YBX3

General Information

Gene Name : YBX3
Gene ID : ENSG00000060138.12
Essential Gene : No

Functions

RNA stability & decay

Localization(RBPImage: YBX3)

Nuclei
Unknown Nuclear Territory
Cytoplasm
Compartment/Organelle
Mitochondria

Domains (AlphaFold: YBX3)

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

Antibody Validation

Bethyl Labs: A303-070A

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	YBX3	ENSG00000060138.12	102.49	143.93	123.21	ENCSR000AEF
HepG2	YBX3	ENSG00000060138.12	118.67	110.18	114.43	ENCSR985KAT
K562	YBX3	ENSG00000060138.12	139.69	160.45	150.07	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: 551	ENCSR529FKI	YBX3	K562	Released	ENCAB021IRD	ENCSR660VTT
eCLIP	eCLIP: 729	ENCSR735HOK	YBX3	HepG2	Released	ENCAB021IRD	ENCSR700UGT
knockdown followed by RNA-seq	YBX3-BGKLV24-K562	ENCSR306EIU	YBX3	K562	Released		ENCSR667PLJ	shRNA	KD% = 79.2,77.8
knockdown followed by RNA-seq	YBX3-BGHLV20-HepG2	ENCSR494VSD	YBX3	HepG2	Released		ENCSR305XWT	shRNA	KD% = 57.6,79.6

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
YBX3	551	K562	ENCSR529FKI	ENCSR660VTT	ENCAB021IRD	A303-070A	1	Released	ENCODE3
YBX3	729	HepG2	ENCSR735HOK	ENCSR700UGT	ENCAB021IRD	A303-070A	1	Released	ENCODE4

Antibody Validation

GeneName	Antibody_DCC_ID	Product_ID	Lot_ID	Phosphate	HepG2 Primary Validation	K562 Primary Validation	HepG2 Secondary Validation	K562 Secondary Validation
YBX3	ENCAB021IRD	A303-070A	1		Released, ENCODE3	Released, ENCODE3	BGHLV20-9, Released, ENCODE3	BGKLV24-11, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
YBX3	K562	shRNA	ENCSR306EIU	ENCSR667PLJ	CSDA_BGKLV24_11_17602,CSDA_BGKLV24_12_17603	non-target_BGKLV24_1_17594,non-target_BGKLV24_2_17595	79.2,77.8	Released	ENCODE3
YBX3	HepG2	shRNA			BGHLV17-51,BGHLV17-52	BGHLV17-1,BGHLV17-2		NotSatisfied	ENCODE3
YBX3	HepG2	shRNA	ENCSR494VSD	ENCSR305XWT	CSDA-30-BGHLV20-9_17710,CSDA-30-BGHLV20-10_17711	non-target-BGHLV20-1_17706,non-target-BGHLV20-2_17707	57.6,79.6	Released	ENCODE3

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

YBX3: Click to RBP Image Database

Nuclei

Unknown Nuclear Territory

Cytoplasm

Compartment/Organelle

Mitochondria

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
YBX3	Product_ID: A303-070A Lot_ID: 1 Source: Bethyl Labs Target Name: YBX3-human

RNA Targets

YBX3 protein binds to 20,298 RNA regions.

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Proteins bound to RNA

YBX3 RNA is bound by 26 proteins.

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YBX3 protein has 20,298 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
YBX3	chr11	61732225	61732231	-	4.24806	400.00000	K562	FTH1	3'-UTR,CDS,intron-Distal,intron-Proximal
YBX3	chr19	42373141	42373150	+	4.02499	400.00000	K562	RPS19	3'-UTR,CDS
YBX3	chr6	34392482	34392508	-	3.34766	400.00000	K562	RPS10, RPS10-NUDT3	CDS,intron-Distal
YBX3	chr19	42373210	42373233	+	4.28511	400.00000	K562	RPS19	3'-UTR,CDS
YBX3	chr6	33240451	33240454	+	3.42510	400.00000	K562	RPS18	5'-UTR,CDS
YBX3	chr11	18422415	18422420	+	3.75287	400.00000	K562	LDHA	3'-UTR,5'-UTR,CDS,intron-Distal,intron-Proximal
YBX3	chr11	2152452	2152462	-	5.98843	400.00000	HepG2	IGF2	3'-UTR,intron-Distal
YBX3	chr3	12877666	12877682	-	3.27266	400.00000	K562	RPL32	CDS,intron-Distal
YBX3	chr6	26199126	26199132	-	4.41347	63.81132	K562	HIST1H3D, HIST1H2AD	5'-UTR,CDS,intron-Distal
YBX3	chr9	127622504	127622532	-	3.66507	62.08362	K562	RPL35	CDS,intron-Distal

Showing 1 to 10 of 100 entries

26 proteins are bound to YBX3 RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr12	10862820	10862923	-	intron-Distal,intron-Proximal	4.19984	25.23211	HepG2	XPO5
chr12	10865850	10865935	-	CDS,intron-Distal,intron-Proximal	3.82910	22.36185	HepG2	BCLAF1
chr12	10862713	10862763	-	intron-Distal,intron-Proximal	5.19210	19.80012	HepG2	SF3B4
chr12	10865786	10865897	-	CDS,intron-Distal,intron-Proximal	3.29445	18.62182	HepG2	GRWD1
chr12	10875387	10875488	-	CDS,intron-Distal	3.42897	17.32904	HepG2	PRPF8
chr12	10875597	10875725	-	5'-UTR,CDS,intron-Distal,intron-Proximal	4.14894	16.67790	K562	METAP2
chr12	10862645	10862742	-	CDS,intron-Distal,intron-Proximal	3.26819	14.92292	HepG2	PPIG
chr12	10865897	10865933	-	CDS,intron-Distal,intron-Proximal	4.12286	13.34751	HepG2	GRWD1
chr12	10868292	10868337	-	CDS,intron-Distal,intron-Proximal	4.59427	13.33970	HepG2	GRWD1
chr12	10851997	10852134	-	3'-UTR,intron-Distal,intron-Proximal	3.58734	13.04208	HepG2	PABPN1
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 74 entries

The YBX3 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
YBX3	chr12	10853851	10853942	-	3.45720	12.53487	K562	YBX3	3'-UTR,CDS,intron-Distal,intron-Proximal
YBX3	chr12	10852072	10852094	-	3.88078	9.88356	K562	YBX3	3'-UTR,intron-Distal,intron-Proximal
YBX3	chr12	10875726	10875778	-	4.26005	8.68374	K562	YBX3	5'-UTR,intron-Distal
YBX3	chr12	10852035	10852072	-	3.11391	8.56198	K562	YBX3	3'-UTR,intron-Distal,intron-Proximal
YBX3	chr12	10862505	10862552	-	3.17817	8.03396	K562	YBX3	CDS,intron-Distal,intron-Proximal
YBX3	chr12	10875778	10875826	-	3.35172	7.76316	K562	YBX3	5'-UTR,intron-Distal
YBX3	chr12	10862552	10862578	-	3.62219	7.24294	K562	YBX3	CDS,intron-Distal
YBX3	chr12	10852245	10852253	-	4.23181	4.48692	K562	YBX3	3'-UTR,intron-Distal

Showing 1 to 8 of 8 entries

Diffrential Expression

3,033 differentially expressed genes after Knockdown/Knockout YBX3 protein.

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121 RBPs can affect the levels of YBX3.

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3,033 differentially expressed genes after Knockdown/Knockout YBX3 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
CYP24A1	ENSG00000019186.5	190.11520	709.91620	-1.90080	44.85820	41.27690	HepG2	YBX3
IFRD1	ENSG00000006652.9	1307.29690	645.48380	1.01800	24.21370	21.58670	HepG2	YBX3
ASB4	ENSG00000005981.8	67.63530	197.15070	-1.54340	11.66530	9.66190	HepG2	YBX3
RNH1	ENSG00000023191.12	656.73050	361.56420	0.86090	10.72510	8.78400	HepG2	YBX3
DBNDD1	ENSG00000003249.9	331.90970	590.48220	-0.83110	10.12640	8.24260	HepG2	YBX3
RABGAP1	ENSG00000011454.12	668.61390	1049.86630	-0.65100	9.80420	7.94580	HepG2	YBX3
MTMR11	ENSG00000014914.15	31.67730	105.36090	-1.73380	8.08080	6.35680	HepG2	YBX3
RPS20	ENSG00000008988.5	5676.52250	4042.72270	0.48960	7.88830	6.18590	HepG2	YBX3
ANKIB1	ENSG00000001629.5	616.20090	993.83580	-0.68960	7.87290	6.17140	HepG2	YBX3
CX3CL1	ENSG00000006210.6	1753.57030	1245.75940	0.49320	7.85620	6.15580	HepG2	YBX3
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".

121 RBPs can affect the gene expression of YBX3 :

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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
YBX3	ENSG00000060138.8	898.19750	2843.30450	-1.66250	102.14240	100.22160	HepG2	SSB
YBX3	ENSG00000060138.8	6482.46190	3274.77760	0.98500	60.54590	58.98600	HepG2	SRFBP1
YBX3	ENSG00000060138.8	3537.29360	1826.05020	0.95380	44.79080	43.10690	HepG2	SRSF9
YBX3	ENSG00000060138.8	1944.12600	3298.86210	-0.76280	28.04120	26.05680	K562	UPF1
YBX3	ENSG00000060138.8	801.75540	2023.64420	-1.33570	27.74150	25.65050	HepG2	CIRBP
YBX3	ENSG00000060138.8	1624.41120	3470.98150	-1.09540	24.97700	23.40310	K562	AQR
YBX3	ENSG00000060138.8	1090.69800	1955.22280	-0.84210	24.08350	22.57160	HepG2	DKC1
YBX3	ENSG00000060138.8	888.44550	2250.08480	-1.34060	23.73910	21.90920	HepG2	EIF4A3
YBX3	ENSG00000060138.8	4821.61720	2899.39930	0.73370	22.47570	21.28520	HepG2	RBM22
YBX3	ENSG00000060138.8	1241.11310	2048.37670	-0.72280	22.77160	21.18090	HepG2	ZC3H8
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 151 entries

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

59 alternative splicing events after Knockdown/Knockout YBX3 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	TXNL4A	ENSG00000141759.10	chr18	-	77737597	77737701	77732874	77733856	77748239	77748593	0.13000	0.02051	included	K562	YBX3
SE	HIST1H2AC	ENSG00000180573.8	chr6	+	26127925	26127989	26124430	26124861	26138281	26139344	0.14000	0.00049	included	K562	YBX3
SE	NT5DC2	ENSG00000168268.6	chr3	-	52566178	52566342	52563165	52563350	52567521	52567793	0.09500	0.01144	included	K562	YBX3
SE	ADAT2	ENSG00000189007.11	chr6	-	143751401	143751614	143749748	143749821	143753641	143753748	-0.09900	0.02312	excluded	K562	YBX3
SE	UHRF2	ENSG00000147854.12	chr9	+	6465743	6465846	6460572	6460791	6475390	6475500	0.30900	0.00402	included	HepG2	YBX3
SE	C17orf76-AS1	ENSG00000175061.13	chr17	+	16342841	16343017	16342640	16342728	16343498	16343567	0.16400	0.00000	included	HepG2	YBX3
SE	FAM60A	ENSG00000139146.9	chr12	-	31457915	31458057	31451010	31451158	31478957	31479070	0.20000	0.00049	included	HepG2	YBX3
SE	CLDND1	ENSG00000080822.12	chr3	-	98240496	98240562	98239976	98240286	98241692	98241829	0.15400	0.00402	included	HepG2	YBX3
SE	MYL6	ENSG00000092841.14	chr12	+	56554409	56554454	56554026	56554104	56555170	56555358	-0.10100	0.00000	excluded	HepG2	YBX3
SE	SLC26A6	ENSG00000225697.6	chr3	-	48669677	48669829	48669312	48669477	48670406	48670545	-0.25500	0.00301	excluded	HepG2	YBX3

Showing 1 to 10 of 59 entries

22 RBPs can affect the splicing of YBX3 :

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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
SE	YBX3	ENSG00000060138.8	chr12	-	10862506	10862713	10856649	10856747	10865809	10865932	-0.31100	0.00000	0.00001	excluded	K562	SRSF1
SE	YBX3	ENSG00000060138.8	chr12	-	10862506	10862713	10856649	10856747	10865809	10865932	0.18500	0.00000	0.01560	included	K562	LIN28B
SE	YBX3	ENSG00000060138.8	chr12	-	10862506	10862713	10856649	10856747	10865809	10865932	0.19500	0.00000	0.00001	included	K562	WDR43
SE	YBX3	ENSG00000060138.8	chr12	-	10862506	10862713	10856649	10856747	10865809	10865932	-0.20700	0.00000	0.00029	excluded	HepG2	SRSF1
A3SS	YBX3	ENSG00000060138.8	chr12	-	10852208	10852274	10852208	10852242	10853852	10853952	-0.10600	0.00000	0.00000	shorter	HepG2	SF3A3
A3SS	YBX3	ENSG00000060138.8	chr12	-	10852208	10852274	10852208	10852253	10853852	10853952	0.05600	0.00000	0.00000	longer	K562	AQR
RI	YBX3	ENSG00000060138.8	chr12	-	10854558	10856747	10854558	10854733	10856649	10856747	0.05900	0.00001	0.00027	included	HepG2	PRPF8
SE	YBX3	ENSG00000060138.8	chr12	-	10871678	10871742	10868292	10868382	10875448	10875906	-0.11300	0.00002	0.00066	excluded	K562	PUS1
RI	YBX3	ENSG00000060138.8	chr12	-	10862506	10865932	10862506	10862713	10865809	10865932	-0.11200	0.00002	0.00552	excluded	HepG2	SRSF7
RI	YBX3	ENSG00000060138.8	chr12	-	10862506	10865932	10862506	10862713	10865809	10865932	0.22900	0.00002	0.00213	included	HepG2	XRN2

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".

YBX3

General Information

Functions

Localization(RBPImage: YBX3)

Domains (AlphaFold: YBX3)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

YBX3 protein has 20,298 RNA targets:

26 proteins are bound to YBX3 RNA:

The YBX3 protein binds to its own RNA.

Diffrential Expression

3,033 differentially expressed genes after Knockdown/Knockout YBX3 protein :

121 RBPs can affect the gene expression of YBX3 :

59 alternative splicing events after Knockdown/Knockout YBX3 protein :

22 RBPs can affect the splicing of YBX3 :

No autoregularoty alternative splicing events between protein YBX3 and its RNA.