UPF2

General Information

Gene Name : UPF2
Gene ID : ENSG00000151461.19
Essential Gene : Yes

Functions

RNA stability & decay

Localization(RBPImage: UPF2)

Nuclei
Nucleoplasm
Mutually Exclusive from Nucleolus
Speckles
Cytoplasm
Compartment/Organelle
Unknown Cyto Foci
Cytosolic
Nuclear release mitosis

Domains (AlphaFold: UPF2)

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

Antibody Validation

Bethyl Labs: A303-929A

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	UPF2	ENSG00000151461.19	36.21	30.25	33.23	ENCSR000AEF
HepG2	UPF2	ENSG00000151461.19	10.33	14.30	12.32	ENCSR985KAT
K562	UPF2	ENSG00000151461.19	21.01	25.33	23.17	ENCSR000AEO

Assays

2 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	UPF2-BGKLV21-K562	ENCSR810FHY	UPF2	K562	Released		ENCSR438MDN	shRNA	KD% = 82.7,85.4
knockdown followed by RNA-seq	UPF2-BGHLV17-HepG2	ENCSR318OXM	UPF2	HepG2	Released		ENCSR856ZRV	shRNA	KD% = 23.2,35.8

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
UPF2	ENCAB821QZM	A303-929A	1					BGKLV21-65, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
UPF2	K562	shRNA			BGKLV19-61,BGKLV19-62	BGKLV19-1,BGKLV19-2		NotSatisfied	ENCODE3
UPF2	K562	shRNA	ENCSR810FHY	ENCSR438MDN	UPF2_BGKLV21-65B,UPF2_BGKLV21-66B	NT_BGKLV21-1B,NT_BGKLV21-2B	82.7,85.4	Released	ENCODE3
UPF2	HepG2	shRNA			BGHLV16-65,BGHLV16-66	BGHLV16-1,BGHLV16-2		NotSatisfied	ENCODE3
UPF2	HepG2	shRNA	ENCSR318OXM	ENCSR856ZRV	UPF2_BGHLV17_39,UPF2_BGHLV17_40	NT_BGHLV17_63,NT_BGHLV17_64	23.2,35.8	Released	ENCODE3
UPF2	HepG2	CRISPR			BGHcLV12-81,BGHcLV12-82	BGHcLV12-1,BGHcLV12-2	0.0,0.0	NotSatisfied	ENCODE4
UPF2	HepG2	CRISPR			BGHcLV12-83,BGHcLV12-84	BGHcLV12-1,BGHcLV12-2	0.0,0.0	NotSatisfied	ENCODE4

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

UPF2: Click to RBP Image Database

Nuclei

Nucleoplasm

Mutually Exclusive from Nucleolus

Speckles

Cytoplasm

Compartment/Organelle

Unknown Cyto Foci

Cytosolic

Nuclear release mitosis

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
UPF2	Product_ID: A303-929A Lot_ID: 1 Source: Bethyl Labs Target Name: UPF2-human

Summary
Proteins Bound to RBP RNA

RNA Targets

eCLIP assay for UPF2 is not avaliable on ENCORE database.

Proteins bound to RNA

UPF2 RNA is bound by 25 proteins.

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eCLIP assay for UPF2 is not avaliable on ENCORE database.

25 proteins are bound to UPF2 RNA:

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Search:

Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr10	12077082	12077140	-	CDS,intron-Distal	5.87358	25.14802	K562	TRA2A
chr10	12071379	12071472	-	CDS,intron-Distal	4.30943	21.65691	K562	ZNF622
chr10	12077057	12077133	-	CDS,intron-Distal,intron-Proximal	5.53344	21.07039	K562	UCHL5
chr10	12071029	12071094	-	CDS,intron-Distal	5.03183	20.37416	K562	ZNF622
chr10	12071095	12071192	-	CDS,intron-Distal	3.30970	19.50455	K562	ZNF622
chr10	12084755	12084820	-	5'-UTR,intron-Distal	6.37430	18.52282	K562	UCHL5
chr10	12071247	12071312	-	CDS,intron-Distal	5.17822	16.95500	K562	UCHL5
chr10	12071312	12071412	-	CDS,intron-Distal	4.10000	16.00088	K562	UCHL5
chr10	12071025	12071093	-	CDS,intron-Distal	3.87833	15.56303	K562	UCHL5
chr10	12077143	12077224	-	CDS,intron-Distal	6.05427	15.43541	K562	TRA2A
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 107 entries

eCLIP assay for UPF2 is not avaliable on ENCORE database.

Diffrential Expression

3,413 differentially expressed genes after Knockdown/Knockout UPF2 protein.

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57 RBPs can affect the levels of UPF2.

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3,413 differentially expressed genes after Knockdown/Knockout UPF2 protein :

Only display 100 entries as example. Please click "View All" button to see all 3,413 entries.

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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	140.69320	656.62950	-2.22250	29.76950	26.74490	HepG2	UPF2
ACSM3	ENSG00000005187.7	1497.66580	479.00450	1.64450	23.83940	21.08520	HepG2	UPF2
NR1H4	ENSG00000012504.9	1880.84330	688.49290	1.44980	19.97530	17.31590	HepG2	UPF2
MLXIPL	ENSG00000009950.11	5716.37740	1837.53090	1.63720	19.41620	16.78980	HepG2	UPF2
SLC4A7	ENSG00000033867.12	268.04180	811.35730	-1.59790	18.45300	15.86450	HepG2	UPF2
LAP3	ENSG00000002549.8	605.14680	1576.44490	-1.38130	16.84600	14.38750	HepG2	UPF2
ANLN	ENSG00000011426.6	980.84720	2204.64680	-1.16840	13.80690	11.49300	HepG2	UPF2
JHDM1D	ENSG00000006459.6	511.69420	1140.19400	-1.15590	11.17750	9.08930	HepG2	UPF2
NUP160	ENSG00000030066.9	882.93040	1874.08390	-1.08580	11.15040	9.06890	HepG2	UPF2
AGPS	ENSG00000018510.8	1296.90570	2568.82410	-0.98600	10.08090	8.10660	HepG2	UPF2
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".

57 RBPs can affect the gene expression of UPF2 :

Show entries

Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
UPF2	ENSG00000151461.15	793.81040	1859.44440	-1.22800	31.86970	27.49150	K562	UPF2
UPF2	ENSG00000151461.15	3881.63340	2709.44630	0.51860	14.22040	12.74510	K562	UPF1
UPF2	ENSG00000151461.15	3578.49050	2367.44500	0.59590	8.27350	7.38330	K562	PUS1
UPF2	ENSG00000151461.15	299.44820	620.52560	-1.05120	8.05520	6.29620	HepG2	UPF2
UPF2	ENSG00000151461.15	3086.07460	2410.80990	0.35620	7.42320	6.10120	K562	WDR43
UPF2	ENSG00000151461.15	4280.99720	3402.94220	0.33110	6.12360	5.20770	K562	DDX47
UPF2	ENSG00000151461.15	854.59450	1261.93580	-0.56230	5.92610	5.08990	HepG2	BOP1
UPF2	ENSG00000151461.15	480.11520	692.73010	-0.52890	5.51090	4.54800	HepG2	DNAJC21
UPF2	ENSG00000151461.15	2959.62070	2306.88700	0.35940	5.32820	4.52970	K562	RBM15
UPF2	ENSG00000151461.15	2133.88420	1331.82950	0.68000	6.39550	4.43090	K562	EEF2
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".

The Knockdown/knockout RNA-Seq assay for UPF2 is not available on ENCORE database.

4 RBPs can affect the splicing of UPF2 :

Show entries

Search:

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	UPF2	ENSG00000151461.15	chr10	-	11968920	11969014			11962020	11963306	11971863	11971984	0.25900	0.00000	0.00003	included	HepG2	U2AF1
A3SS	UPF2	ENSG00000151461.15	chr10	-	12006007	12006170			12006007	12006124	12009339	12009513	0.20900	0.00000	0.00000	longer	K562	AQR
A3SS	UPF2	ENSG00000151461.15	chr10	-	12056022	12056211			12056022	12056183	12070743	12071523	0.14200	0.00000	0.00000	longer	K562	AQR
A3SS	UPF2	ENSG00000151461.15	chr10	-	11985062	11985250			11985062	11985167	11990367	11990570	0.06300	0.00001	0.00007	longer	K562	AQR
A3SS	UPF2	ENSG00000151461.15	chr10	-	12039670	12039825			12039670	12039756	12041904	12042008	0.05700	0.00001	0.00010	longer	K562	AQR
SE	UPF2	ENSG00000151461.15	chr10	-	12043674	12043824			12041904	12042008	12046528	12046726	-0.18100	0.00002	0.00040	excluded	HepG2	U2AF2
MXE	UPF2	ENSG00000151461.15	chr10	-	12041904	12042008	12043674	12043824	12039670	12039756	12046528	12046726	-0.29600	0.00002	0.00031	2included	HepG2	U2AF2
SE	UPF2	ENSG00000151461.15	chr10	-	11994064	11994248			11990388	11990507	11997230	11997506	-0.08000	0.00004	0.00073	excluded	K562	AQR
MXE	UPF2	ENSG00000151461.15	chr10	-	11990388	11990507	11994064	11994248	11985062	11985167	11997230	11997506	-0.10600	0.00007	0.00086	2included	K562	AQR
MXE	UPF2	ENSG00000151461.15	chr10	-	12041904	12042008	12043674	12043824	12039670	12039756	12046528	12046726	-0.24500	0.00040	0.00778	2included	HepG2	SFPQ

Showing 1 to 10 of 16 entries

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

UPF2

General Information

Functions

Localization(RBPImage: UPF2)

Domains (AlphaFold: UPF2)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

eCLIP assay for UPF2 is not avaliable on ENCORE database.

25 proteins are bound to UPF2 RNA:

eCLIP assay for UPF2 is not avaliable on ENCORE database.

Diffrential Expression

3,413 differentially expressed genes after Knockdown/Knockout UPF2 protein :

57 RBPs can affect the gene expression of UPF2 :

The Knockdown/knockout RNA-Seq assay for UPF2 is not available on ENCORE database.

4 RBPs can affect the splicing of UPF2 :

The Knockdown/knockout RNA-Seq assay for UPF2 is not avaliable on ENCORE database.