycomb-Associated Non-Coding RNAs.
MA563511 - JP 2018138019-A/135437: Polycomb-Associated Non-Coding RNAs.
MA563512 - JP 2018138019-A/135438: Polycomb-Associated Non-Coding RNAs.
MN577637 - UNVERIFIED: Homo sapiens mRNA sequence.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04120 - Ubiquitin mediated proteolysis

BioCarta from NCI Cancer Genome Anatomy Project
h_atrbrcaPathway - Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility
h_bard1Pathway - BRCA1-dependent Ub-ligase activity
h_g2Pathway - Cell Cycle: G2/M Checkpoint
h_carm-erPathway - CARM1 and Regulation of the Estrogen Receptor
h_atmPathway - ATM Signaling Pathway

-  Other Names for This Gene
  Alternate Gene Symbols: C6YB45, C6YB45_HUMAN, DQ333386
UCSC ID: uc010whm.2
RefSeq Accession: NR_027676
Protein: C6YB45

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene BRCA1:
brca1 (BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer)
fa (Fanconi Anemia)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: DQ333386.1
exon count: 8CDS single in 3' UTR: no RNA size: 781
ORF size: 522CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1195.00frame shift in genome: no % Coverage: 99.23
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.