DDX3X

General Information

Gene Name : DDX3X
Gene ID : ENSG00000215301.10
Essential Gene : No

Functions

Translation regulation
Viral RNA regulation

Localization(RBPImage: DDX3X)

Nuclei
Unknown Nuclear Territory
Cytoplasm
Compartment/Organelle
Cytosolic

Domains (AlphaFold: DDX3X)

Helicase

Antibody Validation

View validation images for all DDX3X antibodies

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	DDX3X	ENSG00000215301.10	175.91	151.05	163.48	ENCSR000AEF
HepG2	DDX3X	ENSG00000215301.10	101.62	156.16	128.89	ENCSR985KAT
K562	DDX3X	ENSG00000215301.10	121.07	120.00	120.53	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: 350	ENCSR930BZL	DDX3X	K562	Released	ENCAB173JTT	ENCSR028CRL
eCLIP	eCLIP: 492	ENCSR648LAH	DDX3X	HepG2	Released	ENCAB173JTT	ENCSR090VXV
knockdown followed by RNA-seq	DDX3X-BGKLV08-K562	ENCSR000KYM	DDX3X	K562	Released		ENCSR913CAE	shRNA	KD% = 80.1,67.9
knockdown followed by RNA-seq	DDX3X-BGHLV12-HepG2	ENCSR637JLM	DDX3X	HepG2	Released		ENCSR237YZT	shRNA	KD% = 95.7,94.3

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
DDX3X	350	K562	ENCSR930BZL	ENCSR028CRL	ENCAB173JTT	A300-474A	1	Released	ENCODE3
DDX3X	492	HepG2	ENCSR648LAH	ENCSR090VXV	ENCAB173JTT	A330-474A	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
DDX3X	ENCAB173JTT	A300-474A	1		Released, ENCODE3	Released, ENCODE3	BGHLV12-15, Released, ENCODE3	BGKLV08-15, Released, ENCODE3
DDX3X	ENCAB273OGW	201041	DD0527		Released, ENCODE3	Released, ENCODE3		BGKLV08-15, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project	Note
DDX3X	K562	shRNA	ENCSR000KYM	ENCSR913CAE	DDX3X-LV08-15,DDX3X-LV08-16	Nontarget-LV08-1_00003527,nontarget-LV08-2_00003527	80.1,67.9	Released	ENCODE3
DDX3X	HepG2	shRNA	ENCSR637JLM	ENCSR237YZT	DDX3X-BGHLV12-15,DDX3X-BGHLV12-16	NT-BGHLV12-01,NT-BGHLV12-02	95.7,94.3	Released	ENCODE3

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

DDX3X: Click to RBP Image Database

Nuclei

Unknown Nuclear Territory

Cytoplasm

Compartment/Organelle

Cytosolic

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX3X	Product_ID: A300-474A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX3X-human
DDX3X	Product_ID: 201041 Lot_ID: DD0527 Source: Zen Bioscience Target Name: DDX3X-human

RNA Targets

DDX3X protein binds to 15,712 RNA regions.

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Proteins bound to RNA

DDX3X RNA is bound by 56 proteins.

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DDX3X protein has 15,712 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
DDX3X	chr8	126010978	126011029	+	5.92089	400.00000	HepG2	SQLE	5'-UTR,intron-Distal,intron-Proximal
DDX3X	chr20	31596430	31596468	+	4.39096	400.00000	HepG2	BPIFB2	CDS
DDX3X	chr1	20987805	20987869	-	5.49924	400.00000	HepG2	DDOST	5'-UTR,CDS,intron-Distal,intron-Proximal
DDX3X	chr20	60962376	60962378	+	4.19636	400.00000	K562	RPS21	5'-UTR,intron-Proximal
DDX3X	chr8	146017522	146017525	-	3.55940	78.20181	K562	RPL8	5'-UTR,intron-Distal,intron-Proximal
DDX3X	chr6	167369792	167369809	-	5.31155	72.91916	HepG2	RNASET2	5'-UTR,intron-Distal
DDX3X	chr17	80275367	80275468	-	5.32167	71.34755	HepG2	CD7	5'-UTR,CDS,intron-Distal,intron-Proximal
DDX3X	chr20	34252716	34252807	-	3.65404	70.56338	HepG2	RBM12, RP1-309K20.6, CPNE1	5'-UTR,intron-Distal,intron-Proximal
DDX3X	chr2	74756609	74756627	-	5.38877	60.23797	HepG2	AUP1	CDS,intron-Distal,intron-Proximal
DDX3X	chr12	56121108	56121125	-	5.08654	58.24662	K562	CD63	5'-UTR,CDS,intron-Distal,intron-Proximal

Showing 1 to 10 of 100 entries

56 proteins are bound to DDX3X RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chrX	41193459	41193550	+	5'-UTR,CDS	5.05079	69.47285	K562	DDX3X
chrX	41201698	41201745	+	intron-Proximal	5.43013	44.71070	K562	SF3B4
chrX	41204377	41204414	+	intron-Distal,intron-Proximal	5.46323	41.53925	K562	QKI
chrX	41201745	41201802	+	CDS,intron-Proximal	4.09820	37.29515	K562	SF3B4
chrX	41209208	41209274	+	3'-UTR,intron-Distal	4.14799	35.88492	K562	PABPC4
chrX	41204325	41204377	+	intron-Distal,intron-Proximal	5.70230	30.20735	K562	QKI
chrX	41193414	41193459	+	5'-UTR	4.82403	28.21421	K562	DDX3X
chrX	41196679	41196797	+	CDS,intron-Proximal	4.23029	27.85883	K562	EFTUD2
chrX	41194334	41194394	+	intron-Distal	6.56713	27.52100	K562	CSTF2T
chrX	41204840	41204872	+	intron-Distal,intron-Proximal	4.78570	26.22879	K562	AQR
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 189 entries

The DDX3X protein binds to its own RNA.

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
DDX3X	chrX	41193459	41193550	+	5.05079	69.47285	K562	DDX3X	5'-UTR,CDS
DDX3X	chrX	41193414	41193459	+	4.82403	28.21421	K562	DDX3X	5'-UTR
DDX3X	chrX	41196660	41196720	+	3.11220	16.89984	K562	DDX3X	CDS,intron-Proximal
DDX3X	chrX	41193412	41193451	+	4.99376	3.99162	HepG2	DDX3X	5'-UTR

Showing 1 to 4 of 4 entries

Diffrential Expression

9,929 differentially expressed genes after Knockdown/Knockout DDX3X protein.

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76 RBPs can affect the levels of DDX3X.

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9,929 differentially expressed genes after Knockdown/Knockout DDX3X 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
ITGA3	ENSG00000005884.13	301.20940	15.60760	4.27030	47.14530	44.86340	HepG2	DDX3X
SLC7A2	ENSG00000003989.12	5723.59860	15049.71760	-1.39470	36.78920	34.79230	HepG2	DDX3X
RHBDD2	ENSG00000005486.12	2585.66000	936.71850	1.46470	31.98500	30.11340	HepG2	DDX3X
MYLIP	ENSG00000007944.10	523.50350	126.91830	2.04420	28.06560	26.30090	HepG2	DDX3X
LIG3	ENSG00000005156.7	284.81010	844.26890	-1.56770	24.79020	23.11030	HepG2	DDX3X
MAP3K9	ENSG00000006432.11	1190.32010	482.42250	1.30290	20.40070	18.86860	HepG2	DDX3X
LAP3	ENSG00000002549.8	1086.25100	2374.71150	-1.12840	19.93040	18.41470	HepG2	DDX3X
SLC25A5	ENSG00000005022.5	6071.69070	11601.70510	-0.93420	17.19970	15.78240	HepG2	DDX3X
C1orf112	ENSG00000000460.12	87.62070	307.69220	-1.81210	16.91880	15.51240	HepG2	DDX3X
ENPP4	ENSG00000001561.6	99.15970	6.47440	3.93680	16.82120	15.41570	HepG2	DDX3X
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".

76 RBPs can affect the gene expression of DDX3X :

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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
DDX3X	ENSG00000215301.5	1244.68010	8058.60230	-2.69480	115.12360	111.59330	HepG2	DDX3X
DDX3X	ENSG00000215301.5	1417.02520	5001.64390	-1.81950	84.83920	80.95320	K562	DDX3X
DDX3X	ENSG00000215301.5	9967.94820	5434.29230	0.87510	38.56380	36.45800	K562	FXR1
DDX3X	ENSG00000215301.5	3780.09950	5897.89140	-0.64180	32.56470	30.42050	HepG2	ILF2
DDX3X	ENSG00000215301.5	3505.69670	5130.23900	-0.54930	22.04660	20.36600	HepG2	DNAJC2
DDX3X	ENSG00000215301.5	3384.67980	5610.37270	-0.72910	19.03900	17.94400	HepG2	TIAL1
DDX3X	ENSG00000215301.5	4039.74470	7840.72220	-0.95670	16.60410	15.15950	HepG2	GPKOW
DDX3X	ENSG00000215301.5	11577.33580	8408.12570	0.46130	16.88710	15.04740	K562	WDR43
DDX3X	ENSG00000215301.5	10510.32480	7323.37730	0.52110	14.75230	13.84530	HepG2	SRSF1
DDX3X	ENSG00000215301.5	9415.52650	6246.18760	0.59200	15.76020	13.80420	K562	EIF3G
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 86 entries

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

754 alternative splicing events after Knockdown/Knockout DDX3X 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	LPHN2	ENSG00000117114.15	chr1	+	82452584	82452713	82450942	82451039	82456074	82458106	0.34400	0.00000	included	HepG2	DDX3X
SE	SNRNP70	ENSG00000104852.10	chr19	+	49605370	49606844	49604646	49604728	49607890	49607992	0.23600	0.00000	included	HepG2	DDX3X
SE	TMEM59	ENSG00000116209.7	chr1	-	54512939	54513045	54509045	54509198	54518672	54518865	0.06400	0.00060	included	HepG2	DDX3X
SE	DHX9	ENSG00000135829.12	chr1	+	182824711	182824848	182823175	182823313	182825666	182825707	0.08500	0.00006	included	HepG2	DDX3X
SE	ZFAS1	ENSG00000177410.8	chr20	+	47897021	47897107	47895640	47895745	47905581	47905797	0.13100	0.00006	included	HepG2	DDX3X
SE	EIF4H	ENSG00000106682.10	chr7	+	73604576	73604636	73604151	73604248	73609070	73609208	0.12200	0.00000	included	HepG2	DDX3X
SE	G3BP2	ENSG00000138757.10	chr4	-	76649239	76649360	76587114	76587233	76649459	76649654	0.49700	0.00000	included	HepG2	DDX3X
SE	SEC31A	ENSG00000138674.12	chr4	-	83782783	83782861	83778841	83778917	83784470	83784545	0.18400	0.00000	included	HepG2	DDX3X
SE	WNK1	ENSG00000060237.12	chr12	+	989886	990165	987377	987527	990857	990955	0.48400	0.00000	included	HepG2	DDX3X
SE	PICALM	ENSG00000073921.13	chr11	-	85701292	85701442	85694908	85695016	85707868	85707972	0.24000	0.00000	included	HepG2	DDX3X

Showing 1 to 10 of 100 entries

6 RBPs can affect the splicing of DDX3X :

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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
SE	DDX3X	ENSG00000215301.5	chrX	+	41198288	41198336			41196660	41196718	41200736	41200869	-0.12300	0.00000	0.00000	excluded	K562	AQR
SE	DDX3X	ENSG00000215301.5	chrX	+	41196660	41196718			41193414	41193550	41200736	41200869	-0.08500	0.00000	0.00004	excluded	K562	PUS1
SE	DDX3X	ENSG00000215301.5	chrX	+	41199888	41200067			41198288	41198336	41200736	41200869	0.06900	0.00000	0.00003	included	K562	RBM15
SE	DDX3X	ENSG00000215301.5	chrX	+	41199888	41200067			41198288	41198336	41200736	41200869	0.27800	0.00000	0.00001	included	K562	DDX3X
A3SS	DDX3X	ENSG00000215301.5	chrX	+	41204406	41204577			41204432	41204577	41203508	41203652	0.06600	0.00000	0.00000	longer	K562	AQR
A3SS	DDX3X	ENSG00000215301.5	chrX	+	41202954	41203075			41202989	41203075	41202412	41202604	0.08200	0.00000	0.00000	longer	K562	AQR
MXE	DDX3X	ENSG00000215301.5	chrX	+	41202468	41202604	41202989	41203075	41201747	41201906	41203282	41203381	0.06500	0.00000	0.00000	1included	K562	AQR
MXE	DDX3X	ENSG00000215301.5	chrX	+	41196618	41196718	41198288	41198336	41193414	41193550	41200736	41200869	0.22100	0.00000	0.00000	1included	K562	AQR
MXE	DDX3X	ENSG00000215301.5	chrX	+	41201989	41202089	41202468	41202604	41201747	41201906	41203282	41203381	-0.05200	0.00000	0.00000	2included	K562	AQR
SE	DDX3X	ENSG00000215301.5	chrX	+	41199888	41200067			41198288	41198336	41200736	41200869	0.05100	0.00002	0.00055	included	K562	PUS1

Showing 1 to 10 of 15 entries

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

The DDX3X 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	DDX3X	ENSG00000215301.5	chrX	+	41199888	41200067			41198288	41198336	41200736	41200869	0.27800	0.00000	0.00001	included	K562	DDX3X

Showing 1 to 1 of 1 entries