U2AF2

General Information

Gene Name : U2AF2
Gene ID : ENSG00000063244.12
Essential Gene : Yes

Functions

Splicing regulation
Spliceosome
RNA export

Localization(RBPImage: U2AF2)

Nuclei
Nucleoplasm
Mutually Exclusive from Nucleolus
Speckles
Variable Nuclear Intensity
Cytoplasm
Cytosolic
Nuclear release mitosis

Domains (AlphaFold: U2AF2)

RRM

Antibody Validation

Bethyl Labs: A303-665A

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	U2AF2	ENSG00000063244.12	32.15	95.91	64.03	ENCSR000AEF
HepG2	U2AF2	ENSG00000063244.12	193.07	83.49	138.28	ENCSR985KAT
K562	U2AF2	ENSG00000063244.12	161.74	113.78	137.76	ENCSR000AEO

Assays

5 Released experiments are available on ENCORE database.

Assay Type	Exp_Name	ENCODE ID	Target label	Biosample	Status	Linked Antibody	Controls	Method	Note
eCLIP	eCLIP: 242	ENCSR893RAV	U2AF2	K562	Released	ENCAB511TCT	ENCSR871RTL
eCLIP	eCLIP: 272	ENCSR202BFN	U2AF2	HepG2	Released	ENCAB511TCT	ENCSR049GND
knockdown followed by RNA-seq	U2AF2-BGKLV08-K562	ENCSR904CJQ	U2AF2	K562	Released		ENCSR344XID	shRNA	KD% = 80.7,85.4
knockdown followed by RNA-seq	U2AF2-BGHLV14-HepG2	ENCSR622MCX	U2AF2	HepG2	Released		ENCSR491FOC	shRNA	KD% = 77.8,63.4
knockdown followed by RNA-seq	U2AF2-BGHLV26-HepG2	ENCSR426UUG	U2AF2	HepG2	Released		ENCSR104ABF	shRNA	KD% = 90.7,93.5

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
U2AF2	242	K562	ENCSR893RAV	ENCSR871RTL	ENCAB511TCT	A303-665A	1	Released	ENCODE3
U2AF2	272	HepG2	ENCSR202BFN	ENCSR049GND	ENCAB511TCT	A303-665A	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
U2AF2	ENCAB511TCT	A303-665A	1		Released, ENCODE3	Released, ENCODE3	BGHLV14-65, Released, ENCODE3	BGKLV08-63, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
U2AF2	K562	shRNA	ENCSR904CJQ	ENCSR344XID	U2AF2-LV08-63,U2AF2-LV08-64	Nontarget-LV08-1_00003531,nontarget-LV08-2_00003531	80.7,85.4	Released	ENCODE3
U2AF2	HepG2	shRNA			BGHLV12-91,BGHLV12-92	BGHLV12-1,BGHLV12-2		NotSatisfied	ENCODE3
U2AF2	HepG2	shRNA	ENCSR622MCX	ENCSR491FOC	U2AF2_BGHLV14-65,U2AF2_BGHLV14-66	NT_BGHLV14-1,NT_BGHLV14-2	77.8,63.4	Released	ENCODE3
U2AF2	HepG2	shRNA	ENCSR426UUG	ENCSR104ABF	U2AF2_BGHLV26_63,U2AF2_BGHLV26_64	non-target_BGHLV26-1,non-target_BGHLV26-2	90.7,93.5	Released	ENCODE3

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

U2AF2: Click to RBP Image Database

Nuclei

Nucleoplasm

Mutually Exclusive from Nucleolus

Speckles

Variable Nuclear Intensity

Cytoplasm

Cytosolic

Nuclear release mitosis

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
U2AF2	Product_ID: A303-665A Lot_ID: 1 Source: Bethyl Labs Target Name: U2AF2-human

RNA Targets

U2AF2 protein binds to 14,077 RNA regions.

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Proteins bound to RNA

U2AF2 RNA is bound by 60 proteins.

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U2AF2 protein has 14,077 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
U2AF2	chr17	57917100	57917126	+	4.76371	73.56141	HepG2	VMP1	intron-Proximal
U2AF2	chr16	87397299	87397341	-	4.93830	46.51930	HepG2	FBXO31	intron-Distal
U2AF2	chr2	190647572	190647648	-	4.10912	45.74912	HepG2	ORMDL1	5'-UTR,intron-Distal,intron-Proximal
U2AF2	chr22	45726464	45726536	+	5.74546	32.67939	K562	FAM118A	5'-UTR,CDS,intron-Proximal
U2AF2	chr22	29192339	29192398	-	3.88509	30.39039	HepG2	XBP1	intron-Distal
U2AF2	chr20	61299564	61299635	+	4.49349	28.31712	HepG2	SLCO4A1	3'-UTR,intron-Distal,intron-Proximal
U2AF2	chr3	42671616	42671662	+	4.67788	24.18603	HepG2	NKTR	intron-Distal
U2AF2	chr6	4064868	4064918	+	4.44481	19.62278	HepG2	PRPF4B	3'-UTR,intron-Distal
U2AF2	chr8	30567379	30567430	-	5.29944	18.56966	HepG2	GSR	3'-UTR,CDS,intron-Distal,intron-Proximal
U2AF2	chr20	34329985	34329993	-	3.79734	17.22032	K562	RBM39	5'-UTR,intron-Distal,intron-Proximal

Showing 1 to 10 of 100 entries

60 proteins are bound to U2AF2 RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr19	56181842	56181913	+	intron-Distal	7.50562	400.00000	K562	PCBP1
chr19	56181850	56181883	+	intron-Distal	5.41965	400.00000	HepG2	DROSHA
chr19	56172575	56172674	+	intron-Distal,intron-Proximal	6.93472	400.00000	HepG2	PCBP2
chr19	56172717	56172815	+	intron-Distal	6.49140	400.00000	HepG2	PCBP2
chr19	56181842	56181914	+	intron-Distal	4.61390	400.00000	K562	DROSHA
chr19	56181782	56181840	+	intron-Distal	6.70189	400.00000	HepG2	RBFOX2
chr19	56173054	56173108	+	intron-Distal,intron-Proximal	6.16650	400.00000	HepG2	DDX59
chr19	56181841	56181850	+	intron-Distal	5.37400	400.00000	HepG2	DROSHA
chr19	56181789	56181840	+	intron-Distal	5.14393	400.00000	K562	MTPAP
chr19	56181789	56181842	+	intron-Distal	7.73938	400.00000	K562	PCBP1
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 394 entries

The U2AF2 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
U2AF2	chr19	56173841	56173903	+	4.12491	15.96646	HepG2	U2AF2	5'-UTR,CDS,intron-Proximal
U2AF2	chr19	56173136	56173177	+	3.58567	7.15738	HepG2	U2AF2	3'-UTR,5'-UTR,intron-Distal,intron-Proximal

Showing 1 to 2 of 2 entries

Diffrential Expression

8,048 differentially expressed genes after Knockdown/Knockout U2AF2 protein.

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93 RBPs can affect the levels of U2AF2.

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8,048 differentially expressed genes after Knockdown/Knockout U2AF2 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
TNFRSF12A	ENSG00000006327.9	1108.19290	124.60240	3.15270	19.91980	17.10360	HepG2	U2AF2
DEPDC1	ENSG00000024526.12	115.14140	1051.34140	-3.19080	17.69780	15.06300	HepG2	U2AF2
PHLDB1	ENSG00000019144.12	1992.58090	395.72380	2.33200	13.49100	11.23580	HepG2	U2AF2
GPRC5A	ENSG00000013588.5	312.20990	42.59280	2.87370	12.81570	10.60760	HepG2	U2AF2
CD74	ENSG00000019582.10	3707.39190	1049.95980	1.82000	9.24640	7.32870	HepG2	U2AF2
NCAPD2	ENSG00000010292.8	581.35570	2640.12760	-2.18310	9.14610	7.24350	HepG2	U2AF2
POLA2	ENSG00000014138.4	47.92800	247.29610	-2.36730	8.87970	7.01240	HepG2	U2AF2
DPM1	ENSG00000000419.8	684.84000	2289.37420	-1.74110	8.26210	6.47280	HepG2	U2AF2
IDS	ENSG00000010404.13	2719.02260	868.10890	1.64700	7.68860	5.95760	HepG2	U2AF2
TACC3	ENSG00000013810.14	315.06790	1576.74670	-2.32320	7.42110	5.72440	HepG2	U2AF2
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".

93 RBPs can affect the gene expression of U2AF2 :

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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
U2AF2	ENSG00000063244.8	7200.82020	4223.68870	0.76960	35.47280	33.50550	K562	AGGF1
U2AF2	ENSG00000063244.8	6166.43540	2938.73850	1.06910	25.05860	23.10860	HepG2	U2AF1
U2AF2	ENSG00000063244.8	7054.97860	4246.77050	0.73220	22.23610	20.48600	K562	RBM15
U2AF2	ENSG00000063244.8	4321.16140	2980.86590	0.53560	21.74640	20.40710	HepG2	PUM1
U2AF2	ENSG00000063244.8	8356.56800	4358.29340	0.93900	20.70730	19.25340	K562	PUS1
U2AF2	ENSG00000063244.8	1269.37260	3411.30470	-1.42620	20.03850	18.00270	HepG2	SNRNP70
U2AF2	ENSG00000063244.8	4275.31570	2301.91100	0.89310	17.57300	15.96990	HepG2	HNRNPK
U2AF2	ENSG00000063244.8	455.78470	1543.55960	-1.75980	17.21210	15.15890	K562	U2AF2
U2AF2	ENSG00000063244.8	5058.72430	3417.33150	0.56580	14.99580	13.70000	K562	FXR1
U2AF2	ENSG00000063244.8	413.70110	1542.87260	-1.89900	13.74210	11.91050	K562	G3BP2
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 119 entries

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

9,621 alternative splicing events after Knockdown/Knockout U2AF2 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	RP11-566K11.7	ENSG00000267048.1	chr16	+	89973412	89973496	89972564	89972692	89973650	89973730	0.14500	0.00000	included	HepG2	U2AF2
SE	FNDC3B	ENSG00000075420.8	chr3	+	171979658	171979873	171969049	171969331	172003715	172003774	0.05800	0.00013	included	HepG2	U2AF2
SE	ING5	ENSG00000168395.10	chr2	+	242663540	242663589	242662624	242662686	242664403	242668893	0.39000	0.00000	included	HepG2	U2AF2
SE	ILF3	ENSG00000129351.13	chr19	+	10798021	10798384	10794592	10794646	10799225	10799354	0.10900	0.00005	included	HepG2	U2AF2
SE	KTN1	ENSG00000126777.13	chr14	+	56130672	56130759	56128239	56128330	56133958	56134048	0.37700	0.00000	included	HepG2	U2AF2
SE	PUM2	ENSG00000055917.11	chr2	-	20478343	20478580	20462953	20463221	20482707	20482992	0.29600	0.00000	included	HepG2	U2AF2
SE	LUC7L3	ENSG00000108848.11	chr17	+	48814647	48814840	48814320	48814387	48817666	48817706	0.23300	0.00000	included	HepG2	U2AF2
SE	SPRED2	ENSG00000198369.5	chr2	-	65571569	65571728	65561762	65561907	65571852	65571920	0.17400	0.00000	included	HepG2	U2AF2
SE	DDX18	ENSG00000088205.8	chr2	+	118580328	118580421	118579722	118579837	118582144	118582284	0.08300	0.00000	included	HepG2	U2AF2
SE	TBCEL	ENSG00000154114.8	chr11	+	120943693	120943749	120930677	120930794	120957486	120957648	0.27600	0.00012	included	HepG2	U2AF2

Showing 1 to 10 of 100 entries

4 RBPs can affect the splicing of U2AF2 :

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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
SE	U2AF2	ENSG00000063244.8	chr19	+	56173136	56173196	56172403	56172555	56173867	56173984	0.09900	0.00000	0.00000	included	K562	SF3B4
A5SS	U2AF2	ENSG00000063244.8	chr19	+	56174971	56175207	56174971	56175110	56179872	56179952	0.09300	0.00000	0.00000	longer	K562	AQR
A5SS	U2AF2	ENSG00000063244.8	chr19	+	56180448	56180547	56180448	56180535	56180809	56181058	0.16000	0.00000	0.00041	longer	HepG2	PCBP1
A3SS	U2AF2	ENSG00000063244.8	chr19	+	56180380	56180535	56180448	56180535	56180035	56180158	0.10200	0.00067	0.01923	longer	HepG2	U2AF2

Showing 1 to 4 of 4 entries

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

The U2AF2 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	Bound by RBP
A3SS	U2AF2	ENSG00000063244.8	chr19	+	56180380	56180535			56180448	56180535	56180035	56180158	0.10200	0.00067	0.01923	longer	HepG2	U2AF2

Showing 1 to 1 of 1 entries