SAFB2

General Information

Gene Name : SAFB2
Gene ID : ENSG00000130254.11
Essential Gene : No

Functions

Novel RBP

Localization(RBPImage: SAFB2)

Nuclei
Nucleoplasm
Mutually Exclusive from Nucleolus
Speckles
Cytoplasm
Nuclear release mitosis

Domains (AlphaFold: SAFB2)

RRM

Antibody Validation

Bethyl Labs: A301-112A

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	SAFB2	ENSG00000130254.11	33.60	33.78	33.69	ENCSR000AEF
HepG2	SAFB2	ENSG00000130254.11	48.48	41.47	44.97	ENCSR985KAT
K562	SAFB2	ENSG00000130254.11	30.56	36.87	33.71	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: 267	ENCSR943MHU	SAFB2	K562	Released	ENCAB303CHK	ENCSR978JXM
knockdown followed by RNA-seq	SAFB2-BGKLV24-K562	ENCSR770LYW	SAFB2	K562	Released		ENCSR154OBA	shRNA	KD% = 60.1,68.9
knockdown followed by RNA-seq	SAFB2-BGHLV20-HepG2	ENCSR110ZYD	SAFB2	HepG2	Released		ENCSR305XWT	shRNA	KD% = 71.0,73.8
RNA Bind-n-Seq	RBNS: SAFB2	ENCSR558RBK	SAFB2	cell-free sample	Released		ENCSR537ATS

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
SAFB2	267	K562	ENCSR943MHU	ENCSR978JXM	ENCAB303CHK	A301-112A	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
SAFB2	ENCAB303CHK	A301-112A	1			Released, ENCODE3	BGHLV20-53, Released, ENCODE3	BGKLV24-51, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
SAFB2	K562	shRNA	ENCSR770LYW	ENCSR154OBA	SAFB2_BGKLV24-51C,SAFB2_BGKLV24-52C	NT_BGKLV24-1C,NT_BGKLV24-2C	60.1,68.9	Released	ENCODE3
SAFB2	HepG2	shRNA			BGHLV16-49,BGHLV16-50	BGHLV16-1,BGHLV16-2		NotSatisfied	ENCODE3
SAFB2	HepG2	shRNA			BGHLV17-27,BGHLV17-28	BGHLV17-1,BGHLV17-2		NotSatisfied	ENCODE3
SAFB2	HepG2	shRNA	ENCSR110ZYD	ENCSR305XWT	SAFB2-57-BGHLV20-53_17734,SAFB2-57-BGHLV20-54_17735	non-target-BGHLV20-1_17706,non-target-BGHLV20-2_17707	71.0,73.8	Released	ENCODE3

RNA Bind-n-Seqn

GeneName	gene_aliases	Status	Project	Note
SAFB2	SAFB2		Released	ENCODE4

Localization Image in HepG2

SAFB2: Click to RBP Image Database

Nuclei

Nucleoplasm

Mutually Exclusive from Nucleolus

Speckles

Cytoplasm

Nuclear release mitosis

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SAFB2	Product_ID: A301-112A Lot_ID: 1 Source: Bethyl Labs Target Name: SAFB2-human

RNA Targets

SAFB2 protein binds to 3,582 RNA regions.

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The binding motifs of SAFB2

Proteins bound to RNA

SAFB2 RNA is bound by 34 proteins.

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SAFB2 protein has 3,582 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
SAFB2	chr18	75689466	75689518	-	4.72326	30.29418	K562	LINC01029	intron-Distal
SAFB2	chr16	23949171	23949284	+	6.20813	20.91332	K562	PRKCB	intron-Distal
SAFB2	chr7	119346607	119346624	-	4.29892	19.54407	K562	RP11-328J2.1	intron-Distal
SAFB2	chr8	91493630	91493785	+	4.99508	17.28254	K562	LINC00534	intron-Distal
SAFB2	chr7	119437139	119437239	-	3.51780	17.00979	K562	RP11-328J2.1	intron-Distal
SAFB2	chr7	119526255	119526341	-	5.82424	16.21225	K562	RP11-328J2.1	intron-Distal
SAFB2	chr3	37368461	37368580	+	3.79273	14.69396	K562	GOLGA4	CDS,intron-Distal
SAFB2	chr7	76224730	76224794	+	4.69308	12.61905	K562	UPK3B, AC004980.7	intron-Distal
SAFB2	chr22	17535451	17535542	+	4.08598	11.58826	K562	CECR7	intron-Distal
SAFB2	chr10	49560479	49560574	+	5.16183	10.39744	K562	MAPK8	intron-Distal

Showing 1 to 10 of 100 entries

34 proteins are bound to SAFB2 RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr19	5610590	5610651	-	5'-UTR,CDS,intron-Distal,intron-Proximal	4.15790	39.19838	K562	AQR
chr19	5598801	5598867	-	3'-UTR,CDS,intron-Distal,intron-Proximal	7.17902	36.74259	K562	UCHL5
chr19	5595328	5595358	-	intron-Distal,intron-Proximal	5.41128	36.59993	K562	AQR
chr19	5610121	5610156	-	intron-Distal,intron-Proximal	4.24899	33.64390	K562	SF3B4
chr19	5600163	5600256	-	3'-UTR,CDS,intron-Distal,intron-Proximal	4.48854	33.31082	K562	UCHL5
chr19	5610064	5610121	-	5'-UTR,CDS,intron-Distal,intron-Proximal	4.26104	31.81936	K562	SF3B4
chr19	5591662	5591722	-	intron-Distal,intron-Proximal	5.45154	31.35979	K562	AQR
chr19	5591747	5591763	-	CDS,intron-Distal,intron-Proximal	4.38650	28.57710	K562	AQR
chr19	5594065	5594144	-	CDS,intron-Distal	4.91330	28.35922	K562	UCHL5
chr19	5591722	5591743	-	intron-Distal,intron-Proximal	4.49211	28.23402	K562	AQR
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 232 entries

No autoregularoty interactions between protein SAFB2 and its RNA.

Diffrential Expression

6,729 differentially expressed genes after Knockdown/Knockout SAFB2 protein.

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92 RBPs can affect the levels of SAFB2.

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6,729 differentially expressed genes after Knockdown/Knockout SAFB2 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
RPS20	ENSG00000008988.5	7593.48690	3943.39350	0.94520	28.32550	26.57450	HepG2	SAFB2
MLXIPL	ENSG00000009950.11	2350.64900	1166.97200	1.01020	26.91130	25.19260	HepG2	SAFB2
CCDC124	ENSG00000007080.6	335.47610	105.58690	1.66770	22.71350	21.11160	HepG2	SAFB2
VTA1	ENSG00000009844.11	1009.42610	1688.93320	-0.74260	20.58370	19.05550	HepG2	SAFB2
LASP1	ENSG00000002834.13	4207.98950	6015.87340	-0.51560	18.77390	17.31640	HepG2	SAFB2
TSPAN6	ENSG00000000003.10	1091.44920	1716.08070	-0.65290	16.53950	15.16050	HepG2	SAFB2
UPF1	ENSG00000005007.8	1652.90020	1053.46870	0.64980	16.16290	14.79880	HepG2	SAFB2
MASP2	ENSG00000009724.12	241.50210	83.17340	1.53770	14.99110	13.67350	HepG2	SAFB2
CD99	ENSG00000002586.13	2207.88130	1504.36800	0.55340	14.30210	13.00810	HepG2	SAFB2
PAFAH1B1	ENSG00000007168.8	1078.66170	1641.64100	-0.60590	14.15280	12.86480	HepG2	SAFB2
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".

92 RBPs can affect the gene expression of SAFB2 :

Show entries

Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
SAFB2	ENSG00000130254.7	5146.16330	3216.02780	0.67810	23.30660	21.60290	K562	DDX47
SAFB2	ENSG00000130254.7	2180.83810	1253.03780	0.79940	17.12040	15.07570	K562	U2AF2
SAFB2	ENSG00000130254.7	2416.32980	1286.36660	0.90940	16.23280	14.66410	HepG2	U2AF1
SAFB2	ENSG00000130254.7	1324.06030	636.49400	1.05660	14.18680	12.75230	HepG2	MAGOH
SAFB2	ENSG00000130254.7	1272.75650	639.99920	0.99170	11.85370	10.61310	HepG2	MATR3
SAFB2	ENSG00000130254.7	984.50020	599.03460	0.71670	11.14810	10.14120	HepG2	TAF15
SAFB2	ENSG00000130254.7	1167.43660	1844.21660	-0.65970	11.56530	9.99740	HepG2	RBM15
SAFB2	ENSG00000130254.7	1786.68520	1169.88030	0.61080	10.95820	9.85900	HepG2	SUCLG1
SAFB2	ENSG00000130254.7	1036.05670	666.36430	0.63660	10.30130	9.51740	HepG2	SRSF1
SAFB2	ENSG00000130254.7	3451.37120	2566.29520	0.42740	10.75240	9.21370	K562	WDR43
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 103 entries

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

4 alternative splicing events after Knockdown/Knockout SAFB2 protein :

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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	NSUN6	ENSG00000241058.1	chr10	-	18932497	18932569	18931404	18931484	18937418	18937574	0.07200	0.00000	0.00679	included	K562	SAFB2
SE	WNK1	ENSG00000060237.12	chr12	+	977031	978270	971248	971436	987377	987527	0.08700	0.00000	0.04575	included	K562	SAFB2
SE	RPS24	ENSG00000138326.14	chr10	+	79799961	79799983	79796951	79797062	79800372	79800455	0.09400	0.00000	0.00104	included	K562	SAFB2
SE	CRYBB2P1	ENSG00000100058.8	chr22	+	25851678	25851807	25844071	25844251	25853225	25853368	-0.38100	0.00001	0.08065	excluded	K562	SAFB2

Showing 1 to 4 of 4 entries

19 RBPs can affect the splicing of SAFB2 :

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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	SAFB2	ENSG00000130254.7	chr19	-	5616432	5616497	5616142	5616346	5621319	5621407	-0.12700	0.00002	excluded	K562	SF3B4
SE	SAFB2	ENSG00000130254.7	chr19	-	5611130	5611641	5610005	5610106	5612550	5612578	-0.50100	0.00000	excluded	K562	AKAP8L
SE	SAFB2	ENSG00000130254.7	chr19	-	5611882	5612024	5611130	5611641	5612550	5612652	0.08000	0.00000	included	K562	AQR
SE	SAFB2	ENSG00000130254.7	chr19	-	5611130	5611641	5610649	5610699	5612550	5612578	0.21000	0.00021	included	K562	FXR1
SE	SAFB2	ENSG00000130254.7	chr19	-	5610649	5610699	5610005	5610106	5612550	5612578	-0.60200	0.00000	excluded	K562	PUS1
SE	SAFB2	ENSG00000130254.7	chr19	-	5616432	5616497	5616142	5616346	5621319	5621407	-0.06000	0.00007	excluded	HepG2	SF3A3
SE	SAFB2	ENSG00000130254.7	chr19	-	5611130	5611641	5610005	5610106	5612550	5612578	-0.35500	0.00005	excluded	K562	UTP18
SE	SAFB2	ENSG00000130254.7	chr19	-	5610649	5610699	5610005	5610106	5612550	5612578	-0.59500	0.00000	excluded	K562	AGGF1
SE	SAFB2	ENSG00000130254.7	chr19	-	5616432	5616497	5616142	5616346	5621319	5621407	-0.06100	0.00012	excluded	K562	SF3B1
A3SS	SAFB2	ENSG00000130254.7	chr19	-	5595371	5595600	5595371	5595508	5598803	5599009	0.10700	0.00000	longer	K562	AQR

Showing 1 to 10 of 38 entries

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

SAFB2

General Information

Functions

Localization(RBPImage: SAFB2)

Domains (AlphaFold: SAFB2)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

SAFB2 protein has 3,582 RNA targets:

34 proteins are bound to SAFB2 RNA:

No autoregularoty interactions between protein SAFB2 and its RNA.

Diffrential Expression

6,729 differentially expressed genes after Knockdown/Knockout SAFB2 protein :

92 RBPs can affect the gene expression of SAFB2 :

4 alternative splicing events after Knockdown/Knockout SAFB2 protein :

19 RBPs can affect the splicing of SAFB2 :

No autoregularoty alternative splicing events between protein SAFB2 and its RNA.