USP39

General Information

Gene Name : USP39
Gene ID : ENSG00000168883.19
Essential Gene : Yes

Functions

Not Available

Localization

Not Available

Domains (AlphaFold: USP39)

Not Available

Antibody Validation

Cell Signaling Technology: 23303S

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	USP39	ENSG00000168883.19	50.69	49.57	50.13	ENCSR000AEF
HepG2	USP39	ENSG00000168883.19	81.42	90.88	86.15	ENCSR985KAT
K562	USP39	ENSG00000168883.19	110.14	112.64	111.39	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	USP39-BGRSLV05-RS293		USP39	Ribo-STAMP-293T	Released			shRNA	KD% = ,

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
USP39		23303S	1			Submitted, ENCORE2	BGHcLV43-61, Experimented, ENCORE2	BGKcLV42-101, Submitted, ENCORE2

KD RNA-Seq

GeneName	Cell_Line	Method	Sample_reps	Control_reps	KD%	Status	Project
USP39	K562	CRISPR	USP39-BGKcLV42-101,USP39-BGKcLV42-102	NT-BGKcLV42-1,NT-BGKcLV42-2	89.4,88.5	Submitting	ENCORE2
USP39	HepG2	CRISPR	USP39-BGHcLV43-61,USP39-BGHcLV43-62	NT-BGHcLV43-1,NT-BGHcLV43-2	63.6,63.3	Submitting	ENCORE2
USP39	Ribo-STAMP-293T	shRNA	USP39-BGRSLV05-39,USP39-BGRSLV05-40	NT-BGRSLV05-1,NT-BGRSLV05-2	,	Released	ENCORE2

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
USP39	Product_ID: 23303S Lot_ID: 1 Source: Cell Signaling Technology Target Name: USP39-human

Summary
Proteins Bound to RBP RNA

RNA Targets

eCLIP assay for USP39 is not avaliable on ENCORE database.

Proteins bound to RNA

USP39 RNA is bound by 20 proteins.

CanvasJS.com

eCLIP assay for USP39 is not avaliable on ENCORE database.

20 proteins are bound to USP39 RNA:

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Search:

Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr2	85872111	85872197	+	CDS,intron-Distal	3.47571	23.27691	K562	YBX3
chr2	85846350	85846409	+	CDS	4.44850	14.66124	HepG2	PPIG
chr2	85843298	85843439	+	5'-UTR,CDS,intron-Distal	4.46294	12.22508	K562	DDX3X
chr2	85843500	85843589	+	CDS,intron-Distal,intron-Proximal	5.44749	10.96987	K562	RPS3
chr2	85846407	85846459	+	CDS,intron-Proximal	5.43374	10.28689	HepG2	PRPF8
chr2	85876216	85876293	+	3'-UTR	3.73554	10.01865	HepG2	SUB1
chr2	85872082	85872111	+	CDS,intron-Distal	3.62453	8.91050	K562	YBX3
chr2	85875905	85875983	+	3'-UTR,CDS,intron-Proximal	4.26192	8.84200	K562	PABPC4
chr2	85846291	85846416	+	CDS,intron-Proximal	4.35593	8.60557	HepG2	AQR
chr2	85872206	85872253	+	intron-Distal,intron-Proximal	4.59162	8.52787	K562	AQR
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 38 entries

eCLIP assay for USP39 is not avaliable on ENCORE database.

Diffrential Expression

The Knockdown/knockout assay for USP39 is not available on ENCORE database.
106 RBPs can affect the levels of USP39.

CanvasJS.com

The Knockdown/knockout RNA-Seq assay for USP39 is not available on ENCORE database.

106 RBPs can affect the gene expression of USP39 :

Show entries

Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
USP39	ENSG00000168883.15	1411.29180	2578.71160	-0.86960	18.38050	16.92250	K562	HNRNPC
USP39	ENSG00000168883.15	859.03340	1687.24380	-0.97390	13.55000	12.21450	HepG2	NCBP2
USP39	ENSG00000168883.15	1207.53200	1864.02690	-0.62640	13.41170	12.17430	HepG2	SRSF5
USP39	ENSG00000168883.15	757.22620	1469.66570	-0.95670	13.28360	12.05320	HepG2	EIF2S1
USP39	ENSG00000168883.15	3954.84270	2651.02430	0.57700	12.65220	11.38630	K562	RBM15
USP39	ENSG00000168883.15	3715.21940	2636.61240	0.49470	12.46830	11.35750	K562	AGGF1
USP39	ENSG00000168883.15	951.10250	1547.84560	-0.70260	10.86250	9.58840	HepG2	RBM25
USP39	ENSG00000168883.15	4283.23850	2720.90280	0.65450	9.85280	8.87640	K562	PUS1
USP39	ENSG00000168883.15	1087.86710	1574.72270	-0.53360	9.18940	8.30850	HepG2	PTBP1
USP39	ENSG00000168883.15	1285.66450	1810.28780	-0.49370	8.77010	7.63260	HepG2	SLBP
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 128 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 USP39 is not available on ENCORE database.

22 RBPs can affect the splicing of USP39 :

Show entries

Search:

Event Type	Gene Name	Gene ID	chr	Strand	ExonStart	ExonEnd	2ndExonStart	2ndExonEnd	upstreamES	upstreamEE	downstreamES	downstreamEE	dPSI	FDR	is_included	Cell Line	Affected by RBP
SE	USP39	ENSG00000168883.15	chr2	+	85872936	85873022			85872070	85872206	85875052	85875139	0.08500	0.00000	included	HepG2	G3BP1
SE	USP39	ENSG00000168883.15	chr2	+	85872070	85872206			85868098	85868241	85875052	85875139	-0.07000	0.00000	excluded	K562	AQR
SE	USP39	ENSG00000168883.15	chr2	+	85872936	85873022			85872070	85872206	85875052	85875139	0.05800	0.00058	included	HepG2	IGF2BP3
SE	USP39	ENSG00000168883.15	chr2	+	85872936	85873022			85872070	85872206	85875052	85875139	0.10000	0.00000	included	K562	HNRNPC
A3SS	USP39	ENSG00000168883.15	chr2	+	85846287	85846412			85846342	85846412	85843308	85843586	0.07500	0.00000	longer	K562	AQR
A3SS	USP39	ENSG00000168883.15	chr2	+	85850748	85850905			85850768	85850905	85848607	85848702	0.06800	0.00207	longer	HepG2	HNRNPC
A3SS	USP39	ENSG00000168883.15	chr2	+	85850748	85850905			85850768	85850905	85848607	85848702	0.06800	0.00007	longer	K562	HNRNPC
MXE	USP39	ENSG00000168883.15	chr2	+	85868065	85868241	85872070	85872206	85866325	85866514	85875052	85875139	0.08000	0.00000	1included	K562	AQR
MXE	USP39	ENSG00000168883.15	chr2	+	85850728	85850905	85852661	85852814	85848607	85848702	85857843	85858069	0.06200	0.00000	1included	K562	AQR
MXE	USP39	ENSG00000168883.15	chr2	+	85868077	85868241	85872070	85872206	85866325	85866514	85875052	85875139	0.06700	0.00000	1included	K562	AQR

Showing 1 to 10 of 35 entries

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

USP39

General Information

Functions

Localization

Domains (AlphaFold: USP39)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

eCLIP assay for USP39 is not avaliable on ENCORE database.

20 proteins are bound to USP39 RNA:

eCLIP assay for USP39 is not avaliable on ENCORE database.

Diffrential Expression

The Knockdown/knockout RNA-Seq assay for USP39 is not available on ENCORE database.

106 RBPs can affect the gene expression of USP39 :

The Knockdown/knockout RNA-Seq assay for USP39 is not available on ENCORE database.

22 RBPs can affect the splicing of USP39 :

The Knockdown/knockout RNA-Seq assay for USP39 is not avaliable on ENCORE database.