Protein:BRCA1 |
Protein Summary |
 Gene summary |
| Gene name: BRCA1 | ASpdb.0 ID: 672 | Gene | Gene symbol | BRCA1 | Gene ID | 672 |
| Gene name | BRCA1 DNA repair associated |
| Synonyms | BRCAI|BRCC1|BROVCA1|FANCS|IRIS|PNCA4|PPP1R53|PSCP|RNF53 |
| Cytomap | 17q21.31 |
| Type of gene | protein-coding |
| Description | breast cancer type 1 susceptibility proteinBRCA1/BRCA2-containing complex, subunit 1Fanconi anemia, complementation group SRING finger protein 53breast and ovarian cancer susceptibility protein 1breast cancer 1, early onsetearly onset breast cancer |
| Modification date | 20240416 |
| UniProtAcc | P38398 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | BRCA1 | GO:0000152 | nuclear ubiquitin ligase complex | 14636569 |
| Gene | BRCA1 | GO:0000724 | double-strand break repair via homologous recombination | 17349954|28398198 |
| Gene | BRCA1 | GO:0000800 | lateral element | 9774970 |
| Gene | BRCA1 | GO:0000976 | transcription cis-regulatory region binding | 20820192 |
| Gene | BRCA1 | GO:0001216 | DNA-binding transcription activator activity | 20820192 |
| Gene | BRCA1 | GO:0002039 | p53 binding | 15571721 |
| Gene | BRCA1 | GO:0003723 | RNA binding | 12419249 |
| Gene | BRCA1 | GO:0004842 | ubiquitin-protein transferase activity | 12890688|17349954|19117993|20351172 |
| Gene | BRCA1 | GO:0005634 | nucleus | 9342365|14636569|17525340|17643121|20160719|23855721|26833090 |
| Gene | BRCA1 | GO:0005654 | nucleoplasm | - |
| Gene | BRCA1 | GO:0005737 | cytoplasm | 20160719 |
| Gene | BRCA1 | GO:0005886 | plasma membrane | 21282464 |
| Gene | BRCA1 | GO:0006301 | postreplication repair | 17349954 |
| Gene | BRCA1 | GO:0006302 | double-strand break repair | 22186889 |
| Gene | BRCA1 | GO:0008630 | intrinsic apoptotic signaling pathway in response to DNA damage | 14654789 |
| Gene | BRCA1 | GO:0016567 | protein ubiquitination | 17349954 |
| Gene | BRCA1 | GO:0016604 | nuclear body | - |
| Gene | BRCA1 | GO:0031436 | BRCA1-BARD1 complex | 12890688|15265711|19117993|20351172 |
| Gene | BRCA1 | GO:0032991 | protein-containing complex | 9774970 |
| Gene | BRCA1 | GO:0043232 | intracellular non-membrane-bounded organelle | 9008167 |
| Gene | BRCA1 | GO:0045892 | negative regulation of DNA-templated transcription | 16288014 |
| Gene | BRCA1 | GO:0045893 | positive regulation of DNA-templated transcription | 20160719 |
| Gene | BRCA1 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 16331276 |
| Gene | BRCA1 | GO:0051179 | localization | 9008167 |
| Gene | BRCA1 | GO:0051726 | regulation of cell cycle | 21102443 |
| Gene | BRCA1 | GO:0051865 | protein autoubiquitination | 12890688|20351172 |
| Gene | BRCA1 | GO:0070063 | RNA polymerase binding | 9662397 |
| Gene | BRCA1 | GO:0070531 | BRCA1-A complex | 17525340|17525341|17525342|19261748|19261749 |
| Gene | BRCA1 | GO:0071681 | cellular response to indole-3-methanol | 10868478 |
| Gene | BRCA1 | GO:0085020 | protein K6-linked ubiquitination | 12890688|20351172 |
| Gene | BRCA1 | GO:1990904 | ribonucleoprotein complex | 18809582 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| P38398-1 | P38398-1_4igk_A.pdb | 4IGK | X-ray | 1.75 | A | 1646 | 1859 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| P38398 | BRCA1 | P38398-1 | P38398-2 | 1863 | 63 | 64 | 1863 | Deletion | none | none | 63 | 63 |
| P38398 | BRCA1 | P38398-1 | P38398-3 | 1863 | 759 | 264 | 1366 | Deletion | none | none | 263 | 263 |
| P38398 | BRCA1 | P38398-1 | P38398-3 | 1863 | 759 | 1453 | 1453 | Deletion | none | none | 349 | 349 |
| P38398 | BRCA1 | P38398-1 | P38398-5 | 1863 | 721 | 224 | 1365 | Deletion | none | none | 223 | 223 |
| P38398 | BRCA1 | P38398-1 | P38398-6 | 1863 | 699 | 264 | 1366 | Deletion | none | none | 263 | 263 |
| P38398 | BRCA1 | P38398-1 | P38398-6 | 1863 | 699 | 1453 | 1453 | Deletion | none | none | 349 | 349 |
| P38398 | BRCA1 | P38398-1 | P38398-6 | 1863 | 699 | 1778 | 1863 | Substitution | DQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY | GCPPNCGCAARCLDRGQWLPCNWADV | 674 | 699 |
| Multiple sequence alignment of our canonical and alternatively spliced BRCA1 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of BRCA1 |
| UniProt-id | ENSG | ENST | ENSP |
| P38398-1 | ENSG00000012048.25 | ENST00000357654.9 | ENSP00000350283.3 |
| P38398-1 | ENSG00000012048.25 | ENST00000470026.6 | ENSP00000419274.2 |
| P38398-1 | ENSG00000012048.25 | ENST00000494123.6 | ENSP00000419103.2 |
| P38398-1 | ENSG00000012048.25 | ENST00000618469.2 | ENSP00000478114.2 |
| P38398-2 | ENSG00000012048.25 | ENST00000461221.5 | ENSP00000418548.1 |
| P38398-2 | ENSG00000012048.25 | ENST00000461798.5 | ENSP00000417988.1 |
| P38398-3 | ENSG00000012048.25 | ENST00000491747.6 | ENSP00000420705.2 |
| P38398-5 | ENSG00000012048.25 | ENST00000352993.7 | ENSP00000312236.5 |
| P38398-6 | ENSG00000012048.25 | ENST00000468300.5 | ENSP00000417148.1 |
| UniProt-id | NM ID | NP ID |
| P38398-1 | NM_007294.3 | NP_009225.1 |
| P38398-3 | NM_007298.3 | NP_009229.2 |
| P38398-6 | NM_007299.3 | NP_009230.2 |
| Amino acid sequences of our canonical and alternatively spliced BRCA1 |
| accession_id | Protein sequence |
| P38398-1 | MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKII CAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPENPSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYI ELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEISLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLH VEPCGTNTHASSLQHENSSLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLLASDPHEALICKSERVHSK SVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKRKRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTE QNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEKESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRN LSPPNCTELQIDSCSSSEEIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLGKAKTEPNKCVSQCAAFEN PKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVSKRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVT FECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKDKPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFV KTKCKKNLLEENFEEHSMSPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDDLLDDGEIKEDTSFAENDI KESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELPCFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENL LSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLFSSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTG LEENNQEEQSMDSNLGEAASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHSCSGSLQNRNYPSQEELIK VVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRAPESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTT DTAGYNAMEESVSREKPELTASTERVNKRMSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGG KWVVSYFWVTQSIKERKMLNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL |
| P38398-2 | |
| P38398-3 | MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKII CAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPENPSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYI ELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEISLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGEAASGCE SETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALEDLRNPEQSTSEKVLTSQKSSEYP ISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHSCSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLP RQDLEGTPYLESGISLFSDDPESDPSEDRAPESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTE RVNKRMSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKMLNEHDF EVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAI |
| P38398-5 | MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKII CAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPENPSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYI ELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEISLDSAKKGEAASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMA ELEAVLEQHGSQPSNSYPSIISDSSALEDLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCP SLDDRWYMHSCSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRAPESARVGN IPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSGLTPEEFMLVYKFARKHHITLTNLITE ETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKMLNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPF TNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSH |
| P38398-6 | MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKII CAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPENPSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYI ELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEISLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGEAASGCE SETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALEDLRNPEQSTSEKVLTSQKSSEYP ISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHSCSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLP RQDLEGTPYLESGISLFSDDPESDPSEDRAPESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTE RVNKRMSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKMLNEHDF |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| BRCA1 (go to UniProt):P38398 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| P38398 | Domain | 1642 | 1736 | Note=BRCT 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00033 | Type=Deletion;Start=64;End=1863 |
| P38398 | Domain | 1756 | 1855 | Note=BRCT 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00033 | Type=Deletion;Start=64;End=1863 |
| P38398 | Domain | 1756 | 1855 | Note=BRCT 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00033 | Type=Substitution;Start=1778;End=1863 |
| P38398 | Zinc finger | 24 | 65 | Note=RING-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00175 | Type=Deletion;Start=64;End=1863 |
| P38398 | Region | 230 | 270 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Region | 230 | 270 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 230 | 270 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Region | 230 | 270 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 306 | 338 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Region | 306 | 338 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 306 | 338 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Region | 306 | 338 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 534 | 570 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Region | 534 | 570 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 534 | 570 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Region | 534 | 570 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 654 | 709 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Region | 654 | 709 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 654 | 709 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Region | 654 | 709 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 1181 | 1216 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Region | 1181 | 1216 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 1181 | 1216 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Region | 1181 | 1216 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 1322 | 1387 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Region | 1322 | 1387 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 1322 | 1387 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Region | 1322 | 1387 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Region | 1397 | 1424 | Note=Interaction with PALB2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19369211;Dbxref=PMID:19369211 | Type=Deletion;Start=64;End=1863 |
| P38398 | Region | 1440 | 1505 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Region | 1440 | 1505 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1453;End=1453 |
| P38398 | Region | 1440 | 1505 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1453;End=1453 |
| P38398 | Region | 1565 | 1596 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Compositional bias | 230 | 248 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Compositional bias | 230 | 248 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Compositional bias | 324 | 338 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Compositional bias | 324 | 338 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 324 | 338 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Compositional bias | 324 | 338 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 534 | 569 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Compositional bias | 534 | 569 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 534 | 569 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Compositional bias | 534 | 569 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 676 | 698 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Compositional bias | 676 | 698 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 676 | 698 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Compositional bias | 676 | 698 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 1181 | 1196 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Compositional bias | 1181 | 1196 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 1181 | 1196 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Compositional bias | 1181 | 1196 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 1338 | 1353 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Compositional bias | 1338 | 1353 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 1338 | 1353 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Compositional bias | 1338 | 1353 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 1354 | 1387 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Compositional bias | 1354 | 1387 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 1354 | 1387 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=224;End=1365 |
| P38398 | Compositional bias | 1354 | 1387 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=264;End=1366 |
| P38398 | Compositional bias | 1440 | 1468 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
| P38398 | Compositional bias | 1440 | 1468 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1453;End=1453 |
| P38398 | Compositional bias | 1440 | 1468 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1453;End=1453 |
| P38398 | Compositional bias | 1478 | 1492 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=64;End=1863 |
Gene Isoform Structures and Expression Levels for BRCA1 |
| Gene structures of our canonical and alternative spliced genes of BRCA1 * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of P38398-1 |
| 3D view using mol* of P38398-2 |
| 3D view using mol* of P38398-3 |
| 3D view using mol* of P38398-5 |
| 3D view using mol* of P38398-6 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of P38398-1 |
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| pLDDT distribution across the protein length of P38398-2 |
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| pLDDT distribution across the protein length of P38398-3 |
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| pLDDT distribution across the protein length of P38398-5 |
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| pLDDT distribution across the protein length of P38398-6 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of P38398-1 |
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| Ramachandran plot of P38398-2 |
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| Ramachandran plot of P38398-3 |
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| Ramachandran plot of P38398-5 |
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| Ramachandran plot of P38398-6 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| P38398-1 | 0.98 | 96 | 1.014 | 403.368 | 0.73 | 0.657 | 0.774 | 0.433 | 0.926 | 0.467 | 0.735 | 1395,1398,1399,1401,1402,1405,1406,1409,1410,1654, 1655,1656,1657,1659,1662,1678,1679,1680,1699,1700, 1701,1702,1704,1705,1773,1774,1775,1779,1811,1813, 1835,1839 |
| P38398-2 | 0.409 | 11 | 0.291 | 52.136 | 0.82 | 0.546 | 0.76 | 0.215 | 1.07 | 0.201 | 1.316 | 21,25,31,41,42,63
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| P38398-3 | 0.864 | 62 | 0.89 | 181.447 | 0.738 | 0.629 | 0.757 | 0.647 | 0.699 | 0.926 | 0.83 | 29,30,31,32,33,34,44,45,46,47,75,80,83,84,87,90,94 ,103,104,105,107 |
| P38398-5 | 0.767 | 46 | 0.79 | 131.026 | 0.799 | 0.57 | 0.669 | 0.8 | 0.58 | 1.379 | 0.636 | 29,30,31,32,33,34,35,44,45,46,75,77,80,83,84,87,10 5,107 |
| P38398-6 | 1.03 | 522 | 1.079 | 1416.247 | 0.579 | 0.68 | 0.903 | 0.85 | 0.826 | 1.029 | 1.081 | 175,177,178,179,180,181,182,183,184,291,294,295,29 7,298,301,550,551,552,553,554,555,558,574,575,576, 577,578,596,597,598,600,601,603,604,605,607,642,64 4,647,648,651,652,654,655,656,657,658,659,660,661, 662,663,664,665,666,667,668,669,670,671,672,673,67 4,675,676,681,683,684,685,686,687,688,689,690,691, 692,693,694,695,696,697,698,699 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of P38398-1_P38398-1_4igk_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P38398-1_4igk_A_P38398-2.pdb |
| 3D view using mol* of P38398-1_4igk_A_P38398-3.pdb |
| 3D view using mol* of P38398-1_4igk_A_P38398-5.pdb |
| 3D view using mol* of P38398-1_4igk_A_P38398-6.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P38398-1_P38398-2.pdb |
| 3D view using mol* of P38398-1_P38398-3.pdb |
| 3D view using mol* of P38398-1_P38398-5.pdb |
| 3D view using mol* of P38398-1_P38398-6.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/P38398-1_vs_P38398-2.png |
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| ./stats/secondary_structure/figure/P38398-1_vs_P38398-3.png |
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| ./stats/secondary_structure/figure/P38398-1_vs_P38398-5.png |
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| ./stats/secondary_structure/figure/P38398-1_vs_P38398-6.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/P38398-1_vs_P38398-2.png |
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| ./stats/relative_asa/P38398-1_vs_P38398-3.png |
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| ./stats/relative_asa/P38398-1_vs_P38398-5.png |
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| ./stats/relative_asa/P38398-1_vs_P38398-6.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| P38398 | Region | 1397 | 1424 | Note=Interaction with PALB2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19369211;Dbxref=PMID:19369211 | Type=Deletion;Start=64;End=1863 |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to BRCA1 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to BRCA1 |
| Previous studies relating to the alternative splicing of BRCA1 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| BRCA1 | 9115959 | Mutations and alternative splicing of the BRCA1 gene in UK breast/ovarian cancer families. | BRCA1 is a tumour suppressor gene located on chromosome band 17q21. It is estimated that mutations in the BRCA1 gene account for approximately 45% of the breast cancer families and almost all of the breast/ovarian cancer families. We have used single strand conformation polymorphism analysis, direct sequencing, allele specific oligonucleotide hybridisation, and reverse transcription polymerase chain reaction (RT-PCR) to look for mutations in the BRCA1 gene in 49 breast or breast/ovarian cancer families. Five distinct mutations, three novel and two previously observed, were detected in seven families. Each novel mutation was identified in one family: 3896delT in exon 11, a splicing mutation in the intron 9-exon 10 junction, and an inferred regulatory mutation. The 185delAG in exon 2 was found in three families sharing the same haplotype, but this haplotype is different from that shared by the Ashkenazi Jewish families, suggesting that the 185delAG in our families may have arisen independently. Another previously reported mutation, the 3875del4 in exon 11, was identified in one family. Of the 49 families examined, linkage analyses for both the BRCA1 and the BRCA2 regions were performed on 33 families, and mutations in the BRCA1 gene were identified in all but one family that have a lod score above 0.8 for BRCA1. All of the mutations cause either a truncated BRCA1, or loss of a BRCA1 transcript, thus are likely to be functionally disruptive. In addition, we found that alternative splicing is a common phenomenon in the processing of the BRCA1 gene. Seven variant BRCA1 transcripts were identified by RT-PCR; all but one maintained the BRCA1 open reading frame. We believe that alternative splicing may play a significant role in modulating the physiological function of BRCA1. | D001943 | Breast Neoplasms |
| BRCA1 | 9115959 | Mutations and alternative splicing of the BRCA1 gene in UK breast/ovarian cancer families. | BRCA1 is a tumour suppressor gene located on chromosome band 17q21. It is estimated that mutations in the BRCA1 gene account for approximately 45% of the breast cancer families and almost all of the breast/ovarian cancer families. We have used single strand conformation polymorphism analysis, direct sequencing, allele specific oligonucleotide hybridisation, and reverse transcription polymerase chain reaction (RT-PCR) to look for mutations in the BRCA1 gene in 49 breast or breast/ovarian cancer families. Five distinct mutations, three novel and two previously observed, were detected in seven families. Each novel mutation was identified in one family: 3896delT in exon 11, a splicing mutation in the intron 9-exon 10 junction, and an inferred regulatory mutation. The 185delAG in exon 2 was found in three families sharing the same haplotype, but this haplotype is different from that shared by the Ashkenazi Jewish families, suggesting that the 185delAG in our families may have arisen independently. Another previously reported mutation, the 3875del4 in exon 11, was identified in one family. Of the 49 families examined, linkage analyses for both the BRCA1 and the BRCA2 regions were performed on 33 families, and mutations in the BRCA1 gene were identified in all but one family that have a lod score above 0.8 for BRCA1. All of the mutations cause either a truncated BRCA1, or loss of a BRCA1 transcript, thus are likely to be functionally disruptive. In addition, we found that alternative splicing is a common phenomenon in the processing of the BRCA1 gene. Seven variant BRCA1 transcripts were identified by RT-PCR; all but one maintained the BRCA1 open reading frame. We believe that alternative splicing may play a significant role in modulating the physiological function of BRCA1. | D010051 | Ovarian Neoplasms |
| BRCA1 | 12890739 | Emerging roles of BRCA1 alternative splicing. | Germline mutations of the BRCA1 gene predispose individuals mainly to the development of breast and/or ovarian cancer. However, the exact function of the gene is still unclear, although the encoded proteins are involved in various cellular processes, including transcriptional regulation and DNA repair pathways. Several BRCA1 splice variants are found in different tissues, but in spite of intense investigations, their regulation and possible functions are poorly understood at the moment. This review summarises current knowledge on the roles of these splice variants and the mechanisms responsible for their formation. Because alternative splicing is now widely accepted as an important source of genetic diversity, elucidating the functions of the BRCA1 splice variants would help in the understanding of the exact role(s) of this tumour suppressor. This should help to resolve the current paradox that, despite its seemingly vital cellular functions, mutations of this gene are associated with tissue specific tumour formation predominantly in the breast and the ovary. | D001943 | Breast Neoplasms |
| BRCA1 | 12890739 | Emerging roles of BRCA1 alternative splicing. | Germline mutations of the BRCA1 gene predispose individuals mainly to the development of breast and/or ovarian cancer. However, the exact function of the gene is still unclear, although the encoded proteins are involved in various cellular processes, including transcriptional regulation and DNA repair pathways. Several BRCA1 splice variants are found in different tissues, but in spite of intense investigations, their regulation and possible functions are poorly understood at the moment. This review summarises current knowledge on the roles of these splice variants and the mechanisms responsible for their formation. Because alternative splicing is now widely accepted as an important source of genetic diversity, elucidating the functions of the BRCA1 splice variants would help in the understanding of the exact role(s) of this tumour suppressor. This should help to resolve the current paradox that, despite its seemingly vital cellular functions, mutations of this gene are associated with tissue specific tumour formation predominantly in the breast and the ovary. | D020022 | Genetic Predisposition to Disease |
| BRCA1 | 12890739 | Emerging roles of BRCA1 alternative splicing. | Germline mutations of the BRCA1 gene predispose individuals mainly to the development of breast and/or ovarian cancer. However, the exact function of the gene is still unclear, although the encoded proteins are involved in various cellular processes, including transcriptional regulation and DNA repair pathways. Several BRCA1 splice variants are found in different tissues, but in spite of intense investigations, their regulation and possible functions are poorly understood at the moment. This review summarises current knowledge on the roles of these splice variants and the mechanisms responsible for their formation. Because alternative splicing is now widely accepted as an important source of genetic diversity, elucidating the functions of the BRCA1 splice variants would help in the understanding of the exact role(s) of this tumour suppressor. This should help to resolve the current paradox that, despite its seemingly vital cellular functions, mutations of this gene are associated with tissue specific tumour formation predominantly in the breast and the ovary. | D010051 | Ovarian Neoplasms |
| BRCA1 | 16185777 | A new alternative splice variant of BRCA1 containing an additional in-frame exon. | The breast/ovarian cancer susceptibility gene BRCA1 interact with multiple protein complexes involved in cellular mechanisms, such as DNA repair, transcription, homologous recombination and cell cycle regulation. Extensive analyses over the past decade led to the detection of several BRCA1 alternative splice variants. Here, we identify the first BRCA1 alternative splice variant containing an additional in-frame exon. This previously unknown exon 13A-containing transcript is generated by the insertion of 66 nucleotides between exons 13 and 14, due to alternative splicing in intron 13 (IVS13-2786-2720). Furthermore, exon 13A-containing transcript was detectable in total RNA samples from 12 normal tissues and several breast and other cancer cell lines. As revealed by real-time PCR analysis, this transcript corresponds to 20 to 25% of the total BRCA1 mRNA expression levels in leukocytes, brain and cerebellum tissues, whereas its relative level of expression is less than 5% in other tested tissues and cancer cell lines. This novel alternative transcript adds 22 amino acids after residue 1452, thus modifying the primary structure of the trans-activation domain 1 (AD1) and the protein-protein interacting domain of BRCA1 with BRCA2, AR and MSH2. No sequence variant has been detected by direct genomic sequencing of exon 13A in individuals originating from high-risk breast/ovarian cancer families. | D001943 | Breast Neoplasms |
| BRCA1 | 16185777 | A new alternative splice variant of BRCA1 containing an additional in-frame exon. | The breast/ovarian cancer susceptibility gene BRCA1 interact with multiple protein complexes involved in cellular mechanisms, such as DNA repair, transcription, homologous recombination and cell cycle regulation. Extensive analyses over the past decade led to the detection of several BRCA1 alternative splice variants. Here, we identify the first BRCA1 alternative splice variant containing an additional in-frame exon. This previously unknown exon 13A-containing transcript is generated by the insertion of 66 nucleotides between exons 13 and 14, due to alternative splicing in intron 13 (IVS13-2786-2720). Furthermore, exon 13A-containing transcript was detectable in total RNA samples from 12 normal tissues and several breast and other cancer cell lines. As revealed by real-time PCR analysis, this transcript corresponds to 20 to 25% of the total BRCA1 mRNA expression levels in leukocytes, brain and cerebellum tissues, whereas its relative level of expression is less than 5% in other tested tissues and cancer cell lines. This novel alternative transcript adds 22 amino acids after residue 1452, thus modifying the primary structure of the trans-activation domain 1 (AD1) and the protein-protein interacting domain of BRCA1 with BRCA2, AR and MSH2. No sequence variant has been detected by direct genomic sequencing of exon 13A in individuals originating from high-risk breast/ovarian cancer families. | D020022 | Genetic Predisposition to Disease |
| BRCA1 | 16185777 | A new alternative splice variant of BRCA1 containing an additional in-frame exon. | The breast/ovarian cancer susceptibility gene BRCA1 interact with multiple protein complexes involved in cellular mechanisms, such as DNA repair, transcription, homologous recombination and cell cycle regulation. Extensive analyses over the past decade led to the detection of several BRCA1 alternative splice variants. Here, we identify the first BRCA1 alternative splice variant containing an additional in-frame exon. This previously unknown exon 13A-containing transcript is generated by the insertion of 66 nucleotides between exons 13 and 14, due to alternative splicing in intron 13 (IVS13-2786-2720). Furthermore, exon 13A-containing transcript was detectable in total RNA samples from 12 normal tissues and several breast and other cancer cell lines. As revealed by real-time PCR analysis, this transcript corresponds to 20 to 25% of the total BRCA1 mRNA expression levels in leukocytes, brain and cerebellum tissues, whereas its relative level of expression is less than 5% in other tested tissues and cancer cell lines. This novel alternative transcript adds 22 amino acids after residue 1452, thus modifying the primary structure of the trans-activation domain 1 (AD1) and the protein-protein interacting domain of BRCA1 with BRCA2, AR and MSH2. No sequence variant has been detected by direct genomic sequencing of exon 13A in individuals originating from high-risk breast/ovarian cancer families. | D011471 | Prostatic Neoplasms |
| BRCA1 | 17244477 | Alternative splicing of breast cancer associated gene BRCA1 from breast cancer cell line. | Breast cancer is the most common malignancy among women, and mutations in the BRCA1 gene produce increased susceptibility to these malignancies in certain families. In this study, the forward 1-13 exons of breast cancer associated gene BRCA1 were cloned from breast cancer cell line ZR-75-30 by RT-PCR method. Sequence analysis showed that nine BRCA1 splice forms were isolated and characterized, compared with wild-type BRCA1 gene, five splice forms of which were novel. These splice isoforms were produced from the molecular mechanism of 5' and 3' alternative splicing. All these splice forms deleting exon 11b and the locations of alternative splicing were focused on two parts:one was exons 2 and 3, and the other was exons 9 and 10. These splice forms accorded with GT-AG rule. Most these BRCA1 splice variants still kept the original reading frame. Western blot analysis indicated that some BRCA1 splice variants were expressed in ZR-75-30 cell line at the protein level. In addition, we confirmed the presence of these new transcripts of BRCA1 gene in MDA-MB-435S, K562, Hela, HLA, HIC, H9, Jurkat and human fetus samples by RT-PCR analysis. These results suggested that breast cancer associated gene BRCA1 may have unexpectedly a large number of splice variants. We hypothesized that alternative splicing of BRCA1 possibly plays a major role in the tumorigenesis of breast and/or ovarian cancer. Thus, the identification of cancer-specific splice forms will provide a novel source for the discovery of diagnostic or prognostic biomarkers and tumor antigens suitable as targets for therapeutic intervention. | D001943 | Breast Neoplasms |
| BRCA1 | 19892845 | Alternative splicing and molecular characterization of splice site variants: BRCA1 c.591C>T as a case study. | Deleterious mutations in BRCA1 (breast cancer 1, early onset; MIM 113705) increase breast and ovarian cancer [B(O)C] risk; however, many variants cannot be readily classified as deleterious or neutral. Unclassified variants (UVs) pose serious problems in genetic counseling. RNA-splicing analysis is essential for the assessment of many UVs. | D001943 | Breast Neoplasms |
| BRCA1 | 21697133 | Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. | PURPOSE. To collect an entire set of full-length cDNA clones derived from human retina-derived cell lines and to identify full-length transcripts for retinal preferentially expressed genes. METHODS. The full-length cDNA libraries were constructed from a retinoblastoma cell line, Y79, and a retinal pigment epithelium cell line, ARPE-19, using the vector-capping method, which generates a genuine full-length cDNA. By single-pass sequencing of the 5'-end of cDNA clones and subsequent mapping to the human genome, the authors determined their transcriptional start sites and annotated the cDNA clones. RESULTS. Of the 23,616 clones isolated from Y79-derived cDNA libraries, 19,229 full-length cDNA clones were identified and classified into 4808 genes, including genes of >10 kbp. Of the 7067 genes obtained from the Y79 and ARPE-19 libraries, the authors selected 72 genes that were preferentially expressed in the eye, of which 131 clones corresponding to 57 genes were fully sequenced. As a result, we discovered many variants that were produced by different transcriptional start sites, alternative splicing, and alternative polyadenylation. CONCLUSIONS. The bias-free, full-length cDNA libraries constructed using the vector-capping method were shown to be useful for collecting an entire set of full-length cDNA clones for these retinal cell lines. Full-length transcriptome analysis of these cDNA libraries revealed that there were, unexpectedly, many transcript variants for each gene, indicating that obtaining the full-length cDNA for each variant is indispensable for analyzing its function. The full-length cDNA clones (approximately 80,000 clones each for ARPE-19 and Y79) will be useful as a resource for investigating the human retina. | D019572 | Retinal Neoplasms |
| BRCA1 | 21697133 | Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. | PURPOSE. To collect an entire set of full-length cDNA clones derived from human retina-derived cell lines and to identify full-length transcripts for retinal preferentially expressed genes. METHODS. The full-length cDNA libraries were constructed from a retinoblastoma cell line, Y79, and a retinal pigment epithelium cell line, ARPE-19, using the vector-capping method, which generates a genuine full-length cDNA. By single-pass sequencing of the 5'-end of cDNA clones and subsequent mapping to the human genome, the authors determined their transcriptional start sites and annotated the cDNA clones. RESULTS. Of the 23,616 clones isolated from Y79-derived cDNA libraries, 19,229 full-length cDNA clones were identified and classified into 4808 genes, including genes of >10 kbp. Of the 7067 genes obtained from the Y79 and ARPE-19 libraries, the authors selected 72 genes that were preferentially expressed in the eye, of which 131 clones corresponding to 57 genes were fully sequenced. As a result, we discovered many variants that were produced by different transcriptional start sites, alternative splicing, and alternative polyadenylation. CONCLUSIONS. The bias-free, full-length cDNA libraries constructed using the vector-capping method were shown to be useful for collecting an entire set of full-length cDNA clones for these retinal cell lines. Full-length transcriptome analysis of these cDNA libraries revealed that there were, unexpectedly, many transcript variants for each gene, indicating that obtaining the full-length cDNA for each variant is indispensable for analyzing its function. The full-length cDNA clones (approximately 80,000 clones each for ARPE-19 and Y79) will be useful as a resource for investigating the human retina. | D012175 | Retinoblastoma |
| BRCA1 | 22615956 | Evolutionary constraint helps unmask a splicing regulatory region in BRCA1 exon 11. | Alternative splicing across exon 11 produces several BRCA1 isoforms. Their proportion varies during the cell cycle, between tissues and in cancer suggesting functional importance of BRCA1 splicing regulation around this exon. Although the regulatory elements driving exon 11 splicing have never been identified, a selective constraint against synonymous substitutions (silent nucleotide variations that do not alter the amino acid residue sequence) in a critical region of BRCA1 exon 11 has been reported to be associated with the necessity to maintain regulatory sequences. | D001943 | Breast Neoplasms |
| BRCA1 | 25884417 | BRCA1 Alternative splicing landscape in breast tissue samples. | BRCA1 is a key protein in cell network, involved in DNA repair pathways and cell cycle. Recently, the ENIGMA consortium has reported a high number of alternative splicing (AS) events at this locus in blood-derived samples. However, BRCA1 splicing pattern in breast tissue samples is unknown. Here, we provide an accurate description of BRCA1 splicing events distribution in breast tissue samples. | D001943 | Breast Neoplasms |
Clinically important variants in BRCA1 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
| P38398 | P38398-1 | BRCA1 | single nucleotide variant | p.Leu999Ile | Conflicting classifications of pathogenicity |
| P38398 | P38398-1 | BRCA1 | single nucleotide variant | p.Leu999Ile | Conflicting classifications of pathogenicity |
| P38398 | P38398-1 | BRCA1 | Deletion | p.Gln148del | Uncertain significance |
| P38398 | P38398-1 | BRCA1 | Deletion | p.Gln148del | Uncertain significance |
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