UPF1

General Information

Gene Name : UPF1
Gene ID : ENSG00000005007.12
Essential Gene : Yes

Functions

RNA stability & decay
RNA export
Translation regulation

Localization(RBPImage: UPF1)

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

Domains (AlphaFold: UPF1)

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

Antibody Validation

View validation images for all UPF1 antibodies

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	UPF1	ENSG00000005007.12	16.53	22.79	19.66	ENCSR000AEF
HepG2	UPF1	ENSG00000005007.12	47.71	29.17	38.44	ENCSR985KAT
K562	UPF1	ENSG00000005007.12	35.45	31.70	33.58	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: 465	ENCSR456ASB	UPF1	K562	Released	ENCAB730BOO	ENCSR461LGW
eCLIP	eCLIP: 726	ENCSR539BEV	UPF1	HepG2	Released	ENCAB730BOO	ENCSR042RCU
knockdown followed by RNA-seq	UPF1-BGKLV34-K562	ENCSR251ABP	UPF1	K562	Released		ENCSR174OYC	shRNA	KD% = 66.6,53.2
knockdown followed by RNA-seq	UPF1-BGHLV33-HepG2	ENCSR689MIY	UPF1	HepG2	Released		ENCSR691IVR	shRNA	KD% = 51.6,67.3

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
UPF1	465	K562	ENCSR456ASB	ENCSR461LGW	ENCAB730BOO	RN108PW	1	Released	ENCODE3
UPF1	726	HepG2	ENCSR539BEV	ENCSR042RCU	ENCAB730BOO	RN108PW	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
UPF1	ENCAB730BOO	RN108PW	1		Released, ENCODE3	Released, ENCODE3	BGHLV33-33, Released, ENCODE3	BGKLV34-43, Released, ENCODE3
UPF1		12040S	3		Released, ENCODE3	Submitted, ENCORE2	BGHLV33-33, Released, ENCODE3	BGKLV34-43, Submitted, ENCORE2

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
UPF1	K562	shRNA	ENCSR251ABP	ENCSR174OYC	UPF1_BGKLV34-43,UPF1_BGKLV34-44	NT_BGKLV34-1,NT_BGKLV34-2	66.6,53.2	Released	ENCODE3
UPF1	K562	shRNA			BGKLV34-45,BGKLV34-46	BGKLV34-1,BGKLV34-2		NotSatisfied	ENCODE3
UPF1	HepG2	shRNA	ENCSR689MIY	ENCSR691IVR	UPF1_BGHLV33-33,UPF1_BGHLV33-34	NT_BGHLV33-1,NT_BGHLV33-2	51.6,67.3	Released	ENCODE3

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

UPF1: Click to RBP Image Database

Nuclei

Nucleoplasm

Mutually Exclusive from Nucleolus

Cytoplasm

Compartment/Organelle

Unknown Cyto Foci

Cytosolic

Mitotic-Apparatus (Spindle; Centrosomes)

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
UPF1	Product_ID: RN108PW Lot_ID: 1 Source: MBLI Target Name: UPF1-human
UPF1	Product_ID: 12040S Lot_ID: 3 Source: Cell Signaling Technology Target Name: UPF1-human

RNA Targets

UPF1 protein binds to 22,887 RNA regions.

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Proteins bound to RNA

UPF1 RNA is bound by 47 proteins.

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UPF1 protein has 22,887 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
UPF1	chr17	47126799	47126886	+	7.23833	400.00000	HepG2	IGF2BP1	3'-UTR,CDS
UPF1	chr17	38078083	38078152	-	6.69229	400.00000	HepG2	ORMDL3	3'-UTR,intron-Distal,intron-Proximal
UPF1	chr1	228286624	228286686	+	4.86100	400.00000	K562	ARF1	3'-UTR
UPF1	chr12	49414939	49415044	-	4.76313	80.84964	K562	KMT2D	3'-UTR,intron-Distal
UPF1	chr3	47893524	47893574	-	5.59380	73.19000	K562	MAP4	3'-UTR,intron-Distal,intron-Proximal
UPF1	chr11	118915174	118915240	-	4.56878	71.68546	K562	HYOU1	3'-UTR,intron-Distal
UPF1	chr1	12072249	12072356	+	6.70398	68.84366	K562	MFN2	3'-UTR
UPF1	chr4	1809190	1809227	+	5.69570	64.70038	HepG2	FGFR3	3'-UTR
UPF1	chr17	40732686	40732759	-	5.78033	57.23745	HepG2	FAM134C	3'-UTR,intron-Distal
UPF1	chr20	43954602	43954683	-	5.70090	57.00133	HepG2	SDC4	3'-UTR,intron-Distal

Showing 1 to 10 of 100 entries

47 proteins are bound to UPF1 RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr19	18977425	18977554	+	3'-UTR	5.00709	48.06247	K562	UPF1
chr19	18978292	18978371	+	3'-UTR	5.93917	43.54384	K562	UPF1
chr19	18978057	18978134	+	3'-UTR	5.71537	43.07891	K562	UPF1
chr19	18977670	18977715	+	3'-UTR	5.58906	41.87180	K562	UPF1
chr19	18963464	18963570	+	intron-Distal	6.87412	40.51599	HepG2	PCBP2
chr19	18977497	18977579	+	3'-UTR	6.23917	40.25634	HepG2	UPF1
chr19	18978875	18978945	+	3'-UTR	5.73941	36.73164	K562	UPF1
chr19	18977554	18977628	+	3'-UTR	6.30453	35.54329	K562	UPF1
chr19	18977430	18977497	+	3'-UTR	5.09138	33.45043	HepG2	UPF1
chr19	18977933	18977985	+	3'-UTR	4.83114	33.34254	K562	UPF1
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 260 entries

The UPF1 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
UPF1	chr19	18977425	18977554	+	5.00709	48.06247	K562	UPF1	3'-UTR
UPF1	chr19	18978292	18978371	+	5.93917	43.54384	K562	UPF1	3'-UTR
UPF1	chr19	18978057	18978134	+	5.71537	43.07891	K562	UPF1	3'-UTR
UPF1	chr19	18977670	18977715	+	5.58906	41.87180	K562	UPF1	3'-UTR
UPF1	chr19	18977497	18977579	+	6.23917	40.25634	HepG2	UPF1	3'-UTR
UPF1	chr19	18978875	18978945	+	5.73941	36.73164	K562	UPF1	3'-UTR
UPF1	chr19	18977554	18977628	+	6.30453	35.54329	K562	UPF1	3'-UTR
UPF1	chr19	18977430	18977497	+	5.09138	33.45043	HepG2	UPF1	3'-UTR
UPF1	chr19	18977933	18977985	+	4.83114	33.34254	K562	UPF1	3'-UTR
UPF1	chr19	18978749	18978812	+	4.06045	32.16511	K562	UPF1	3'-UTR

Showing 1 to 10 of 28 entries

Diffrential Expression

12,512 differentially expressed genes after Knockdown/Knockout UPF1 protein.

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107 RBPs can affect the levels of UPF1.

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12,512 differentially expressed genes after Knockdown/Knockout UPF1 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
GDE1	ENSG00000006007.7	4214.83180	1677.60850	1.32900	86.72740	84.09020	HepG2	UPF1
ANLN	ENSG00000011426.6	559.35700	2479.39560	-2.14810	70.91950	68.45840	HepG2	UPF1
NCAPD2	ENSG00000010292.8	1626.85730	3381.08380	-1.05540	51.88300	49.69900	HepG2	UPF1
RPS20	ENSG00000008988.5	3470.14870	6484.58390	-0.90200	49.73170	47.57930	HepG2	UPF1
CD99	ENSG00000002586.13	1475.05730	3022.55490	-1.03500	47.71690	45.58430	HepG2	UPF1
IL32	ENSG00000008517.12	4546.78380	2320.24370	0.97050	37.53340	35.57940	HepG2	UPF1
SCMH1	ENSG00000010803.12	1010.13080	1959.28030	-0.95580	33.15020	31.28980	HepG2	UPF1
RHBDD2	ENSG00000005486.12	1405.29180	676.77050	1.05400	32.88490	31.03480	HepG2	UPF1
TSPAN9	ENSG00000011105.7	2249.59230	1232.07650	0.86850	30.33570	28.54030	HepG2	UPF1
CSDE1	ENSG00000009307.11	8056.68920	11812.73770	-0.55210	22.41230	20.80070	HepG2	UPF1
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".

107 RBPs can affect the gene expression of UPF1 :

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Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
UPF1	ENSG00000005007.8	927.42580	4068.15410	-2.13310	185.73640	182.10690	K562	UPF1
UPF1	ENSG00000005007.8	2335.68440	1149.39480	1.02290	27.79760	26.51700	HepG2	TIAL1
UPF1	ENSG00000005007.8	1373.57960	2570.86650	-0.90430	25.81130	24.33030	HepG2	TAF15
UPF1	ENSG00000005007.8	2689.54260	1724.60620	0.64100	21.74610	20.14870	HepG2	SLBP
UPF1	ENSG00000005007.8	3363.86610	1746.16950	0.94580	20.82650	18.34340	K562	MAGOH
UPF1	ENSG00000005007.8	2789.54950	1909.32830	0.54690	17.66460	16.43320	HepG2	PUM1
UPF1	ENSG00000005007.8	1652.90020	1053.46870	0.64980	16.16290	14.79880	HepG2	SAFB2
UPF1	ENSG00000005007.8	2674.65450	1775.88750	0.59070	15.19710	13.89980	HepG2	SRSF5
UPF1	ENSG00000005007.8	3043.84670	1798.63490	0.75890	14.42520	13.20780	HepG2	PUF60
UPF1	ENSG00000005007.8	5042.61120	3315.33910	0.60490	14.07310	12.89600	K562	AGGF1
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 118 entries

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

436 alternative splicing events after Knockdown/Knockout UPF1 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	UBP1	ENSG00000153560.7	chr3	-	33450181	33450289	33444292	33444396	33450727	33450838	0.10200	0.00265	included	HepG2	UPF1
SE	ITGA6	ENSG00000091409.10	chr2	+	173366499	173366629	173362702	173362828	173368818	173369262	0.24100	0.00040	included	HepG2	UPF1
SE	PLOD2	ENSG00000152952.7	chr3	-	145795648	145795711	145794568	145794682	145796902	145797044	0.25700	0.00000	included	HepG2	UPF1
SE	SREK1	ENSG00000153914.11	chr5	+	65451892	65454760	65449290	65449424	65455046	65455162	0.26200	0.00003	included	HepG2	UPF1
SE	SPTAN1	ENSG00000197694.9	chr9	+	131355261	131355321	131353755	131353904	131356453	131356652	0.29300	0.00000	included	HepG2	UPF1
SE	PICALM	ENSG00000073921.13	chr11	-	85701292	85701442	85694908	85695016	85707868	85707972	0.23500	0.00000	included	HepG2	UPF1
SE	MACF1	ENSG00000127603.19	chr1	+	39946591	39946702	39945469	39945681	39950272	39950402	0.10900	0.00000	included	HepG2	UPF1
SE	BAZ2B	ENSG00000123636.13	chr2	-	160253584	160253611	160252279	160252345	160253855	160253900	0.42000	0.00112	included	HepG2	UPF1
SE	ARHGEF10L	ENSG00000074964.12	chr1	+	17961042	17961057	17958815	17958961	17961329	17961511	0.42400	0.00000	included	HepG2	UPF1
SE	LMO7	ENSG00000136153.15	chr13	+	76383289	76383319	76378362	76378677	76391296	76391414	0.16100	0.00156	included	HepG2	UPF1

Showing 1 to 10 of 100 entries

6 RBPs can affect the splicing of UPF1 :

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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	UPF1	ENSG00000005007.8	chr19	+	18974227	18974421	18974246	18974421	18972818	18972961	0.10300	0.00000	0.00000	longer	K562	AQR
A5SS	UPF1	ENSG00000005007.8	chr19	+	18963795	18963913	18963795	18963880	18964060	18964159	-0.21100	0.00000	0.00000	shorter	HepG2	SRSF1
A5SS	UPF1	ENSG00000005007.8	chr19	+	18963795	18963913	18963795	18963880	18964060	18964159	-0.14900	0.00000	0.00000	shorter	HepG2	SRSF7
A5SS	UPF1	ENSG00000005007.8	chr19	+	18963795	18963913	18963795	18963880	18964060	18964159	-0.12300	0.00000	0.00000	shorter	K562	SRSF1
RI	UPF1	ENSG00000005007.8	chr19	+	18976097	18976587	18976097	18976259	18976369	18976587	0.06400	0.00000	0.00000	included	K562	AQR
A5SS	UPF1	ENSG00000005007.8	chr19	+	18963795	18963913	18963795	18963880	18964060	18964159	-0.08400	0.00002	0.02077	shorter	K562	ZC3H8
A5SS	UPF1	ENSG00000005007.8	chr19	+	18963795	18963913	18963795	18963880	18964060	18964159	0.16800	0.00011	0.00952	longer	K562	U2AF2
A5SS	UPF1	ENSG00000005007.8	chr19	+	18963795	18963913	18963795	18963880	18964060	18964159	0.09100	0.00045	0.04468	longer	K562	UTP18
A5SS	UPF1	ENSG00000005007.8	chr19	+	18963795	18963913	18963795	18963880	18964060	18964159	0.15400	0.00167	0.05790	longer	HepG2	U2AF2

Showing 1 to 9 of 9 entries

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

UPF1

General Information

Functions

Localization(RBPImage: UPF1)

Domains (AlphaFold: UPF1)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

UPF1 protein has 22,887 RNA targets:

47 proteins are bound to UPF1 RNA:

The UPF1 protein binds to its own RNA.

Diffrential Expression

12,512 differentially expressed genes after Knockdown/Knockout UPF1 protein :

107 RBPs can affect the gene expression of UPF1 :

436 alternative splicing events after Knockdown/Knockout UPF1 protein :

6 RBPs can affect the splicing of UPF1 :

No autoregularoty alternative splicing events between protein UPF1 and its RNA.