CHD3

General Information

Gene Name : CHD3
Gene ID : ENSG00000170004.16
Essential Gene : No

Functions

Not Available

Localization

Not Available

Domains (AlphaFold: CHD3)

Not Available

Antibody Validation

Zen Bioscience: 200314-7F6

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	CHD3	ENSG00000170004.16	35.44	36.70	36.07	ENCSR000AEF
HepG2	CHD3	ENSG00000170004.16	6.13	4.94	5.54	ENCSR985KAT
K562	CHD3	ENSG00000170004.16	17.81	16.70	17.25	ENCSR000AEO

Assays

1 Released experiments are available on ENCORE database.

Assay Type	Exp_Name	ENCODE ID	Target label	Biosample	Status	Linked Antibody	Controls	Method	Note
knockdown followed by RNA-seq	CHD3-BGHcLV10-HepG2	ENCSR242DBX	CHD3	HepG2	Released		ENCSR775ZWO	CRISPR	KD% = 64.3,76.6

eCLIP

No eCLIP experiment available

Antibody Validation

GeneName	Antibody_DCC_ID	Product_ID	Lot_ID	Phosphate	HepG2 Primary Validation	K562 Primary Validation	HepG2 Secondary Validation	K562 Secondary Validation
CHD3	ENCAB509XJY	200314-7F6	CD1016		Released, ENCODE3	Released, ENCODE3	BGHcLV10-9, Released, ENCODE4

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
CHD3	HepG2	shRNA			BGHLV35-11,BGHLV35-12	BGHLV35-1,BGHLV35-2		NotSatisfied	ENCODE3
CHD3	K562	CRISPR			BGKcLV06-9,BGKcLV06-10	BGKcLV06-1,BGKcLV06-2		NotSatisfied	ENCODE3
CHD3	K562	CRISPR			BGKcLV08-11,BGKcLV08-12	BGKcLV08-1,BGKcLV08-2	0.0,0.0	NotSatisfied	ENCODE4
CHD3	K562	CRISPR			BGKcLV08-13,BGKcLV08-14	BGKcLV08-1,BGKcLV08-2	0.0,0.0	NotSatisfied	ENCODE4
CHD3	K562	CRISPR			BGKcLV11-27,BGKcLV11-28	BGKcLV11-1,BGKcLV11-2	NO CLEAR BAND ON THE POSITION,	NotSatisfied	ENCODE4
CHD3	K562	CRISPR			BGKcLV11-29,BGKcLV11-30	BGKcLV11-1,BGKcLV11-2	NO CLEAR BAND ON THE POSITION,	NotSatisfied	ENCODE4
CHD3	HepG2	CRISPR			BGHcLV07-9,BGHcLV07-10	BGHcLV07-1,BGHcLV07-2	no clear band,	NotSatisfied	ENCODE3
CHD3	HepG2	CRISPR	ENCSR242DBX	ENCSR775ZWO	CHD3-BGHcLV10-9,CHD3-BGHcLV10-10	NT-BGHcLV10-1,NT-BGHcLV10-2	64.3,76.6	Released	ENCODE4
CHD3	HepG2	CRISPR			BGHcLV10-11,BGHcLV10-12	BGHcLV10-1,BGHcLV10-2	18.8,36.5	NotSatisfied	ENCODE4

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
CHD3	Product_ID: 200314-7F6 Lot_ID: CD1016 Source: Zen Bioscience Target Name: CHD3-human

Summary
Proteins Bound to RBP RNA

RNA Targets

eCLIP assay for CHD3 is not avaliable on ENCORE database.

Proteins bound to RNA

CHD3 RNA is bound by 28 proteins.

CanvasJS.com

eCLIP assay for CHD3 is not avaliable on ENCORE database.

28 proteins are bound to CHD3 RNA:

Show entries

Search:

Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr17	7809480	7809498	+	intron-Distal	5.53386	400.00000	HepG2	DKC1
chr17	7809432	7809480	+	intron-Distal	5.30716	400.00000	HepG2	DKC1
chr17	7809528	7809552	+	intron-Distal	6.44601	400.00000	HepG2	DKC1
chr17	7809569	7809635	+	intron-Distal	7.25475	400.00000	HepG2	NOLC1
chr17	7809571	7809630	+	intron-Distal	6.66904	400.00000	HepG2	DKC1
chr17	7809508	7809523	+	intron-Distal	6.26362	400.00000	HepG2	DKC1
chr17	7809423	7809569	+	intron-Distal	5.14711	400.00000	HepG2	NOLC1
chr17	7809575	7809634	+	intron-Distal	4.57714	45.07855	HepG2	SF3A3
chr17	7809568	7809637	+	intron-Distal	5.87129	41.35179	K562	SMNDC1
chr17	7809431	7809509	+	intron-Distal	4.32211	40.63676	HepG2	SF3A3
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 109 entries

eCLIP assay for CHD3 is not avaliable on ENCORE database.

Diffrential Expression

The Knockdown/knockout assay for CHD3 is not available on ENCORE database.
91 RBPs can affect the levels of CHD3.

CanvasJS.com

The Knockdown/knockout RNA-Seq assay for CHD3 is not available on ENCORE database.

91 RBPs can affect the gene expression of CHD3 :

Show entries

Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
CHD3	ENSG00000170004.12	1892.26770	788.81830	1.26230	53.24330	51.03970	HepG2	UPF1
CHD3	ENSG00000170004.12	1842.00130	713.90350	1.36740	52.32830	50.34060	HepG2	ETF1
CHD3	ENSG00000170004.12	1400.02610	585.10530	1.25860	42.84050	41.40370	HepG2	SSB
CHD3	ENSG00000170004.12	1399.44470	490.36110	1.51280	28.48090	27.18770	HepG2	TIAL1
CHD3	ENSG00000170004.12	1257.71870	556.70490	1.17570	20.84190	19.17490	HepG2	CPSF6
CHD3	ENSG00000170004.12	1162.00920	621.76870	0.90210	20.10010	18.55730	HepG2	AUH
CHD3	ENSG00000170004.12	1279.56740	740.86350	0.78830	17.28780	15.57360	HepG2	EIF4G1
CHD3	ENSG00000170004.12	1339.80170	710.79950	0.91440	15.79260	14.52520	HepG2	PUF60
CHD3	ENSG00000170004.12	1076.77430	534.00210	1.01170	14.66980	13.09280	HepG2	NSUN2
CHD3	ENSG00000170004.12	1450.32670	2639.85450	-0.86410	14.14770	12.96510	K562	AQR
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 106 entries

*: "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 CHD3 is not available on ENCORE database.

8 RBPs can affect the splicing of CHD3 :

Show entries

Search:

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	CHD3	ENSG00000170004.12	chr17	+	7810918	7811020	7810670	7810806	7811211	7811337	-0.41900	0.00000	0.00001	excluded	K562	SRSF1
SE	CHD3	ENSG00000170004.12	chr17	+	7810918	7811020	7810670	7810806	7811211	7811337	-0.47700	0.00000	0.00022	excluded	K562	SF3B4
SE	CHD3	ENSG00000170004.12	chr17	+	7810918	7811020	7810670	7810806	7811211	7811337	-0.31800	0.00001	0.00093	excluded	K562	FXR1
A5SS	CHD3	ENSG00000170004.12	chr17	+	7808417	7808655	7808417	7808483	7808938	7809024	0.12400	0.00004	0.00110	longer	K562	AQR
SE	CHD3	ENSG00000170004.12	chr17	+	7810918	7811020	7810670	7810806	7811211	7811337	-0.40200	0.00006	0.00229	excluded	HepG2	SRSF1
SE	CHD3	ENSG00000170004.12	chr17	+	7810918	7811020	7810670	7810806	7811211	7811337	-0.67900	0.00011	0.03659	excluded	HepG2	EFTUD2
SE	CHD3	ENSG00000170004.12	chr17	+	7810918	7811020	7810670	7810806	7811211	7811337	-0.42600	0.00012	0.00832	excluded	HepG2	PCBP1
SE	CHD3	ENSG00000170004.12	chr17	+	7810918	7811020	7810670	7810806	7811211	7811452	-0.30500	0.00081	0.03409	excluded	K562	SF3B1
SE	CHD3	ENSG00000170004.12	chr17	+	7810918	7811020	7810670	7810806	7811211	7811337	-0.32800	0.00103	0.04726	excluded	HepG2	SF3B4
SE	CHD3	ENSG00000170004.12	chr17	+	7810918	7811020	7810670	7810806	7811211	7811337	-0.54700	0.00196	0.09160	excluded	HepG2	NCBP2

Showing 1 to 10 of 11 entries

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

CHD3

General Information

Functions

Localization

Domains (AlphaFold: CHD3)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

eCLIP assay for CHD3 is not avaliable on ENCORE database.

28 proteins are bound to CHD3 RNA:

eCLIP assay for CHD3 is not avaliable on ENCORE database.

Diffrential Expression

The Knockdown/knockout RNA-Seq assay for CHD3 is not available on ENCORE database.

91 RBPs can affect the gene expression of CHD3 :

The Knockdown/knockout RNA-Seq assay for CHD3 is not available on ENCORE database.

8 RBPs can affect the splicing of CHD3 :

The Knockdown/knockout RNA-Seq assay for CHD3 is not avaliable on ENCORE database.