CDC40

General Information

Gene Name : CDC40
Gene ID : ENSG00000168438.14
Essential Gene : Yes

Functions

Splicing regulation
Spliceosome

Localization(RBPImage: CDC40)

Nuclei
Nucleoplasm
Mutually Exclusive from Nucleolus
Speckles
Cytoplasm
Compartment/Organelle
Unknown Cyto Foci
Cytoskeleton
Microtubule
Mitotic-Apparatus (Spindle; Centrosomes)

Domains (AlphaFold: CDC40)

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

Antibody Validation

View validation images for all CDC40 antibodies

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	CDC40	ENSG00000168438.14	23.54	18.59	21.06	ENCSR000AEF
HepG2	CDC40	ENSG00000168438.14	6.76	11.82	9.29	ENCSR985KAT
K562	CDC40	ENSG00000168438.14	12.03	11.15	11.59	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: 556	ENCSR815VVI	CDC40	HepG2	Released	ENCAB127ICL	ENCSR828ALT
knockdown followed by RNA-seq	CDC40-BGKcLV08-K562	ENCSR354DVY	CDC40	K562	Released		ENCSR015KGT	CRISPR	KD% = 57.0,56.0
knockdown followed by RNA-seq	CDC40-BGHcLV05-HepG2	ENCSR278NFF	CDC40	HepG2	Released		ENCSR481WJH	CRISPR	KD% = 70.8,65.7
knockdown followed by RNA-seq	CDC40-BG293LV04-WT293		CDC40	293T	Released			shRNA	KD% = ,
knockdown followed by RNA-seq	CDC40-BG293LV06-WT293		CDC40	293T	Released			shRNA	KD% = ,

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
CDC40	556	HepG2	ENCSR815VVI	ENCSR828ALT	ENCAB127ICL	A303-699A	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
CDC40	ENCAB127ICL	A303-699A	1		Released, ENCODE3	Released, ENCODE3	BGHcLV05-7, Released, ENCODE3	BGKcLV08-3, Released, ENCODE4
CDC40		99086S	1		Released, ENCODE3	Submitted, ENCORE2	BGHcLV05-7, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
CDC40	K562	shRNA			BGKLV28-5,BGKLV28-6	BGKLV28-1,BGKLV28-2		NotSatisfied	ENCODE3
CDC40	K562	shRNA			BGKLV34-11,BGKLV34-12	BGKLV34-1,BGKLV34-2		NotSatisfied	ENCODE3
CDC40	HepG2	shRNA			BGHLV17-49,BGHLV17-50	BGHLV17-1,BGHLV17-2		NotSatisfied	ENCODE3
CDC40	HepG2	shRNA			BGHLV20-7,BGHLV20-8	BGHLV20-1,BGHLV20-2	redo transfection,redo transfection	NotSatisfied	ENCODE3
CDC40	K562	CRISPR			BGKcLV04-3,BGKcLV04-4	BGKcLV04-1,BGKcLV04-2	34.9,9.4	NotSatisfied	ENCODE3
CDC40	K562	CRISPR			BGKcLV04-3-D12,BGKcLV04-4-D12	BGKcLV04-1,BGKcLV04-2	0.0,0.0	NotSatisfied	ENCODE3
CDC40	K562	CRISPR			BGKcLV04-4-D12,BGKcLV04-3-D20	BGKcLV04-1,BGKcLV04-2	0.0,32.1	NotSatisfied	ENCODE3
CDC40	K562	CRISPR			BGKcLV04-3-D20,BGKcLV04-4-D20	BGKcLV04-1,BGKcLV04-2	32.1,38.0	NotSatisfied	ENCODE3
CDC40	K562	CRISPR			BGKcLV04-4-D20,BGKcLV04-3-D30	BGKcLV04-1,BGKcLV04-2	38.0,0.0	NotSatisfied	ENCODE3
CDC40	K562	CRISPR			BGKcLV04-3-D30,BGKcLV04-4-D30	BGKcLV04-1,BGKcLV04-2	0.0,0.0	NotSatisfied	ENCODE3
CDC40	K562	CRISPR			BGKcLV04-4-D30,BGKcLV08-3	BGKcLV04-1,BGKcLV04-2	0.0,57.0	NotSatisfied	ENCODE3
CDC40	K562	CRISPR	ENCSR354DVY	ENCSR015KGT	CDC40-BGKcLV08-3,CDC40-BGKcLV08-4	NT-BGKcLV08-1,NT-BGKcLV08-2	57.0,56.0	Released	ENCODE4
CDC40	K562	CRISPR			BGKcLV08-5,BGKcLV08-6	BGKcLV08-1,BGKcLV08-2	47.0,47.0	NotSatisfied	ENCODE4
CDC40	K562	CRISPR			BGKcLV44-95,BGKcLV44-96	BGKcLV44-1,BGKcLV44-2		NotSatisfied	ENCORE2
CDC40	K562	CRISPR			BGKcLV44-97,BGKcLV44-98	BGKcLV44-1,BGKcLV44-2		NotSatisfied	ENCORE2
CDC40	HepG2	CRISPR	ENCSR278NFF	ENCSR481WJH	CDC40_BGHcLV05_7,CDC40_BGHcLV05_8	NT_BGHcLV05-1,NT_BGHcLV05-2	70.8,65.7	Released	ENCODE3
CDC40	293T	shRNA			BG293LV01-3,BG293LV01-4	BG293LV01-1,BG293LV01-2		NotSatisfied	ENCORE2
CDC40	293T	shRNA			BG293LV01-5,BG293LV01-6	BG293LV01-1,BG293LV01-2		NotSatisfied	ENCORE2
CDC40	293T	shRNA			BG293LV01-7,BG293LV01-8	BG293LV01-1,BG293LV01-2		NotSatisfied	ENCORE2
CDC40	293T	shRNA			BG293LV04-11,BG293LV04-12	BG293LV04-1,BG293LV04-2		NotSatisfied	ENCORE2
CDC40	293T	shRNA			CDC40-BG293LV04-13,CDC40-BG293LV04-14	NT-BG293LV04-1,NT-BG293LV04-2	,	Released	ENCORE2
CDC40	293T	shRNA			CDC40-BG293LV06-119B,CDC40-BG293LV06-120B	NT-BG293LV06-1B,NT-BG293LV06-2B	,	Released	ENCORE2

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

CDC40: Click to RBP Image Database

Nuclei

Nucleoplasm

Mutually Exclusive from Nucleolus

Speckles

Cytoplasm

Compartment/Organelle

Unknown Cyto Foci

Cytoskeleton

Microtubule

Mitotic-Apparatus (Spindle; Centrosomes)

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CDC40	Product_ID: A303-699A Lot_ID: 1 Source: Bethyl Labs Target Name: CDC40-human
CDC40	Product_ID: 99086S Lot_ID: 1 Source: Cell Signaling Technology Target Name: CDC40-human

RNA Targets

CDC40 protein binds to 1,202 RNA regions.

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Proteins bound to RNA

CDC40 RNA is bound by 7 proteins.

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CDC40 protein has 1,202 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
CDC40	chr11	2152211	2152216	-	4.00734	400.00000	HepG2	IGF2	3'-UTR,intron-Distal
CDC40	chr11	2152719	2152724	-	6.54690	400.00000	HepG2	IGF2	3'-UTR,intron-Distal
CDC40	chr11	2153114	2153137	-	5.31108	400.00000	HepG2	IGF2	3'-UTR,intron-Distal
CDC40	chr11	2153097	2153114	-	5.02472	400.00000	HepG2	IGF2	3'-UTR,intron-Distal
CDC40	chr11	2153507	2153515	-	3.86382	400.00000	HepG2	IGF2	3'-UTR,intron-Distal
CDC40	chr11	2152927	2152945	-	5.74939	400.00000	HepG2	IGF2	3'-UTR,intron-Distal
CDC40	chr11	2152945	2152951	-	5.86642	400.00000	HepG2	IGF2	3'-UTR,intron-Distal
CDC40	chr11	2152682	2152688	-	5.97780	400.00000	HepG2	IGF2	3'-UTR,intron-Distal
CDC40	chr6	159048123	159048307	+	4.25233	64.97931	HepG2	TMEM181, AL591025.1	intron-Distal
CDC40	chr16	2820243	2820312	+	4.13441	33.78378	HepG2	SRRM2	intron-Distal,intron-Proximal

Showing 1 to 10 of 100 entries

7 proteins are bound to CDC40 RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr6	110536489	110536561	+	CDS,intron-Proximal	5.02542	11.09609	HepG2	PRPF8
chr6	110533342	110533476	+	CDS,intron-Proximal	3.70300	7.25346	K562	UCHL5
chr6	110540943	110541081	+	CDS,intron-Proximal	4.14938	6.22576	HepG2	BCLAF1
chr6	110530370	110530426	+	CDS	3.65782	4.76274	K562	UCHL5
chr6	110531908	110531943	+	CDS,intron-Proximal	4.50703	4.16170	K562	UCHL5
chr6	110547385	110547444	+	CDS,intron-Distal	4.18784	3.71570	HepG2	BCLAF1
chr6	110503797	110503946	+	intron-Distal	4.33032	3.55787	K562	PTBP1
chr6	110503832	110504034	+	intron-Distal	3.11323	3.32889	K562	MATR3
chr6	110502920	110503021	+	intron-Distal	4.16602	3.29248	HepG2	SUGP2
chr6	110533183	110533303	+	intron-Distal,intron-Proximal	3.77506	3.24603	K562	KHSRP
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 11 entries

No autoregularoty interactions between protein CDC40 and its RNA.

Diffrential Expression

158 differentially expressed genes after Knockdown/Knockout CDC40 protein.

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54 RBPs can affect the levels of CDC40.

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158 differentially expressed genes after Knockdown/Knockout CDC40 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
MMP3	ENSG00000149968.7	446.22650	9.14360	5.60880	61.29080	56.93770	HepG2	CDC40
IGFBP3	ENSG00000146674.10	3620.52060	8158.22880	-1.17210	12.38870	8.81370	HepG2	CDC40
CPLX2	ENSG00000145920.10	341.74870	110.18260	1.63290	10.57490	7.06680	HepG2	CDC40
ARRDC4	ENSG00000140450.7	625.28230	240.93170	1.37580	10.33880	6.88870	HepG2	CDC40
SORL1	ENSG00000137642.8	5701.47720	11021.50950	-0.95090	8.94840	5.59530	HepG2	CDC40
GCLC	ENSG00000001084.6	1635.92940	827.45010	0.98330	7.81700	4.57780	HepG2	CDC40
FAM13A	ENSG00000138640.10	1212.57390	2274.20460	-0.90730	7.37340	4.16640	HepG2	CDC40
TOMM34	ENSG00000025772.7	1268.36000	649.59260	0.96530	6.84000	3.73700	HepG2	CDC40
TIMP1	ENSG00000102265.7	267.19840	102.03120	1.38880	6.83490	3.73700	HepG2	CDC40
PTGR1	ENSG00000106853.12	188.60180	67.63650	1.47940	6.77730	3.70290	HepG2	CDC40
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".

54 RBPs can affect the gene expression of CDC40 :

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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
CDC40	ENSG00000168438.10	404.21130	737.00050	-0.86660	15.79800	14.30420	HepG2	HNRNPL
CDC40	ENSG00000168438.10	290.59730	562.13150	-0.95190	9.31240	8.12360	HepG2	CPSF6
CDC40	ENSG00000168438.10	318.70360	525.20210	-0.72070	8.72980	7.81590	HepG2	TRIM56
CDC40	ENSG00000168438.10	320.66570	564.34750	-0.81550	7.88980	6.93030	K562	HNRNPC
CDC40	ENSG00000168438.10	270.62850	469.36720	-0.79440	7.19500	5.51270	HepG2	FASTKD2
CDC40	ENSG00000168438.10	486.67700	708.20260	-0.54120	6.23170	5.37630	HepG2	PCBP1
CDC40	ENSG00000168438.10	614.88620	862.27570	-0.48780	6.01220	5.06270	HepG2	AUH
CDC40	ENSG00000168438.10	320.00840	475.97680	-0.57280	5.85110	4.95520	HepG2	DNAJC2
CDC40	ENSG00000168438.10	581.37190	827.46520	-0.50920	5.49700	4.82930	HepG2	RBM22
CDC40	ENSG00000168438.10	600.47550	812.91840	-0.43700	5.59600	4.81450	HepG2	PUM1
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 61 entries

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

178 alternative splicing events after Knockdown/Knockout CDC40 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	EIF4H	ENSG00000106682.10	chr7	+	73604576	73604636	73604151	73604248	73609070	73609208	0.05300	0.00010	included	HepG2	CDC40
SE	AHSA2	ENSG00000173209.18	chr2	+	61410681	61410797	61408472	61408540	61411846	61411935	0.16000	0.00313	included	HepG2	CDC40
SE	TCERG1	ENSG00000113649.7	chr5	+	145847903	145847966	145843197	145843356	145849106	145849307	0.34800	0.00106	included	HepG2	CDC40
SE	R3HDM1	ENSG00000048991.12	chr2	+	136399105	136399360	136396465	136396692	136402948	136403097	0.21100	0.00001	included	HepG2	CDC40
SE	ENTPD5	ENSG00000187097.8	chr14	-	74439586	74439727	74438554	74438611	74440579	74440681	0.13400	0.00017	included	HepG2	CDC40
SE	SEC24B	ENSG00000138802.7	chr4	+	110402832	110402937	110394159	110394342	110412482	110412563	0.23500	0.00148	included	HepG2	CDC40
SE	DENND5A	ENSG00000184014.3	chr11	-	9198318	9198449	9192173	9192324	9199678	9199913	0.08200	0.00041	included	HepG2	CDC40
SE	EIF4A2	ENSG00000156976.10	chr3	+	186506098	186506209	186505616	186505671	186506913	186507080	0.09600	0.00000	included	HepG2	CDC40
SE	ZNF706	ENSG00000120963.7	chr8	-	102214560	102214675	102213842	102213971	102217662	102217960	0.10700	0.00010	included	HepG2	CDC40
SE	RPL17	ENSG00000265681.2	chr18	-	47018105	47018203	47017901	47017954	47018827	47018878	0.06000	0.00148	included	HepG2	CDC40

Showing 1 to 10 of 100 entries

2 RBPs can affect the splicing of CDC40 :

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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	CDC40	ENSG00000168438.10	chr6	+	110549998	110550179	110550034	110550179	110547369	110547446	0.14500	0.00000	0.00000	longer	K562	AQR
SE	CDC40	ENSG00000168438.10	chr6	+	110532985	110533062	110531909	110532006	110533335	110533475	0.06400	0.00003	0.00051	included	K562	AQR
SE	CDC40	ENSG00000168438.10	chr6	+	110532985	110533062	110531909	110532006	110533335	110533475	0.09000	0.00013	0.00381	included	K562	SRSF1
SE	CDC40	ENSG00000168438.10	chr6	+	110522760	110522890	110514384	110514471	110528708	110528792	-0.15700	0.00017	0.00271	excluded	K562	AQR
SE	CDC40	ENSG00000168438.10	chr6	+	110534288	110534363	110533335	110533475	110536488	110536534	-0.06500	0.01154	0.09098	excluded	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".

CDC40

General Information

Functions

Localization(RBPImage: CDC40)

Domains (AlphaFold: CDC40)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

CDC40 protein has 1,202 RNA targets:

7 proteins are bound to CDC40 RNA:

No autoregularoty interactions between protein CDC40 and its RNA.

Diffrential Expression

158 differentially expressed genes after Knockdown/Knockout CDC40 protein :

54 RBPs can affect the gene expression of CDC40 :

178 alternative splicing events after Knockdown/Knockout CDC40 protein :

2 RBPs can affect the splicing of CDC40 :

No autoregularoty alternative splicing events between protein CDC40 and its RNA.