BRCA1

General Information

Gene Name : BRCA1
Gene ID : ENSG00000012048.21
Essential Gene : Yes

Functions

Not Available

Localization

Not Available

Domains (AlphaFold: BRCA1)

Not Available

Antibody Validation

Not Avaiable

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	BRCA1	ENSG00000012048.21	28.48	30.46	29.47	ENCSR000AEF
HepG2	BRCA1	ENSG00000012048.21	25.41	29.03	27.22	ENCSR985KAT
K562	BRCA1	ENSG00000012048.21	54.02	51.88	52.95	ENCSR000AEO

Assays

2 Released experiments are available on ENCORE database.

Assay Type	Exp_Name	ENCODE ID	Target label	Biosample	Status	Linked Antibody	Controls	Method	Note
knockdown followed by RNA-seq	BRCA1-BGRSDLV02-RSD293RBP		BRCA1	Ribo-STAMP-293T	Released			shRNA	KD% =
knockdown followed by RNA-seq	BRCA1-BGRSDLV02-RSD293RBP		BRCA1	Ribo-STAMP-293T	Released			shRNA	KD% = ,

eCLIP

No eCLIP experiment available

Antibody Validation

No Antibody Primary Validation image or Secondary image available

KD RNA-Seq

GeneName	Cell_Line	Method	Sample_reps	Control_reps	KD%	Status	Project
BRCA1	Ribo-STAMP-293T	shRNA	BGRSLV02-57,BGRSLV02-58	BGRSLV02-1,BGRSLV02-2		NotSatisfied	ENCORE2
BRCA1	Ribo-STAMP-293T	shRNA	BGRSLV07-7,BGRSLV07-8	BGRSLV07-1,BGRSLV07-2		NotSatisfied	ENCORE2
BRCA1	Ribo-STAMP-293T	shRNA	BGRSLV09-3,BGRSLV09-4	BGRSLV09-1,BGRSLV09-2		NotSatisfied	ENCORE2
BRCA1	Ribo-STAMP-293T	shRNA	BGRSLV09-5,BGRSLV09-6	BGRSLV09-1,BGRSLV09-2		NotSatisfied	ENCORE2
BRCA1	Ribo-STAMP-293T	shRNA	BGRSDLV02-9,BGRSDLV02-10	BGRSDLV02-1,BGRSDLV02-2		Released	ENCORE2
BRCA1	Ribo-STAMP-293T	shRNA	BRCA1-BGRSDLV02-11dox,BRCA1-BGRSDLV02-12dox	BRCA1-BGRSDLV02-9,BRCA1-BGRSDLV02-10	,	Released	ENCORE2

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

No Localization Information available

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela

Summary
Proteins Bound to RBP RNA

RNA Targets

eCLIP assay for BRCA1 is not avaliable on ENCORE database.

Proteins bound to RNA

BRCA1 RNA is bound by 20 proteins.

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eCLIP assay for BRCA1 is not avaliable on ENCORE database.

20 proteins are bound to BRCA1 RNA:

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Search:

Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr17	41203031	41203053	-	intron-Distal,intron-Proximal	5.94475	11.65826	K562	AQR
chr17	41228694	41228828	-	intron-Distal,intron-Proximal	4.31521	10.35163	K562	KHSRP
chr17	41203053	41203081	-	3'-UTR,CDS,intron-Distal,intron-Proximal	4.81979	9.08030	K562	AQR
chr17	41246486	41246569	-	3'-UTR,5'-UTR,CDS,intron-Distal	3.84424	7.43456	K562	SAFB2
chr17	41277288	41277347	-	5'-UTR,intron-Distal,intron-Proximal	4.10543	7.37356	K562	DDX3X
chr17	41197758	41197817	-	3'-UTR,CDS,intron-Distal	4.76703	7.21258	K562	LIN28B
chr17	41233081	41233200	-	intron-Distal	3.11945	7.14496	K562	KHSRP
chr17	41196322	41196464	-	3'-UTR,intron-Distal	4.90127	7.06234	K562	PUM2
chr17	41245519	41245621	-	5'-UTR,CDS,intron-Distal,intron-Proximal	4.00446	7.00245	K562	SAFB2
chr17	41258471	41258551	-	3'-UTR,5'-UTR,CDS,intron-Distal,intron-Proximal	4.06836	6.81238	K562	ZNF622
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 42 entries

eCLIP assay for BRCA1 is not avaliable on ENCORE database.

Diffrential Expression

The Knockdown/knockout assay for BRCA1 is not available on ENCORE database.
162 RBPs can affect the levels of BRCA1.

CanvasJS.com

The Knockdown/knockout RNA-Seq assay for BRCA1 is not available on ENCORE database.

162 RBPs can affect the gene expression of BRCA1 :

Show entries

Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
BRCA1	ENSG00000012048.15	122.68370	1057.64300	-3.10780	152.21560	149.94380	HepG2	ZNF622
BRCA1	ENSG00000012048.15	130.05850	1597.76020	-3.61880	140.14890	137.45790	HepG2	BOP1
BRCA1	ENSG00000012048.15	246.20060	1500.01600	-2.60710	119.67520	117.62840	HepG2	SRFBP1
BRCA1	ENSG00000012048.15	141.59930	1236.84050	-3.12680	103.73060	101.13230	HepG2	RPLP0
BRCA1	ENSG00000012048.15	247.94970	1328.06160	-2.42120	95.80250	93.61880	HepG2	RBM22
BRCA1	ENSG00000012048.15	335.05140	1546.59660	-2.20660	64.73250	62.10380	HepG2	TARDBP
BRCA1	ENSG00000012048.15	319.95870	1128.07580	-1.81790	63.77250	61.48140	HepG2	SRSF7
BRCA1	ENSG00000012048.15	188.38960	846.27480	-2.16740	58.32970	56.59630	HepG2	TIAL1
BRCA1	ENSG00000012048.15	292.15870	961.65900	-1.71880	54.81870	52.59470	HepG2	UPF1
BRCA1	ENSG00000012048.15	195.93700	982.01530	-2.32540	47.73080	45.61790	HepG2	SUPV3L1
Gene Name	Gene ID	KDMean	CNMean	log2(fold change)	-log(pval)	-log(padj)	Cell Line	Affected by RBP	Bound by RBP

Showing 1 to 10 of 190 entries

*: "Inf" was shown as "99999.99999" and "-Inf" was shown as "-99999.99999".
**: "-log(0)" was displayed as "99999.99999".

The Knockdown/knockout RNA-Seq assay for BRCA1 is not available on ENCORE database.

13 RBPs can affect the splicing of BRCA1 :

Show entries

Search:

Event Type	Gene Name	Gene ID	chr	Strand	ExonStart	ExonEnd	2ndExonStart	2ndExonEnd	upstreamES	upstreamEE	downstreamES	downstreamEE	dPSI	p-value	FDR	is_included	Cell Line	Affected by RBP
SE	BRCA1	ENSG00000012048.15	chr17	-	41228504	41228631			41226347	41226538	41234420	41234592	-0.14300	0.00000	0.00001	excluded	K562	UTP18
SE	BRCA1	ENSG00000012048.15	chr17	-	41219624	41219712			41215890	41215968	41222944	41223255	-0.14200	0.00000	0.00000	excluded	K562	HNRNPC
A3SS	BRCA1	ENSG00000012048.15	chr17	-	41203079	41203225			41203079	41203134	41209068	41209152	0.07000	0.00000	0.00001	longer	K562	AQR
MXE	BRCA1	ENSG00000012048.15	chr17	-	41246760	41246877	41247862	41247939	41242960	41243049	41249260	41249306	-0.36300	0.00000	0.00012	2included	K562	SRSF1
A5SS	BRCA1	ENSG00000012048.15	chr17	-	41243451	41246877			41246760	41246877	41242960	41243049	-0.41500	0.00001	0.00067	shorter	K562	SRSF1
MXE	BRCA1	ENSG00000012048.15	chr17	-	41199659	41199720	41203079	41203185	41196312	41197819	41209068	41209152	0.10300	0.00001	0.00011	1included	K562	AQR
SE	BRCA1	ENSG00000012048.15	chr17	-	41228504	41228631			41226347	41226538	41234420	41234592	-0.06800	0.00004	0.00252	excluded	K562	AKAP8L
MXE	BRCA1	ENSG00000012048.15	chr17	-	41201137	41201211	41203079	41203185	41199659	41199720	41209068	41209152	0.17500	0.00004	0.00047	1included	K562	AQR
SE	BRCA1	ENSG00000012048.15	chr17	-	41247862	41247939			41243451	41246877	41251791	41251894	-0.26800	0.00014	0.00381	excluded	K562	U2AF2
MXE	BRCA1	ENSG00000012048.15	chr17	-	41201137	41201211	41203079	41203134	41199659	41199720	41209068	41209152	-0.15900	0.00014	0.00434	2included	K562	DROSHA

Showing 1 to 10 of 26 entries

*: "Inf" was shown as "99999.99999" and "-Inf" was shown as "-99999.99999".
**: "-log(0)" was displayed as "99999.99999".

BRCA1

General Information

Functions

Localization

Domains (AlphaFold: BRCA1)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

eCLIP assay for BRCA1 is not avaliable on ENCORE database.

20 proteins are bound to BRCA1 RNA:

eCLIP assay for BRCA1 is not avaliable on ENCORE database.

Diffrential Expression

The Knockdown/knockout RNA-Seq assay for BRCA1 is not available on ENCORE database.

162 RBPs can affect the gene expression of BRCA1 :

The Knockdown/knockout RNA-Seq assay for BRCA1 is not available on ENCORE database.

13 RBPs can affect the splicing of BRCA1 :

The Knockdown/knockout RNA-Seq assay for BRCA1 is not avaliable on ENCORE database.