NPHP4

General Information

Gene Name : NPHP4
Gene ID : ENSG00000131697.17
Essential Gene : No

Functions

Not Available

Localization

Not Available

Domains (AlphaFold: NPHP4)

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	NPHP4	ENSG00000131697.17	0.89	1.76	1.32	ENCSR000AEF
HepG2	NPHP4	ENSG00000131697.17	9.89	3.75	6.82	ENCSR985KAT
K562	NPHP4	ENSG00000131697.17	7.50	6.43	6.96	ENCSR000AEO

Assays

0 Released experiments are available on ENCORE database.

eCLIP

No eCLIP experiment available

Antibody Validation

No Antibody Primary Validation image or Secondary image available

KD RNA-Seq

No KD RNA-Seq experiment available

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 NPHP4 is not avaliable on ENCORE database.

Proteins bound to RNA

NPHP4 RNA is bound by 21 proteins.

eCLIP assay for NPHP4 is not avaliable on ENCORE database.

21 proteins are bound to NPHP4 RNA:

Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr1	5950892	5950952	-	3'-UTR,CDS,intron-Distal,intron-Proximal	4.95998	6.59451	HepG2	PRPF8
chr1	5923431	5923489	-	3'-UTR,CDS,intron-Distal	5.95984	12.87452	K562	AQR
chr1	5923379	5923427	-	3'-UTR,CDS,intron-Distal	4.48633	3.81597	K562	RBM15
chr1	5987686	5987740	-	3'-UTR,CDS,intron-Distal,intron-Proximal	4.94339	4.02817	HepG2	PRPF8
chr1	5926359	5926438	-	3'-UTR,CDS,intron-Distal,intron-Proximal	4.16750	6.95612	HepG2	PRPF8
chr1	5940169	5940243	-	3'-UTR,CDS,intron-Distal,intron-Proximal	3.57551	3.59112	HepG2	PPIG
chr1	5937149	5937212	-	3'-UTR,CDS,intron-Distal,intron-Proximal	5.01593	5.27053	HepG2	PPIG
chr1	5923909	5923959	-	3'-UTR,CDS,intron-Distal,intron-Proximal	3.31373	3.59112	HepG2	PPIG
chr1	5923379	5923426	-	3'-UTR,CDS,intron-Distal	3.30843	3.20886	K562	PRPF8
chr1	5923867	5923959	-	3'-UTR,CDS,intron-Distal,intron-Proximal	4.37296	15.19374	HepG2	PRPF8
chr1	5937283	5937347	-	3'-UTR,CDS,intron-Distal	4.34741	3.79199	HepG2	PPIG
chr1	5946668	5946836	-	3'-UTR,intron-Distal	3.86629	3.99124	K562	FUS
chr1	5927800	5927806	-	3'-UTR,CDS,intron-Distal,intron-Proximal	5.62047	8.38577	HepG2	PRPF8
chr1	5947344	5947529	-	3'-UTR,CDS,intron-Distal,intron-Proximal	3.55966	8.43905	HepG2	PPIG
chr1	5933326	5933433	-	3'-UTR,CDS,intron-Distal,intron-Proximal	4.30470	3.25089	HepG2	AQR
chr1	5934456	5934551	-	3'-UTR,CDS,intron-Distal,intron-Proximal	3.42642	6.18341	HepG2	PRPF8
chr1	6007159	6007204	-	5'-UTR,CDS,intron-Distal,intron-Proximal	4.27000	4.08604	HepG2	PPIG
chr1	6046272	6046368	-	5'-UTR,CDS,intron-Distal	3.81003	3.12746	HepG2	GRWD1
chr1	6012758	6012840	-	CDS,intron-Distal,intron-Proximal	4.39945	3.82297	K562	NOLC1
chr1	6021880	6021993	-	CDS,intron-Distal	4.28299	3.80143	K562	NOLC1
chr1	6038339	6038402	-	CDS,intron-Distal	3.07078	3.47879	HepG2	PPIG
chr1	5940023	5940131	-	intron-Distal,intron-Proximal	6.65860	20.09939	K562	EIF4G2
chr1	5926384	5926431	-	intron-Distal,intron-Proximal	3.23834	3.18246	K562	PRPF8
chr1	6038148	6038183	-	intron-Distal	3.93302	3.33062	K562	ILF3
chr1	5927759	5927800	-	intron-Distal,intron-Proximal	5.90399	9.40852	HepG2	PRPF8
chr1	5926354	5926433	-	intron-Distal,intron-Proximal	4.65307	4.65563	K562	AQR
chr1	6037441	6037547	-	intron-Distal	4.14950	8.35855	K562	ILF3
chr1	6037270	6037358	-	intron-Distal	4.07731	7.56929	K562	ILF3
chr1	6020822	6020897	-	intron-Distal	3.62716	3.90822	HepG2	HNRNPM
chr1	6031692	6031766	-	intron-Distal	4.70480	4.38558	HepG2	HNRNPM
chr1	6016973	6017038	-	intron-Distal	3.95519	3.07980	HepG2	HNRNPM
chr1	6038239	6038285	-	intron-Distal,intron-Proximal	4.53848	3.03048	HepG2	GTF2F1
chr1	5923860	5923950	-	intron-Distal,intron-Proximal	6.69312	22.44866	K562	AQR
chr1	6052224	6052269	-	intron-Distal	3.76070	3.30664	K562	NONO
chr1	6037892	6037953	-	intron-Distal	4.96695	4.35687	HepG2	DDX59
chr1	6020794	6020867	-	intron-Distal	4.12190	3.78162	K562	HNRNPM
chr1	6038207	6038297	-	intron-Distal,intron-Proximal	4.41555	5.24056	K562	GTF2F1
chr1	5933740	5933865	-	intron-Distal	5.30921	10.49968	K562	EIF4G2
chr1	6038227	6038313	-	intron-Distal,intron-Proximal	5.06007	5.41529	HepG2	CSTF2T
chr1	6037867	6037940	-	intron-Distal	5.73616	11.88842	HepG2	PCBP2
chr1	5939929	5939991	-	intron-Distal	3.95836	3.46495	K562	TARDBP
chr1	6012565	6012628	-	intron-Distal	5.02086	5.24810	K562	GTF2F1
chr1	5933721	5933869	-	intron-Distal	3.42644	4.79863	K562	TARDBP
chr1	5933865	5933945	-	intron-Distal,intron-Proximal	4.59201	6.26655	K562	EIF4G2
chr1	6038039	6038086	-	intron-Distal	4.44486	3.31153	K562	GTF2F1
chr1	5928658	5928714	-	intron-Distal	5.29464	6.10540	K562	EIF4G2
chr1	6038183	6038289	-	intron-Distal,intron-Proximal	4.45390	4.48935	K562	CSTF2T
chr1	6037291	6037345	-	intron-Distal	3.66035	3.77708	K562	GTF2F1
chr1	5940023	5940120	-	intron-Distal,intron-Proximal	5.27590	9.43874	K562	TARDBP
chr1	5944419	5944508	-	intron-Distal	3.42689	3.42785	HepG2	HNRNPM
chr1	5945765	5945840	-	intron-Distal	4.01394	3.53896	K562	NONO
chr1	6037823	6037930	-	intron-Distal	5.08291	9.16886	K562	ILF3
chr1	5943802	5943854	-	intron-Distal	3.96154	3.80512	K562	CSTF2T
chr1	6017026	6017083	-	intron-Distal	4.15504	3.30687	K562	EXOSC5
chr1	6038041	6038083	-	intron-Distal	4.20564	3.30705	HepG2	GTF2F1
chr1	5942550	5942616	-	intron-Distal	3.62139	4.58695	K562	SLTM
chr1	6038214	6038277	-	intron-Distal,intron-Proximal	4.36744	9.23193	K562	ILF3
chr1	5933945	5934003	-	intron-Distal,intron-Proximal	3.84716	3.46495	K562	TARDBP
chr1	5950362	5950469	-	intron-Distal	4.57380	10.85680	HepG2	QKI
chr1	5923853	5923945	-	intron-Distal,intron-Proximal	4.08969	6.71940	K562	PRPF8
chr1	6009682	6009746	-	intron-Distal	4.20111	7.94355	HepG2	HNRNPM
chr1	5929025	5929095	-	intron-Distal	5.67372	7.55693	K562	EIF4G2
chr1	5939757	5939876	-	intron-Distal,intron-Proximal	6.00743	12.46423	K562	EIF4G2
chr1	5940022	5940089	-	intron-Distal,intron-Proximal	3.19276	4.64824	K562	PRPF8
chr1	6037291	6037381	-	intron-Distal	4.82125	6.19429	HepG2	CSTF2T
chr1	5928849	5928923	-	intron-Distal	4.73521	7.66106	K562	EIF4G2
chr1	5934433	5934512	-	intron-Distal,intron-Proximal	5.27856	7.63570	K562	AQR
chr1	5944414	5944507	-	intron-Distal	4.38332	4.48497	K562	NONO
chr1	5939798	5939877	-	intron-Distal	3.84716	3.46495	K562	TARDBP
chr1	5929366	5929421	-	intron-Distal	4.17044	4.00200	K562	EIF4G2
chr1	6052057	6052119	-	intron-Distal	4.00189	3.82910	K562	NONO
chr1	5942711	5942827	-	intron-Distal	4.61548	6.36475	K562	CSTF2T
chr1	6012576	6012636	-	intron-Distal	5.28795	7.81647	HepG2	FAM120A
chr1	6009586	6009738	-	intron-Distal	5.09087	7.63393	K562	HNRNPM
chr1	5933945	5934056	-	intron-Distal,intron-Proximal	4.65622	11.07632	K562	EIF4G2
chr1	5929171	5929241	-	intron-Distal	5.34441	5.14653	K562	EIF4G2
chr1	5934407	5934503	-	intron-Distal,intron-Proximal	4.32166	3.49003	K562	PRPF8
chr1	6019131	6019221	-	intron-Distal	4.23528	3.30696	K562	EXOSC5
chr1	6051389	6051469	-	intron-Distal	4.85689	7.85689	K562	NONO
chr1	5944406	5944457	-	intron-Distal	4.04031	3.87340	HepG2	CSTF2T
chr1	5928549	5928658	-	intron-Distal	6.18237	10.00047	K562	EIF4G2
chr1	5944409	5944498	-	intron-Distal	5.04430	7.56775	K562	EWSR1
chr1	6037462	6037551	-	intron-Distal	4.81334	5.23961	K562	GTF2F1
chr1	5934074	5934136	-	intron-Distal	3.97838	3.87294	K562	TARDBP
chr1	5943923	5944032	-	intron-Distal	3.66497	3.41858	K562	FUS
chr1	5942709	5942798	-	intron-Distal	3.45152	3.93602	K562	EWSR1
chr1	5934885	5934934	-	intron-Distal,intron-Proximal	4.69963	3.62536	K562	AQR
chr1	5944412	5944477	-	intron-Distal	3.97805	3.96304	K562	CSTF2T
chr1	5928731	5928802	-	intron-Distal	6.29095	10.98400	K562	EIF4G2
chr1	6005218	6005304	-	intron-Distal	4.17767	3.99130	HepG2	FAM120A
chr1	6038017	6038148	-	intron-Distal	5.54551	11.69218	K562	ILF3
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

eCLIP assay for NPHP4 is not avaliable on ENCORE database.

Diffrential Expression

The Knockdown/knockout assay for NPHP4 is not available on ENCORE database.
53 RBPs can affect the levels of NPHP4.

The Knockdown/knockout RNA-Seq assay for NPHP4 is not available on ENCORE database.

53 RBPs can affect the gene expression of NPHP4 :

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
NPHP4	ENSG00000131697.13	452.24440	675.47310	-0.57880	6.56660	5.57920	HepG2	AUH
NPHP4	ENSG00000131697.13	199.31540	304.91800	-0.61340	3.46030	2.61100	HepG2	CALR
NPHP4	ENSG00000131697.13	330.40290	230.91600	0.51680	3.16780	2.07830	HepG2	YBX3
NPHP4	ENSG00000131697.13	261.78830	422.30750	-0.68990	4.41500	3.63860	HepG2	DDX3X
NPHP4	ENSG00000131697.13	184.66550	295.92390	-0.68030	2.49800	1.57020	HepG2	DDX59
NPHP4	ENSG00000131697.13	321.94910	224.74540	0.51840	3.69460	2.96050	HepG2	DNAJC2
NPHP4	ENSG00000131697.13	593.07330	385.32360	0.62200	4.02340	3.25640	HepG2	EIF4A3
NPHP4	ENSG00000131697.13	199.36670	299.59760	-0.58760	3.23180	2.38670	HepG2	FUBP3
NPHP4	ENSG00000131697.13	605.66880	388.98890	0.63870	4.70170	3.81560	HepG2	FXR1
NPHP4	ENSG00000131697.13	497.51310	365.53610	0.44460	2.29000	1.65080	HepG2	HNRNPK
NPHP4	ENSG00000131697.13	253.83240	345.26850	-0.44380	2.55220	1.63780	HepG2	HNRNPM
NPHP4	ENSG00000131697.13	406.83970	252.93380	0.68560	6.38420	5.49420	HepG2	HNRNPU
NPHP4	ENSG00000131697.13	793.15470	515.36720	0.62190	3.66590	2.71100	HepG2	LARP4
NPHP4	ENSG00000131697.13	647.05450	389.12570	0.73360	5.97370	5.02080	HepG2	MAGOH
NPHP4	ENSG00000131697.13	678.75500	391.26880	0.79460	6.11200	5.20160	HepG2	MATR3
NPHP4	ENSG00000131697.13	273.28070	404.96160	-0.56740	3.98780	3.02080	HepG2	MSI2
NPHP4	ENSG00000131697.13	351.63060	249.96580	0.49220	2.40870	1.70880	HepG2	NSUN2
NPHP4	ENSG00000131697.13	407.33090	225.59580	0.85240	8.74800	7.48480	HepG2	PPIL4
NPHP4	ENSG00000131697.13	579.95960	421.18300	0.46140	4.92770	4.18260	HepG2	PUM1
NPHP4	ENSG00000131697.13	383.15690	500.56760	-0.38560	2.44540	1.63400	HepG2	RBM15
NPHP4	ENSG00000131697.13	384.76070	648.23920	-0.75260	8.97480	8.16360	HepG2	RBM22
NPHP4	ENSG00000131697.13	577.81980	405.22700	0.51180	3.47300	2.79210	HepG2	RECQL
NPHP4	ENSG00000131697.13	179.45980	336.65930	-0.90760	6.97720	5.96620	HepG2	RPLP0
NPHP4	ENSG00000131697.13	244.06280	136.79900	0.83510	3.98530	3.02450	HepG2	RPS3A
NPHP4	ENSG00000131697.13	377.77400	225.24540	0.74590	5.58430	4.72210	HepG2	SAFB2
NPHP4	ENSG00000131697.13	535.49980	380.45460	0.49310	4.08350	3.25480	HepG2	SLBP
NPHP4	ENSG00000131697.13	161.27640	310.46620	-0.94490	4.61640	3.59720	HepG2	SNRNP70
NPHP4	ENSG00000131697.13	249.26410	732.14080	-1.55440	35.38290	34.12120	HepG2	SRFBP1
NPHP4	ENSG00000131697.13	255.67630	424.76110	-0.73230	3.56000	3.04020	HepG2	SRSF1
NPHP4	ENSG00000131697.13	166.90240	300.24210	-0.84710	4.15730	2.90480	HepG2	SRSF3
NPHP4	ENSG00000131697.13	166.46270	345.59530	-1.05390	6.65160	5.86230	HepG2	SRSF9
NPHP4	ENSG00000131697.13	660.92970	445.51220	0.56890	6.93510	6.02870	HepG2	SUCLG1
NPHP4	ENSG00000131697.13	388.18490	245.75100	0.65940	4.99580	4.36450	HepG2	TIAL1
NPHP4	ENSG00000131697.13	423.40790	247.97090	0.77180	8.07700	7.19260	HepG2	TRIM56
NPHP4	ENSG00000131697.13	1057.36520	836.46930	0.33800	3.48470	2.86100	K562	AGGF1
NPHP4	ENSG00000131697.13	1088.08820	870.38230	0.32200	2.32240	1.72250	K562	AKAP8L
NPHP4	ENSG00000131697.13	558.44960	1001.45190	-0.84260	9.30690	8.33280	K562	AQR
NPHP4	ENSG00000131697.13	601.73470	482.02030	0.31990	2.24140	1.37720	K562	BCLAF1
NPHP4	ENSG00000131697.13	1088.03620	1418.14650	-0.38230	4.18080	2.97410	K562	CELF1
NPHP4	ENSG00000131697.13	522.08280	806.80680	-0.62790	8.56740	7.50120	K562	DDX47
NPHP4	ENSG00000131697.13	676.85430	425.87270	0.66830	5.40100	4.10000	K562	EFTUD2
NPHP4	ENSG00000131697.13	971.91730	660.82160	0.55650	7.33350	6.24450	K562	EIF2S2
NPHP4	ENSG00000131697.13	245.10690	395.46830	-0.69020	4.07920	2.67620	K562	FKBP4
NPHP4	ENSG00000131697.13	489.34310	646.69930	-0.40220	3.22420	2.57890	K562	FXR1
NPHP4	ENSG00000131697.13	62.39400	243.45250	-1.96420	15.53580	13.54250	K562	G3BP2
NPHP4	ENSG00000131697.13	579.74800	776.99730	-0.42250	2.66070	1.60840	K562	HNRNPA1
NPHP4	ENSG00000131697.13	548.42540	729.12540	-0.41090	3.13500	2.00340	K562	HNRNPL
NPHP4	ENSG00000131697.13	234.48520	356.38520	-0.60390	3.11890	2.12640	K562	HNRNPM
NPHP4	ENSG00000131697.13	649.83730	408.79100	0.66860	3.12580	2.01220	K562	IGF2BP2
NPHP4	ENSG00000131697.13	938.49420	1229.14450	-0.38920	3.42510	2.16690	K562	MSI2
NPHP4	ENSG00000131697.13	923.69200	1258.18280	-0.44590	4.08060	3.09660	K562	PUF60
NPHP4	ENSG00000131697.13	1070.75810	1338.47920	-0.32200	3.04960	1.92600	K562	PUM1
NPHP4	ENSG00000131697.13	403.47190	253.01910	0.67310	5.48470	4.25460	K562	SF3B4
NPHP4	ENSG00000131697.13	282.94420	408.94490	-0.53140	2.36670	1.70460	K562	SRSF1
NPHP4	ENSG00000131697.13	595.99620	413.79940	0.52630	2.13780	1.51110	K562	TARDBP
NPHP4	ENSG00000131697.13	665.52720	399.17720	0.73740	8.08910	6.57900	K562	TIA1
NPHP4	ENSG00000131697.13	704.80590	391.89970	0.84660	6.57460	4.71690	K562	TRA2A
NPHP4	ENSG00000131697.13	604.27350	780.48590	-0.36920	3.73040	2.75730	K562	WDR43
Gene Name	Gene ID	KDMean	CNMean	log2(fold change)	-log(pval)	-log(padj)	Cell Line	Affected by RBP	Bound by RBP

*: "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 NPHP4 is not available on ENCORE database.

8 RBPs can affect the splicing of NPHP4 :

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	NPHP4	ENSG00000131697.13	chr1	-	5939405	5939692			5937152	5937358	5940173	5940299	0.27000	0.00564	0.06817	included	K562	PUS1
SE	NPHP4	ENSG00000131697.13	chr1	-	5939405	5939692			5937152	5937358	5940173	5940299	-0.41700	0.00302	0.04681	excluded	K562	HNRNPC
A3SS	NPHP4	ENSG00000131697.13	chr1	-	5927089	5927251			5927089	5927175	5927799	5927956	0.15100	0.00167	0.01100	longer	K562	AQR
RI	NPHP4	ENSG00000131697.13	chr1	-	5922870	5926518			5922870	5924093	5924397	5926518	0.09200	0.00603	0.05793	included	HepG2	SF3A3
RI	NPHP4	ENSG00000131697.13	chr1	-	5922870	5924093			5922870	5923465	5923949	5924093	0.34000	0.00104	0.01499	included	K562	PRPF8
RI	NPHP4	ENSG00000131697.13	chr1	-	5922870	5926518			5922870	5924093	5924397	5926518	0.24800	0.01277	0.09530	included	HepG2	U2AF1
RI	NPHP4	ENSG00000131697.13	chr1	-	5922870	5926518			5922870	5924093	5924397	5926518	0.15600	0.00006	0.00050	included	K562	AQR
RI	NPHP4	ENSG00000131697.13	chr1	-	5922870	5926518			5922870	5924093	5924397	5926518	0.20800	0.00397	0.05511	included	K562	FXR1
RI	NPHP4	ENSG00000131697.13	chr1	-	5922870	5924093			5922870	5923465	5923949	5924093	0.19200	0.00856	0.09965	included	K562	FXR1
MXE	NPHP4	ENSG00000131697.13	chr1	-	5924397	5924577	5925161	5925333	5923949	5924093	5926432	5926518	-0.37000	0.00188	0.08997	2included	HepG2	IGF2BP3

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

NPHP4

General Information

Functions

Localization

Domains (AlphaFold: NPHP4)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

eCLIP assay for NPHP4 is not avaliable on ENCORE database.

21 proteins are bound to NPHP4 RNA:

eCLIP assay for NPHP4 is not avaliable on ENCORE database.

Diffrential Expression

The Knockdown/knockout RNA-Seq assay for NPHP4 is not available on ENCORE database.

53 RBPs can affect the gene expression of NPHP4 :

The Knockdown/knockout RNA-Seq assay for NPHP4 is not available on ENCORE database.

8 RBPs can affect the splicing of NPHP4 :

The Knockdown/knockout RNA-Seq assay for NPHP4 is not avaliable on ENCORE database.