NCBP2

General Information

Gene Name : NCBP2
Gene ID : ENSG00000114503.10
Essential Gene : Yes

Functions

Splicing regulation
RNA stability & decay
RNA localization
RNA export
Translation regulation

Localization(RBPImage: NCBP2)

Nuclei
Nucleoplasm
Mutually Exclusive from Nucleolus
Cytoplasm
Cytosolic
Nuclear release mitosis

Domains (AlphaFold: NCBP2)

RRM

Antibody Validation

Bethyl Labs: A302-553A

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	NCBP2	ENSG00000114503.10	73.90	73.17	73.53	ENCSR000AEF
HepG2	NCBP2	ENSG00000114503.10	51.78	63.96	57.87	ENCSR985KAT
K562	NCBP2	ENSG00000114503.10	60.25	68.48	64.37	ENCSR000AEO

Assays

4 Released experiments are available on ENCORE database.

Assay Type	Exp_Name	ENCODE ID	Target label	Biosample	Status	Linked Antibody	Controls	Method	Note
eCLIP	eCLIP: 477	ENCSR018RVZ	NCBP2	HepG2	Released	ENCAB039KCI	ENCSR257OYO
eCLIP	eCLIP: 566	ENCSR484LTQ	NCBP2	K562	Released	ENCAB039KCI	ENCSR921SHJ
knockdown followed by RNA-seq	NCBP2-BGKLV08-K562	ENCSR361LBE	NCBP2	K562	Released		ENCSR913CAE	shRNA	KD% = 43.9,46.0
knockdown followed by RNA-seq	NCBP2-BGHLV12-HepG2	ENCSR030ARO	NCBP2	HepG2	Released		ENCSR603TCV	shRNA	KD% = 55.4,41.5

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
NCBP2	477	HepG2	ENCSR018RVZ	ENCSR257OYO	ENCAB039KCI	A302-553A	1	Released	ENCODE3
NCBP2	566	K562	ENCSR484LTQ	ENCSR921SHJ	ENCAB039KCI	A302-553A	1	Released	ENCODE3

Antibody Validation

GeneName	Antibody_DCC_ID	Product_ID	Lot_ID	Phosphate	HepG2 Primary Validation	K562 Primary Validation	HepG2 Secondary Validation	K562 Secondary Validation
NCBP2	ENCAB039KCI	A302-553A	1		Released, ENCODE3	Released, ENCODE3	BGHLV12-51, Released, ENCODE3	BGKLV08-35, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project	Note
NCBP2	K562	shRNA	ENCSR361LBE	ENCSR913CAE	NCBP2-LV08-35,NCBP2-LV08-36	Nontarget-LV08-1_00003527,nontarget-LV08-2_00003527	43.9,46.0	Released	ENCODE3
NCBP2	HepG2	shRNA	ENCSR030ARO	ENCSR603TCV	NCBP2-BGHLV12-51,NCBP2-BGHLV12-52	NT-BGHLV12-93,NT-BGHLV12-94	55.4,41.5	Released	ENCODE3

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

NCBP2: Click to RBP Image Database

Nuclei

Nucleoplasm

Mutually Exclusive from Nucleolus

Cytoplasm

Cytosolic

Nuclear release mitosis

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NCBP2	Product_ID: A302-553A Lot_ID: 1 Source: Bethyl Labs Target Name: NCBP2-human

RNA Targets

NCBP2 protein binds to 3,548 RNA regions.

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Proteins bound to RNA

NCBP2 RNA is bound by 16 proteins.

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NCBP2 protein has 3,548 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
NCBP2	chr5	179050621	179050671	-	5.37094	400.00000	HepG2	HNRNPH1	5'-UTR,intron-Distal,intron-Proximal
NCBP2	chr1	28832587	28832600	+	5.71953	41.41167	K562	SNHG3, RCC1	5'-UTR,intron-Proximal
NCBP2	chr3	171757542	171757566	+	3.91331	35.25259	HepG2	FNDC3B	5'-UTR,intron-Proximal
NCBP2	chr1	154600324	154600400	-	4.89889	31.18315	HepG2	ADAR	5'-UTR,CDS,intron-Distal,intron-Proximal
NCBP2	chr17	79953218	79953264	+	3.57977	27.47756	HepG2	ASPSCR1	intron-Distal
NCBP2	chr6	16761602	16761690	-	4.82612	26.20492	HepG2	ATXN1	5'-UTR,intron-Distal,intron-Proximal
NCBP2	chr2	228336873	228336984	+	3.69755	20.62819	HepG2	AGFG1	5'-UTR
NCBP2	chr19	2270197	2270274	+	3.13508	19.67745	K562	OAZ1	intron-Distal
NCBP2	chr16	89882978	89883053	-	4.38448	18.68250	HepG2	FANCA	5'-UTR,CDS,intron-Distal,intron-Proximal
NCBP2	chr7	99156342	99156409	+	5.18268	18.02476	HepG2	ZNF655, GS1-259H13.10	5'-UTR

Showing 1 to 10 of 100 entries

16 proteins are bound to NCBP2 RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr3	196669289	196669407	-	5'-UTR,CDS,intron-Distal,intron-Proximal	5.58407	34.97793	K562	DDX3X
chr3	196666095	196666177	-	3'-UTR,5'-UTR,CDS,intron-Distal,intron-Proximal	3.72757	22.27400	HepG2	BCLAF1
chr3	196666211	196666241	-	3'-UTR,5'-UTR,CDS,intron-Distal,intron-Proximal	4.40638	19.43363	HepG2	BCLAF1
chr3	196662916	196663035	-	3'-UTR,intron-Distal	3.48428	17.17938	K562	UPF1
chr3	196663328	196663486	-	3'-UTR,intron-Distal	3.52202	15.80967	HepG2	UPF1
chr3	196666211	196666238	-	3'-UTR,5'-UTR,CDS,intron-Distal,intron-Proximal	3.77463	13.18813	HepG2	GRWD1
chr3	196666186	196666211	-	3'-UTR,5'-UTR,CDS,intron-Distal,intron-Proximal	3.98431	13.10875	HepG2	BCLAF1
chr3	196666241	196666266	-	3'-UTR,5'-UTR,CDS,intron-Distal,intron-Proximal	3.57459	10.65310	HepG2	BCLAF1
chr3	196666249	196666306	-	3'-UTR,5'-UTR,CDS,intron-Distal,intron-Proximal	3.70518	10.46214	K562	ZNF622
chr3	196664114	196664173	-	intron-Distal,intron-Proximal	3.43509	10.40504	HepG2	U2AF2
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 38 entries

No autoregularoty interactions between protein NCBP2 and its RNA.

Diffrential Expression

8,836 differentially expressed genes after Knockdown/Knockout NCBP2 protein.

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109 RBPs can affect the levels of NCBP2.

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8,836 differentially expressed genes after Knockdown/Knockout NCBP2 protein :

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Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
SLC7A2	ENSG00000003989.12	3331.17020	14267.99870	-2.09870	74.76420	71.80000	HepG2	NCBP2
SPAG9	ENSG00000008294.16	1924.27760	5382.34600	-1.48390	36.31310	34.23060	HepG2	NCBP2
ST3GAL1	ENSG00000008513.10	1009.92600	2868.82060	-1.50620	33.81760	31.81130	HepG2	NCBP2
ADIPOR2	ENSG00000006831.9	2662.72230	7033.21570	-1.40130	33.66310	31.66940	HepG2	NCBP2
SLC25A5	ENSG00000005022.5	4551.40660	10999.49950	-1.27310	29.22830	27.33200	HepG2	NCBP2
MGST1	ENSG00000008394.8	1095.32210	2754.12360	-1.33020	26.67200	24.85270	HepG2	NCBP2
RHBDD2	ENSG00000005486.12	2021.37890	888.28190	1.18620	19.94040	18.34220	HepG2	NCBP2
MAP3K9	ENSG00000006432.11	1138.43410	457.45280	1.31530	19.91330	18.31580	HepG2	NCBP2
MAPK8IP2	ENSG00000008735.10	379.03430	105.81770	1.84060	19.35170	17.77390	HepG2	NCBP2
TFPI	ENSG00000003436.10	10961.08200	22542.70690	-1.04030	17.92650	16.40700	HepG2	NCBP2
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 100 entries

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

109 RBPs can affect the gene expression of NCBP2 :

Show entries

Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
NCBP2	ENSG00000114503.6	597.07770	4121.98670	-2.78730	105.18700	101.71080	HepG2	NCBP2
NCBP2	ENSG00000114503.6	1921.70540	4009.17610	-1.06090	48.94560	47.32690	HepG2	NELFE
NCBP2	ENSG00000114503.6	2051.35690	3914.78480	-0.93240	42.99900	41.62440	HepG2	SRSF1
NCBP2	ENSG00000114503.6	881.91980	2019.39330	-1.19520	33.58830	30.17690	K562	NCBP2
NCBP2	ENSG00000114503.6	1803.35260	4347.90320	-1.26960	27.67290	25.91870	HepG2	DDX3X
NCBP2	ENSG00000114503.6	1466.37340	2424.02720	-0.72520	25.11030	23.56120	HepG2	CKAP4
NCBP2	ENSG00000114503.6	7734.20990	3905.68490	0.98560	24.65040	23.08930	K562	AQR
NCBP2	ENSG00000114503.6	2462.91650	3753.68190	-0.60790	24.34000	22.93820	HepG2	PUM1
NCBP2	ENSG00000114503.6	1175.15720	2183.24010	-0.89360	21.45300	20.30430	HepG2	TIAL1
NCBP2	ENSG00000114503.6	2345.34660	3750.48430	-0.67730	21.51410	20.12310	HepG2	SF3B4
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 134 entries

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

1,765 alternative splicing events after Knockdown/Knockout NCBP2 protein :

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Event Type	Gene Name	Gene ID	chr	Strand	ExonStart	ExonEnd	upstreamES	upstreamEE	downstreamES	downstreamEE	dPSI	FDR	is_included	Cell Line	Affected by RBP
SE	INTS10	ENSG00000104613.7	chr8	+	19701863	19701996	19701638	19701749	19703214	19703308	0.09500	0.00010	included	HepG2	NCBP2
SE	IGF2BP2	ENSG00000073792.11	chr3	-	185410964	185411016	185410486	185410550	185414399	185414451	0.08600	0.00038	included	HepG2	NCBP2
SE	LPHN2	ENSG00000117114.15	chr1	+	82452584	82452713	82450942	82451039	82456074	82458106	0.60300	0.00000	included	HepG2	NCBP2
SE	SNRNP70	ENSG00000104852.10	chr19	+	49605370	49606844	49604646	49604728	49607890	49607992	0.26200	0.00000	included	HepG2	NCBP2
SE	YWHAZ	ENSG00000164924.13	chr8	-	101964156	101964356	101960841	101961128	101965496	101965616	0.19900	0.00028	included	HepG2	NCBP2
SE	ALDOA	ENSG00000149925.12	chr16	+	30077145	30077248	30075781	30075826	30078554	30078687	0.18300	0.00000	included	HepG2	NCBP2
SE	EIF4H	ENSG00000106682.10	chr7	+	73604576	73604636	73604151	73604248	73609070	73609208	0.17200	0.00000	included	HepG2	NCBP2
SE	SREK1	ENSG00000153914.11	chr5	+	65451892	65454760	65449290	65449424	65455046	65455162	0.36000	0.00001	included	HepG2	NCBP2
SE	SEC31A	ENSG00000138674.12	chr4	-	83782783	83782861	83778841	83778917	83784470	83784545	0.31600	0.00000	included	HepG2	NCBP2
SE	WNK1	ENSG00000060237.12	chr12	+	989886	990165	987377	987527	990857	990955	0.39100	0.00000	included	HepG2	NCBP2

Showing 1 to 10 of 100 entries

2 RBPs can affect the splicing of NCBP2 :

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Event Type	Gene Name	Gene ID	chr	Strand	ExonStart	ExonEnd	upstreamES	upstreamEE	downstreamES	downstreamEE	dPSI	p-value	FDR	is_included	Cell Line	Affected by RBP
A3SS	NCBP2	ENSG00000114503.6	chr3	-	196664380	196664558	196664380	196664502	196666263	196666303	-0.17700	0.00000	0.00000	shorter	HepG2	SF3A3
A3SS	NCBP2	ENSG00000114503.6	chr3	-	196666121	196666363	196666121	196666303	196669296	196669468	0.07200	0.00000	0.00000	longer	K562	AQR
A5SS	NCBP2	ENSG00000114503.6	chr3	-	196666082	196666303	196666263	196666303	196664322	196664502	0.25600	0.00002	0.00071	longer	K562	AQR
SE	NCBP2	ENSG00000114503.6	chr3	-	196668357	196668473	196666121	196666303	196669240	196669307	0.07200	0.00040	0.00556	included	K562	AQR
A3SS	NCBP2	ENSG00000114503.6	chr3	-	196666121	196666363	196666121	196666303	196668579	196668640	-0.26400	0.00745	0.04102	shorter	K562	AQR

Showing 1 to 5 of 5 entries

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

NCBP2

General Information

Functions

Localization(RBPImage: NCBP2)

Domains (AlphaFold: NCBP2)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

NCBP2 protein has 3,548 RNA targets:

16 proteins are bound to NCBP2 RNA:

No autoregularoty interactions between protein NCBP2 and its RNA.

Diffrential Expression

8,836 differentially expressed genes after Knockdown/Knockout NCBP2 protein :

109 RBPs can affect the gene expression of NCBP2 :

1,765 alternative splicing events after Knockdown/Knockout NCBP2 protein :

2 RBPs can affect the splicing of NCBP2 :

No autoregularoty alternative splicing events between protein NCBP2 and its RNA.