NPM1

General Information

Gene Name : NPM1
Gene ID : ENSG00000181163.13
Essential Gene : No

Functions

rRNA processing

Localization(RBPImage: NPM1)

Nuclei
Nucleolus

Domains (AlphaFold: NPM1)

No checked domain (RRM, ZNF, KH, Helicase, Nuclease, dRBM or PUM_HD)

Antibody Validation

View validation images for all NPM1 antibodies

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	NPM1	ENSG00000181163.13	5276.24	3363.64	4319.94	ENCSR000AEF
HepG2	NPM1	ENSG00000181163.13	2085.08	3320.04	2702.56	ENCSR985KAT
K562	NPM1	ENSG00000181163.13	3021.17	3831.25	3426.21	ENCSR000AEO

Assays

5 Released experiments are available on ENCORE database.

Assay Type	Exp_Name	ENCODE ID	Target label	Biosample	Status	Linked Antibody	Controls	Method	Note
eCLIP	eCLIP: 354	ENCSR867DSZ	NPM1	K562	Released	ENCAB881HTO	ENCSR468ZQA
eCLIP	eCLIP: 4010	ENCSR448IDP	NPM1	K562	Released	ENCAB147WFE	ENCSR206NIG
knockdown followed by RNA-seq	NPM1-BGKLV28-K562	ENCSR346DZQ	NPM1	K562	Released		ENCSR164MUK	shRNA	KD% = 55.6,59.4
knockdown followed by RNA-seq	NPM1-BGHLV26-HepG2	ENCSR016XPB	NPM1	HepG2	Released		ENCSR104ABF	shRNA	KD% = 66.4,61.2
knockdown followed by RNA-seq	NPM1-BGKcLV15-K562	ENCSR034NAT	NPM1	K562	Released		ENCSR404OHQ	CRISPR	KD% = 92.1,86.4

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
NPM1	354	K562	ENCSR867DSZ	ENCSR468ZQA	ENCAB881HTO	A302-402A	1	Released	ENCODE3
NPM1	4010	K562	ENCSR448IDP	ENCSR206NIG	ENCAB147WFE	325200	TD268297	Released	ENCODE4

Antibody Validation

GeneName	Antibody_DCC_ID	Product_ID	Lot_ID	HepG2 Primary Validation	K562 Primary Validation	HepG2 Secondary Validation	K562 Secondary Validation
NPM1	ENCAB881HTO	A302-402A	1		Released, ENCODE3	BGHLV26-27, Released, ENCODE3	BGKLV28-31, Released, ENCODE3
NPM1	ENCAB147WFE	325200	TD268297		NotSatisfied, ENCODE4	BGHLV26-27, Released, ENCODE4	BGKcLV15-41, Released, ENCODE4
NPM1	ENCAB365CVY	200143	AD0811	Released, ENCODE3	NotSatisfied, ENCODE4		BGKcLV15-41, Released, ENCODE4

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
NPM1	K562	shRNA	ENCSR346DZQ	ENCSR164MUK	NPM1_BGKLV28-31,NPM1_BGKLV28-32	non-target_BGKLV28-1,non-target_BGKLV28-2	55.6,59.4	Released	ENCODE3
NPM1	HepG2	shRNA	ENCSR016XPB	ENCSR104ABF	NPM1_BGHLV26_27,NPM1_BGHLV26_28	non-target_BGHLV26-1,non-target_BGHLV26-2	66.4,61.2	Released	ENCODE3
NPM1	K562	CRISPR	ENCSR034NAT	ENCSR404OHQ	NPM1-BGKcLV15-41,NPM1-BGKcLV15-42	NT-BGKcLV15-1,NT-BGKcLV15-2	92.1,86.4	Released	ENCODE4

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

NPM1: Click to RBP Image Database

Nuclei

Nucleolus

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NPM1	Product_ID: A302-402A Lot_ID: 1 Source: Bethyl Labs Target Name: NPM1-human
NPM1	Product_ID: 325200 Lot_ID: TD268297 Source: Thermo Fisher Target Name: NPM1-human
NPM1	Product_ID: 200143 Lot_ID: AD0811 Source: Zen Bioscience Target Name: NPM1-human

RNA Targets

NPM1 protein binds to 36 RNA regions.

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Proteins bound to RNA

NPM1 RNA is bound by 50 proteins.

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NPM1 protein has 36 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
NPM1	chr12	98993465	98993514	+	3.94970	84.10436	K562	SLC25A3	intron-Distal
NPM1	chr20	17943421	17943452	-	3.46938	62.21151	K562	SNX5, OVOL2	intron-Distal
NPM1	chr20	17943402	17943421	-	3.16493	47.52247	K562	SNX5, OVOL2	intron-Distal
NPM1	chr20	17943356	17943402	-	3.34861	46.46233	K562	OVOL2, SNX5	intron-Distal
NPM1	chr4	174253084	174253224	-	3.12934	41.68980	K562	HMGB2	3'-UTR,intron-Distal
NPM1	chr9	100777644	100777770	+	3.42034	18.14591	K562	ANP32B	3'-UTR,CDS,intron-Proximal
NPM1	chr4	174253224	174253279	-	4.17709	13.62082	K562	HMGB2	3'-UTR,CDS,intron-Distal
NPM1	chr19	56181801	56181926	+	3.96230	12.00164	K562	U2AF2	intron-Distal
NPM1	chr4	83817004	83817014	-	3.50233	11.37340	K562	SEC31A, THAP9-AS1	intron-Distal,intron-Proximal
NPM1	chr7	103029414	103029425	-	4.79344	11.10608	K562	SLC26A5	intron-Distal,intron-Proximal

Showing 1 to 10 of 36 entries

50 proteins are bound to NPM1 RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr5	170814863	170814931	+	5'-UTR,intron-Proximal	4.16455	400.00000	HepG2	SUB1
chr5	170817054	170817106	+	CDS,intron-Distal,intron-Proximal	3.86837	400.00000	K562	UCHL5
chr5	170827170	170827211	+	CDS	3.54706	400.00000	K562	UCHL5
chr5	170814999	170815010	+	5'-UTR,CDS	4.60261	88.11682	K562	UCHL5
chr5	170832315	170832358	+	CDS	4.66747	86.01882	HepG2	BCLAF1
chr5	170827166	170827214	+	CDS	3.86046	83.28736	HepG2	BCLAF1
chr5	170827872	170827919	+	CDS,intron-Distal	4.60847	82.93603	HepG2	BCLAF1
chr5	170827211	170827214	+	CDS	3.60263	82.15435	K562	UCHL5
chr5	170814972	170814999	+	5'-UTR,CDS	4.43951	77.98313	K562	UCHL5
chr5	170827842	170827873	+	CDS,intron-Distal,intron-Proximal	3.42958	73.34833	K562	UCHL5
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 259 entries

No autoregularoty interactions between protein NPM1 and its RNA.

Diffrential Expression

57 differentially expressed genes after Knockdown/Knockout NPM1 protein.

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173 RBPs can affect the levels of NPM1.

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57 differentially expressed genes after Knockdown/Knockout NPM1 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
MAGEA9B	ENSG00000123584.7	0.00000	348.47940	-99999.99999	26.85520	22.46790	K562	NPM1
SDHAP2	ENSG00000215837.7	0.00000	64.89650	-99999.99999	14.10930	9.74880	HepG2	NPM1
PLA2G2A	ENSG00000188257.6	1067.53310	199.28590	2.42130	13.19350	9.13400	HepG2	NPM1
NPM1	ENSG00000181163.9	9512.09010	39559.36750	-2.05620	11.31110	7.42760	HepG2	NPM1
TM9SF1	ENSG00000254692.1	446.61610	91.68320	2.28420	9.85110	6.09270	HepG2	NPM1
MSANTD3-TMEFF1	ENSG00000251349.3	0.00000	174.46620	-99999.99999	8.43360	4.77210	HepG2	NPM1
RP11-274B21.2	ENSG00000243302.3	314.88250	47.71780	2.72210	8.18110	4.59870	HepG2	NPM1
EEF1E1-BLOC1S5	ENSG00000265818.1	0.00000	32.45390	-99999.99999	7.63490	4.11950	HepG2	NPM1
ZFP41	ENSG00000264668.1	0.00000	31.19710	-99999.99999	7.17040	3.71290	HepG2	NPM1
NPM1P27	ENSG00000249353.2	45.16020	197.23060	-2.12680	6.80810	3.40180	HepG2	NPM1
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 57 entries

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

173 RBPs can affect the gene expression of NPM1 :

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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
NPM1	ENSG00000181163.9	2562.40910	20161.53390	-2.97600	198.91300	195.79590	HepG2	BOP1
NPM1	ENSG00000181163.9	15098.49130	41280.81020	-1.45110	176.02810	173.66700	HepG2	SRFBP1
NPM1	ENSG00000181163.9	12498.44590	32070.63560	-1.35950	115.41390	113.20260	HepG2	PTBP1
NPM1	ENSG00000181163.9	14808.37090	35840.45790	-1.27520	105.75800	103.81950	HepG2	SSB
NPM1	ENSG00000181163.9	6069.90230	18498.52050	-1.60770	95.66160	93.53170	HepG2	TIAL1
NPM1	ENSG00000181163.9	15935.23700	35691.51400	-1.16340	92.99530	90.99270	HepG2	NELFE
NPM1	ENSG00000181163.9	10162.16100	19652.80230	-0.95150	70.23150	68.03370	HepG2	PUS1
NPM1	ENSG00000181163.9	16901.57170	33389.61880	-0.98220	69.12680	66.93600	HepG2	SF3B4
NPM1	ENSG00000181163.9	9553.51330	17431.43150	-0.86760	68.19790	65.80120	HepG2	ZC3H8
NPM1	ENSG00000181163.9	14882.68540	34733.22800	-1.22270	67.43820	65.16950	HepG2	QKI
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 219 entries

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

441 alternative splicing events after Knockdown/Knockout NPM1 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	GOLGA8A	ENSG00000175265.13	chr15	-	34720815	34720905	34699816	34699936	34727583	34727672	0.06200	0.00134	included	K562	NPM1
SE	PI4KAP2	ENSG00000183506.12	chr22	-	21830932	21830993	21830280	21830449	21832078	21832204	0.46600	0.00000	included	K562	NPM1
SE	TRNT1	ENSG00000072756.12	chr3	+	3184577	3184742	3182193	3182332	3186267	3186394	0.07500	0.00035	included	K562	NPM1
SE	DLGAP5	ENSG00000126787.8	chr14	-	55615311	55615402	55614829	55615191	55617516	55617566	0.09100	0.00247	included	K562	NPM1
SE	SIGIRR	ENSG00000185187.8	chr11	-	406842	406993	406348	406538	407061	407164	0.27200	0.00123	included	K562	NPM1
SE	HNRNPD	ENSG00000138668.14	chr4	-	83276047	83276154	83274986	83275307	83276456	83276554	0.06100	0.00158	included	K562	NPM1
SE	DDX11	ENSG00000013573.12	chr12	+	31237114	31237330	31236900	31236995	31237516	31237603	0.10100	0.00264	included	K562	NPM1
SE	HNRNPDL	ENSG00000152795.13	chr4	-	83346715	83346820	83345781	83346036	83347189	83347274	0.12400	0.00136	included	K562	NPM1
SE	RRP1	ENSG00000160214.8	chr21	+	45223201	45223298	45222154	45222268	45223392	45225174	0.06000	0.00061	included	K562	NPM1
SE	PPP4R1	ENSG00000154845.11	chr18	-	9562919	9563044	9561977	9562073	9563375	9563548	0.24400	0.00249	included	K562	NPM1

Showing 1 to 10 of 100 entries

15 RBPs can affect the splicing of NPM1 :

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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	NPM1	ENSG00000181163.9	chr5	+	170817054	170817092	170814832	170815010	170818308	170818373	-0.12800	0.00000	excluded	K562	SF3B4
SE	NPM1	ENSG00000181163.9	chr5	+	170817068	170817134	170814651	170815010	170818308	170818781	-0.05300	0.00000	excluded	K562	AQR
SE	NPM1	ENSG00000181163.9	chr5	+	170817054	170817092	170814936	170815010	170818308	170818428	-0.06100	0.00061	excluded	K562	LARP4
SE	NPM1	ENSG00000181163.9	chr5	+	170817054	170817092	170814651	170815010	170818308	170818428	-0.17300	0.00000	excluded	HepG2	SF3A3
SE	NPM1	ENSG00000181163.9	chr5	+	170817030	170817092	170814651	170815010	170818308	170818373	0.35800	0.00161	included	K562	RBM22
SE	NPM1	ENSG00000181163.9	chr5	+	170817054	170817092	170814936	170815010	170818308	170818428	-0.14800	0.00000	excluded	K562	HNRNPU
SE	NPM1	ENSG00000181163.9	chr5	+	170817054	170817092	170814936	170815010	170818308	170818428	-0.12300	0.00000	excluded	K562	SF3B1
SE	NPM1	ENSG00000181163.9	chr5	+	170817054	170817092	170814936	170815010	170818308	170818428	-0.06000	0.00000	excluded	HepG2	HNRNPU
SE	NPM1	ENSG00000181163.9	chr5	+	170817054	170817092	170814936	170815010	170818308	170818428	-0.12000	0.00010	excluded	K562	NPM1
SE	NPM1	ENSG00000181163.9	chr5	+	170817054	170817134	170814832	170815010	170818308	170818428	-0.07300	0.00000	excluded	K562	HNRNPC

Showing 1 to 10 of 29 entries

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

The NPM1 protein affects to its own RNA splicing after knockdown/knockout.

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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	Bound by RBP
SE	NPM1	ENSG00000181163.9	chr5	+	170817054	170817092			170814936	170815010	170818308	170818428	-0.12000	0.00000	0.00010	excluded	K562	NPM1

Showing 1 to 1 of 1 entries