U2AF1

General Information

Gene Name : U2AF1
Gene ID : ENSG00000160201.11
Essential Gene : Yes

Functions

Splicing regulation
Spliceosome

Localization(RBPImage: U2AF1)

Nuclei
Nucleoplasm
Mutually Exclusive from Nucleolus
Speckles
Nuclear release mitosis

Domains (AlphaFold: U2AF1)

RRM
ZNF

Antibody Validation

Bethyl Labs: A302-079A

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	U2AF1	ENSG00000160201.11	36.17	69.86	53.02	ENCSR000AEF
HepG2	U2AF1	ENSG00000160201.11	98.45	68.32	83.38	ENCSR985KAT
K562	U2AF1	ENSG00000160201.11	148.33	130.22	139.28	ENCSR000AEO

Assays

7 Released experiments are available on ENCORE database.

Assay Type	Exp_Name	ENCODE ID	Target label	Biosample	Status	Linked Antibody	Controls	Method	Note
eCLIP	eCLIP: 244	ENCSR862QCH	U2AF1	K562	Released	ENCAB298WVV	ENCSR482ZSE
eCLIP	eCLIP: 282	ENCSR328LLU	U2AF1	HepG2	Released	ENCAB298WVV	ENCSR941GJG
knockdown followed by RNA-seq	U2AF1-BGKLV08-K562	ENCSR342EDG	U2AF1	K562	Released		ENCSR344XID	shRNA	KD% = 52.7,63.7
knockdown followed by RNA-seq	U2AF1-BGHLV30-HepG2	ENCSR372UWV	U2AF1	HepG2	Released		ENCSR067GHD	shRNA	KD% = 72.5,76.1
knockdown followed by RNA-seq	U2AF1-BGRSLV02-RS293		U2AF1	Ribo-STAMP-293T	Released			shRNA	KD% = ,
knockdown followed by RNA-seq	U2AF1-BGRSDLV04-RSD293		U2AF1	Ribo-STAMP-293T	Released			shRNA	KD% =
knockdown followed by RNA-seq	U2AF1-BGRSDLV04-RSD293		U2AF1	Ribo-STAMP-293T	Released			shRNA	KD% = ,

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
U2AF1	244	K562	ENCSR862QCH	ENCSR482ZSE	ENCAB298WVV	A302-079A	1	Released	ENCODE3
U2AF1	282	HepG2	ENCSR328LLU	ENCSR941GJG	ENCAB298WVV	A302-079A	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
U2AF1	ENCAB298WVV	A302-079A	1		Released, ENCODE3	Released, ENCODE3	BGHLV30-55, Released, ENCODE3	BGKLV08-61, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
U2AF1	K562	shRNA	ENCSR342EDG	ENCSR344XID	U2AF1-LV08-61,U2AF1-LV08-62	Nontarget-LV08-1_00003531,nontarget-LV08-2_00003531	52.7,63.7	Released	ENCODE3
U2AF1	HepG2	shRNA			BGHLV12-89,BGHLV12-90	BGHLV12-1,BGHLV12-2		NotSatisfied	ENCODE3
U2AF1	HepG2	shRNA			BGHLV14-63,BGHLV14-64	BGHLV14-1,BGHLV14-2	33.5,36.7	NotSatisfied	ENCODE3
U2AF1	HepG2	shRNA			BGHLV26-61,BGHLV26-62	BGHLV26-1,BGHLV26-2	redo transfection,redo transfection	NotSatisfied	ENCODE3
U2AF1	HepG2	shRNA	ENCSR372UWV	ENCSR067GHD	U2AF1_BGHLV30-55,U2AF1_BGHLV30-56	NT_BGHLV30-1,NT_BGHLV30-2	72.5,76.1	Released	ENCODE3
U2AF1	Ribo-STAMP-293T	shRNA			BGRSLV01-19,BGRSLV01-20	BGRSLV01-1,BGRSLV01-2		NotSatisfied	ENCORE2
U2AF1	Ribo-STAMP-293T	shRNA			U2AF1-BGRSLV02-17,U2AF1-BGRSLV02-18	NT-BGRSLV02-1,NT-BGRSLV02-2	,	Released	ENCORE2
U2AF1	Ribo-STAMP-293T	shRNA			BGRSDLV03-37,BGRSDLV03-38	BGRSDLV03-1,BGRSDLV03-2		NotSatisfied	ENCORE2
U2AF1	Ribo-STAMP-293T	shRNA			BGRSDLV03-39dox,BGRSDLV03-40dox	BGRSDLV03-1,BGRSDLV03-2		NotSatisfied	ENCORE2
U2AF1	Ribo-STAMP-293T	shRNA			BGRSDLV04-5,BGRSDLV04-6	BGRSDLV04-1,BGRSDLV04-2		Released	ENCORE2
U2AF1	Ribo-STAMP-293T	shRNA			U2AF1-BGRSDLV04-7dox,U2AF1-BGRSDLV04-8dox	NT-BGRSDLV04-3dox,NT-BGRSDLV04-4dox	,	Released	ENCORE2

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

U2AF1: Click to RBP Image Database

Nuclei

Nucleoplasm

Mutually Exclusive from Nucleolus

Speckles

Nuclear release mitosis

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
U2AF1	Product_ID: A302-079A Lot_ID: 1 Source: Bethyl Labs Target Name: U2AF1-human

RNA Targets

U2AF1 protein binds to 2,202 RNA regions.

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Proteins bound to RNA

U2AF1 RNA is bound by 46 proteins.

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U2AF1 protein has 2,202 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
U2AF1	chr6	32944017	32944067	+	4.88273	50.79940	K562	BRD2	3'-UTR,CDS,intron-Proximal
U2AF1	chr17	57915647	57915675	+	4.08616	44.99255	HepG2	VMP1	3'-UTR,CDS,intron-Proximal
U2AF1	chr9	86585785	86585835	-	6.06503	41.99315	K562	HNRNPK	CDS,intron-Distal,intron-Proximal
U2AF1	chr11	64540940	64540988	-	4.32704	40.77734	K562	SF1	3'-UTR,CDS,intron-Distal,intron-Proximal
U2AF1	chr19	54972422	54972519	+	4.09093	36.87222	HepG2	LENG8	3'-UTR,CDS
U2AF1	chr19	54972298	54972340	+	3.98181	34.86192	K562	LENG8	3'-UTR,intron-Distal,intron-Proximal
U2AF1	chr1	155884099	155884158	-	4.28875	29.33975	K562	KIAA0907	3'-UTR,CDS,intron-Distal
U2AF1	chr4	83276084	83276152	-	4.80856	28.75043	HepG2	HNRNPD	3'-UTR,intron-Distal,intron-Proximal
U2AF1	chr12	69652348	69652376	+	5.23056	28.68379	K562	CPSF6	CDS,intron-Distal,intron-Proximal
U2AF1	chr17	57915596	57915735	+	3.74564	28.40416	K562	VMP1	3'-UTR,CDS,intron-Proximal

Showing 1 to 10 of 100 entries

46 proteins are bound to U2AF1 RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr21	44527434	44527535	-	intron-Distal	4.89125	56.68102	HepG2	EFTUD2
chr21	44524472	44524478	-	5'-UTR,CDS,intron-Distal	4.06929	46.17985	K562	YBX3
chr21	44524478	44524485	-	5'-UTR,CDS,intron-Distal	3.93999	45.91600	K562	YBX3
chr21	44527559	44527614	-	5'-UTR,CDS,intron-Distal	3.68676	43.99238	K562	DDX3X
chr21	44527359	44527409	-	intron-Distal	7.00732	43.57126	HepG2	EFTUD2
chr21	44524485	44524497	-	5'-UTR,CDS,intron-Distal	4.02683	43.39424	K562	YBX3
chr21	44515495	44515591	-	3'-UTR,CDS,intron-Distal,intron-Proximal	4.37045	35.13596	HepG2	PRPF8
chr21	44515569	44515646	-	3'-UTR,CDS,intron-Distal	3.22422	30.76319	K562	UCHL5
chr21	44524433	44524469	-	5'-UTR,CDS,intron-Distal	3.27548	29.59258	K562	YBX3
chr21	44515545	44515569	-	3'-UTR,CDS,intron-Distal,intron-Proximal	3.43407	28.35931	K562	UCHL5
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 132 entries

The U2AF1 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
U2AF1	chr21	44525911	44525965	-	3.71677	7.61895	K562	U2AF1	intron-Distal
U2AF1	chr21	44513322	44513374	-	4.08062	4.16151	HepG2	U2AF1	3'-UTR,CDS,intron-Distal
U2AF1	chr21	44521020	44521058	-	3.95429	3.07225	K562	U2AF1	intron-Distal

Showing 1 to 3 of 3 entries

Diffrential Expression

9,642 differentially expressed genes after Knockdown/Knockout U2AF1 protein.

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75 RBPs can affect the levels of U2AF1.

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9,642 differentially expressed genes after Knockdown/Knockout U2AF1 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
CDK11A	ENSG00000008128.18	2272.42180	989.68600	1.19910	24.74610	22.81180	HepG2	U2AF1
SLC7A2	ENSG00000003989.12	2907.84500	5636.67470	-0.95490	20.32030	18.56170	HepG2	U2AF1
CREBBP	ENSG00000005339.8	5231.87790	2705.25520	0.95150	19.83300	18.10430	HepG2	U2AF1
MAP3K9	ENSG00000006432.11	1411.45870	635.42130	1.15130	18.82570	17.13200	HepG2	U2AF1
REV3L	ENSG00000009413.11	2762.82600	1418.76720	0.96140	18.47990	16.80200	HepG2	U2AF1
PIGQ	ENSG00000007541.10	104.10870	334.59160	-1.68430	16.35630	14.77890	HepG2	U2AF1
CROT	ENSG00000005469.7	461.60510	164.92770	1.48470	16.31120	14.73790	HepG2	U2AF1
SYNRG	ENSG00000006114.11	1502.10530	789.52450	0.92780	14.21000	12.75030	HepG2	U2AF1
SKAP2	ENSG00000005020.8	1147.17510	522.78090	1.13370	14.16440	12.70830	HepG2	U2AF1
DBNDD1	ENSG00000003249.9	620.72050	1220.43390	-0.97540	14.05410	12.60270	HepG2	U2AF1
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".

75 RBPs can affect the gene expression of U2AF1 :

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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
U2AF1	ENSG00000160201.7	735.94380	1723.45140	-1.22760	23.66090	21.75680	HepG2	U2AF1
U2AF1	ENSG00000160201.7	2253.36470	3793.89100	-0.75160	15.73960	14.40020	K562	HNRNPC
U2AF1	ENSG00000160201.7	2202.93190	3167.97040	-0.52410	15.72100	14.20650	HepG2	DAZAP1
U2AF1	ENSG00000160201.7	6621.34800	4919.15280	0.42860	11.91180	10.82560	K562	AGGF1
U2AF1	ENSG00000160201.7	2151.16050	3946.84290	-0.87560	12.86830	10.30140	K562	U2AF1
U2AF1	ENSG00000160201.7	7962.75160	5075.95200	0.64950	10.74910	9.72620	K562	PUS1
U2AF1	ENSG00000160201.7	11862.92740	7791.68030	0.60640	10.39810	9.37050	K562	AQR
U2AF1	ENSG00000160201.7	1978.11030	2998.79680	-0.60030	9.19480	8.19460	HepG2	PUF60
U2AF1	ENSG00000160201.7	1872.50930	2994.13590	-0.67720	9.67210	8.18980	HepG2	EIF4G2
U2AF1	ENSG00000160201.7	1056.87880	1801.28670	-0.76920	8.94440	7.83730	HepG2	GPKOW
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 89 entries

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

7,745 alternative splicing events after Knockdown/Knockout U2AF1 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	RP11-302B13.5	ENSG00000272822.1	chr12	-	49349880	49349980	49334730	49334971	49351092	49351148	0.26000	0.00000	included	HepG2	U2AF1
SE	RPS24	ENSG00000138326.14	chr10	+	79799961	79799983	79796951	79797062	79800372	79800455	0.46500	0.00000	included	HepG2	U2AF1
SE	TMEM242	ENSG00000215712.6	chr6	-	157738961	157739045	157710417	157714031	157739813	157739951	0.29000	0.00000	included	HepG2	U2AF1
SE	GSE1	ENSG00000131149.13	chr16	+	85691380	85691528	85691009	85691210	85694751	85695371	0.30400	0.00019	included	HepG2	U2AF1
SE	EPB41L2	ENSG00000079819.12	chr6	-	131197813	131197915	131190798	131191266	131199243	131199390	0.57100	0.00000	included	HepG2	U2AF1
SE	ING5	ENSG00000168395.10	chr2	+	242663540	242663589	242662624	242662686	242664403	242668893	0.25900	0.00000	included	HepG2	U2AF1
SE	TMEM59	ENSG00000116209.7	chr1	-	54514322	54514355	54512939	54513045	54519028	54519085	0.85800	0.00000	included	HepG2	U2AF1
SE	SPRED2	ENSG00000198369.5	chr2	-	65571569	65571728	65561762	65561907	65571852	65571920	0.17000	0.00001	included	HepG2	U2AF1
SE	METAP1	ENSG00000164024.7	chr4	+	99952658	99952813	99950017	99950069	99955380	99955425	0.09000	0.00001	included	HepG2	U2AF1
SE	DDX18	ENSG00000088205.8	chr2	+	118580328	118580421	118579722	118579837	118582144	118582284	0.63400	0.00000	included	HepG2	U2AF1

Showing 1 to 10 of 100 entries

57 RBPs can affect the splicing of U2AF1 :

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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	U2AF1	ENSG00000160201.7	chr21	-	44520562	44520629	44515803	44515853	44521475	44521542	0.25200	0.00000	included	K562	SRSF1
SE	U2AF1	ENSG00000160201.7	chr21	-	44521475	44521542	44520562	44520629	44524424	44524512	0.27400	0.00000	included	HepG2	HNRNPK
SE	U2AF1	ENSG00000160201.7	chr21	-	44521475	44521542	44520562	44520629	44524424	44524512	-0.13200	0.00088	excluded	HepG2	DDX59
SE	U2AF1	ENSG00000160201.7	chr21	-	44526837	44526937	44524424	44524512	44527560	44527680	0.08800	0.00000	included	HepG2	U2AF2
SE	U2AF1	ENSG00000160201.7	chr21	-	44521475	44521542	44520562	44520629	44524424	44524512	0.25100	0.00000	included	HepG2	U2AF2
SE	U2AF1	ENSG00000160201.7	chr21	-	44520562	44520629	44515803	44515853	44524424	44524531	-0.11000	0.00000	excluded	K562	AQR
SE	U2AF1	ENSG00000160201.7	chr21	-	44515547	44515673	44514776	44514898	44515803	44515874	-0.06100	0.00000	excluded	K562	AQR
SE	U2AF1	ENSG00000160201.7	chr21	-	44520562	44520629	44515803	44515853	44521475	44521542	-0.16400	0.00000	excluded	K562	PUS1
SE	U2AF1	ENSG00000160201.7	chr21	-	44520562	44520629	44515803	44515853	44521475	44521542	0.18600	0.00000	included	HepG2	EFTUD2
SE	U2AF1	ENSG00000160201.7	chr21	-	44521475	44521542	44520562	44520629	44524424	44524512	0.43400	0.00000	included	K562	U2AF1

Showing 1 to 10 of 240 entries

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

The U2AF1 protein affects to its own RNA splicing after knockdown/knockout.

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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	U2AF1	ENSG00000160201.7	chr21	-	44521475	44521542			44520562	44520629	44524424	44524512	0.43400	0.00000	0.00000	included	K562	U2AF1
SE	U2AF1	ENSG00000160201.7	chr21	-	44520562	44520629			44515803	44515853	44524424	44525362	-0.09900	0.00000	0.00000	excluded	K562	U2AF1
A5SS	U2AF1	ENSG00000160201.7	chr21	-	44520562	44524512			44524424	44524512	44515803	44515853	-0.14900	0.00000	0.00000	shorter	K562	U2AF1
RI	U2AF1	ENSG00000160201.7	chr21	-	44520562	44524512			44520562	44520629	44524424	44524512	0.54400	0.00000	0.00000	included	K562	U2AF1
RI	U2AF1	ENSG00000160201.7	chr21	-	44513065	44514673			44513065	44513359	44514580	44514673	0.41000	0.00000	0.00000	included	K562	U2AF1
MXE	U2AF1	ENSG00000160201.7	chr21	-	44520562	44520650	44521475	44521542	44515803	44515853	44524424	44524512	0.26800	0.00000	0.00000	1included	K562	U2AF1
MXE	U2AF1	ENSG00000160201.7	chr21	-	44520562	44520629	44524424	44524512	44515803	44515853	44527560	44527688	0.21200	0.00000	0.00001	1included	K562	U2AF1
MXE	U2AF1	ENSG00000160201.7	chr21	-	44520562	44520629	44521475	44521542	44515803	44515853	44524424	44524512	0.32100	0.00000	0.00000	1included	K562	U2AF1
SE	U2AF1	ENSG00000160201.7	chr21	-	44521475	44521542			44520562	44520629	44524424	44524531	0.21700	0.00001	0.00049	included	HepG2	U2AF1
RI	U2AF1	ENSG00000160201.7	chr21	-	44520562	44524512			44520562	44520629	44524424	44524512	0.08700	0.00006	0.00106	included	HepG2	U2AF1

Showing 1 to 10 of 11 entries