PHF6

General Information

Gene Name : PHF6
Gene ID : ENSG00000156531.16
Essential Gene : No

Functions

Novel RBP

Localization(RBPImage: PHF6)

Nuclei
Nucleoplasm
Nucleolus
Cytoplasm
Cytosolic
Mitotic-Apparatus (Spindle; Centrosomes)

Domains (AlphaFold: PHF6)

ZNF

Antibody Validation

Bethyl Labs: A301-450A

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	PHF6	ENSG00000156531.16	27.71	24.99	26.35	ENCSR000AEF
HepG2	PHF6	ENSG00000156531.16	9.62	15.01	12.31	ENCSR985KAT
K562	PHF6	ENSG00000156531.16	34.75	41.81	38.28	ENCSR000AEO

Assays

3 Released experiments are available on ENCORE database.

Assay Type	Exp_Name	ENCODE ID	Target label	Biosample	Status	Linked Antibody	Controls	Method	Note
eCLIP	eCLIP: 680	ENCSR001KKZ	PHF6	K562	Released	ENCAB411AGR	ENCSR103HDM
knockdown followed by RNA-seq	PHF6-BGKLV21-K562	ENCSR322XVS	PHF6	K562	Released		ENCSR572FFX	shRNA	KD% = 62.2,62.0
knockdown followed by RNA-seq	PHF6-BGHLV18-HepG2	ENCSR681SMT	PHF6	HepG2	Released		ENCSR674KEK	shRNA	KD% = 79.3,67.6

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
PHF6	680	K562	ENCSR001KKZ	ENCSR103HDM	ENCAB411AGR	A301-450A	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
PHF6	ENCAB411AGR	A301-450A	1		Released, ENCODE3	Released, ENCODE3	BGHLV18-39, Released, ENCODE3	BGKLV21-39, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project	Note
PHF6	K562	shRNA	ENCSR322XVS	ENCSR572FFX	PHF6_BGKLV21_39_17580,PHF6_BGKLV21_40_17581	non-target_BGKLV21_1,non-target_BGKLV21_2	62.2,62.0	Released	ENCODE3
PHF6	HepG2	shRNA	ENCSR681SMT	ENCSR674KEK	PHF6_BGHLV18_39,PHF6_BGHLV18_40	NT_BGHLV18_1,NT_BGHLV18_2	79.3,67.6	Released	ENCODE3

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

PHF6: Click to RBP Image Database

Nuclei

Nucleoplasm

Nucleolus

Cytoplasm

Cytosolic

Mitotic-Apparatus (Spindle; Centrosomes)

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PHF6	Product_ID: A301-450A Lot_ID: 1 Source: Bethyl Labs Target Name: PHF6-human

RNA Targets

PHF6 protein binds to 643 RNA regions.

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Proteins bound to RNA

PHF6 RNA is bound by 14 proteins.

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PHF6 protein has 643 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
PHF6	chr19	50000987	50001055	+	3.85439	400.00000	K562	RPS11	intron-Distal
PHF6	chr3	160232887	160232898	-	3.23538	400.00000	K562	KPNA4	intron-Distal
PHF6	chr11	75115513	75115530	+	3.53212	400.00000	K562	RPS3	intron-Distal
PHF6	chr7	98479460	98479472	+	3.65326	400.00000	K562	TRRAP	intron-Distal
PHF6	chr9	136217744	136217748	+	3.72878	400.00000	K562	RPL7A	intron-Distal
PHF6	chr7	98479412	98479417	+	4.94886	400.00000	K562	TRRAP	intron-Distal
PHF6	chr3	186502628	186502653	+	3.16898	85.32084	K562	EIF4A2	intron-Distal,intron-Proximal
PHF6	chr6	133136444	133136454	+	5.38117	64.70154	K562	RPS12	intron-Distal,intron-Proximal
PHF6	chr1	45242162	45242168	+	4.38038	63.82652	K562	RPS8	intron-Distal
PHF6	chr2	203156097	203156113	+	3.82280	63.45399	K562	NOP58	intron-Distal

Showing 1 to 10 of 100 entries

14 proteins are bound to PHF6 RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chrX	133562670	133562798	+	3'-UTR	4.29439	45.70792	K562	PUM2
chrX	133561230	133561345	+	3'-UTR	3.35378	15.37164	K562	FAM120A
chrX	133559228	133559366	+	3'-UTR,CDS,intron-Proximal	3.29707	14.01301	K562	ZNF622
chrX	133562728	133562793	+	3'-UTR	3.99366	13.63735	K562	DDX6
chrX	133562390	133562503	+	3'-UTR	3.93113	13.27237	K562	FAM120A
chrX	133561257	133561355	+	3'-UTR	4.82737	13.19814	K562	TIA1
chrX	133559261	133559365	+	3'-UTR,CDS,intron-Proximal	3.19846	10.78086	K562	UCHL5
chrX	133562427	133562563	+	3'-UTR	5.16717	10.31906	K562	IGF2BP1
chrX	133562076	133562094	+	3'-UTR	4.14810	8.75974	K562	KHSRP
chrX	133561419	133561481	+	3'-UTR	3.29713	8.43850	K562	IGF2BP1
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 32 entries

No autoregularoty interactions between protein PHF6 and its RNA.

Diffrential Expression

1,315 differentially expressed genes after Knockdown/Knockout PHF6 protein.

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95 RBPs can affect the levels of PHF6.

CanvasJS.com

1,315 differentially expressed genes after Knockdown/Knockout PHF6 protein :

Only display 100 entries as example. Please click "View All" button to see all 1,315 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
SYP	ENSG00000102003.6	720.23760	75.49940	3.25380	63.00140	58.63730	HepG2	PHF6
HAL	ENSG00000084110.6	1740.20860	586.85920	1.56810	26.77340	23.01140	HepG2	PHF6
SULT2A1	ENSG00000105398.3	5151.42660	2041.34560	1.33540	24.15710	20.49190	HepG2	PHF6
CHGB	ENSG00000089199.5	293.59660	68.28160	2.10420	20.26610	16.68010	HepG2	PHF6
CPT1A	ENSG00000110090.8	2096.10690	877.21290	1.25660	19.32630	15.86530	HepG2	PHF6
ACSM2B	ENSG00000066813.10	831.23340	314.60790	1.40160	17.05300	13.73020	HepG2	PHF6
MAPK8IP2	ENSG00000008735.10	192.93810	42.05630	2.19760	14.95130	11.73330	HepG2	PHF6
SLC16A6	ENSG00000108932.7	455.44190	177.20250	1.36180	13.58600	10.47720	HepG2	PHF6
SLC26A3	ENSG00000091138.8	112.82320	21.21070	2.41110	12.19870	9.11330	HepG2	PHF6
SCG3	ENSG00000104112.4	44.88930	1.41700	4.98540	11.13660	8.11490	HepG2	PHF6
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".

95 RBPs can affect the gene expression of PHF6 :

Show entries

Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
PHF6	ENSG00000156531.12	787.92700	2431.40320	-1.62570	48.10260	43.73970	K562	PHF6
PHF6	ENSG00000156531.12	2247.70290	3938.79760	-0.80930	33.30050	31.12830	K562	UPF1
PHF6	ENSG00000156531.12	218.37160	582.88780	-1.41640	30.53200	28.59610	HepG2	DNAJC2
PHF6	ENSG00000156531.12	230.39980	637.55780	-1.46840	26.45790	25.20710	HepG2	TIAL1
PHF6	ENSG00000156531.12	1200.74400	2490.40100	-1.05240	25.75670	24.01730	K562	HNRNPC
PHF6	ENSG00000156531.12	266.32610	734.96080	-1.46450	21.05550	19.57570	HepG2	HNRNPLL
PHF6	ENSG00000156531.12	326.25680	644.47220	-0.98210	18.10420	17.00850	HepG2	ZNF622
PHF6	ENSG00000156531.12	269.92060	679.37990	-1.33170	18.01750	16.44470	HepG2	CPSF6
PHF6	ENSG00000156531.12	2115.55890	3302.27710	-0.64240	16.70140	15.32510	K562	FXR1
PHF6	ENSG00000156531.12	3233.85260	4965.82070	-0.61880	17.63030	14.98150	K562	CPEB4
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 113 entries

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

245 alternative splicing events after Knockdown/Knockout PHF6 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	SREK1	ENSG00000153914.11	chr5	+	65454636	65454760	65449290	65449424	65455046	65455162	0.25600	0.00000	included	K562	PHF6
SE	FNBP4	ENSG00000109920.8	chr11	-	47747288	47747388	47746023	47746330	47752925	47753113	0.08800	0.00018	included	K562	PHF6
SE	GNL1	ENSG00000204590.8	chr6	-	30514731	30514790	30514472	30514613	30514888	30515051	0.09100	0.00357	included	K562	PHF6
SE	CREBZF	ENSG00000137504.9	chr11	-	85374222	85374337	85372996	85373501	85374567	85374645	0.22800	0.00003	included	K562	PHF6
SE	HADH	ENSG00000138796.11	chr4	+	108949094	108949225	108948667	108948916	108954331	108954448	0.07200	0.00588	included	K562	PHF6
SE	THAP9-AS1	ENSG00000251022.2	chr4	-	83820865	83820890	83819141	83819215	83821229	83821376	0.16300	0.01296	included	K562	PHF6
SE	GAS5	ENSG00000234741.3	chr1	-	173834647	173834685	173834366	173834420	173835898	173835934	0.05900	0.00049	included	K562	PHF6
SE	ZMYND8	ENSG00000101040.15	chr20	-	45841286	45841370	45839405	45839542	45848908	45848975	0.18300	0.00037	included	K562	PHF6
SE	C1orf63	ENSG00000117616.13	chr1	-	25570944	25570989	25570040	25570124	25571640	25571792	0.33300	0.01277	included	K562	PHF6
SE	SRSF11	ENSG00000116754.9	chr1	+	70697541	70697658	70694104	70694238	70697950	70698058	0.09600	0.00278	included	K562	PHF6

Showing 1 to 10 of 100 entries

19 RBPs can affect the splicing of PHF6 :

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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
RI	PHF6	ENSG00000156531.12	chrX	+	133559230	133562819	133559230	133559360	133559690	133562819	0.22800	0.00000	0.00000	included	K562	PUS1
RI	PHF6	ENSG00000156531.12	chrX	+	133559230	133562819	133559230	133559360	133559690	133562819	0.25900	0.00000	0.00000	included	K562	SRSF1
RI	PHF6	ENSG00000156531.12	chrX	+	133559230	133562819	133559230	133559360	133559690	133562819	-0.21200	0.00000	0.00030	excluded	K562	SUPV3L1
RI	PHF6	ENSG00000156531.12	chrX	+	133559230	133562819	133559230	133559360	133559690	133562819	0.37000	0.00000	0.00000	included	K562	U2AF2
RI	PHF6	ENSG00000156531.12	chrX	+	133559230	133562819	133559230	133559360	133559690	133562819	-0.21500	0.00000	0.00029	excluded	K562	FMR1
RI	PHF6	ENSG00000156531.12	chrX	+	133559230	133562819	133559230	133559360	133559690	133562819	-0.17100	0.00001	0.00069	excluded	K562	PTBP1
SE	PHF6	ENSG00000156531.12	chrX	+	133512034	133512136	133511601	133511785	133527530	133527664	-0.08200	0.00006	0.00173	excluded	K562	U2AF2
SE	PHF6	ENSG00000156531.12	chrX	+	133512034	133512136	133511601	133511785	133527530	133527664	-0.08000	0.00011	0.00335	excluded	K562	SF3B4
RI	PHF6	ENSG00000156531.12	chrX	+	133559230	133562819	133559230	133559360	133559690	133562819	-0.12600	0.00012	0.01415	excluded	K562	EIF4G2
RI	PHF6	ENSG00000156531.12	chrX	+	133559230	133562819	133559230	133559360	133559690	133562819	-0.18000	0.00012	0.01897	excluded	K562	XRN2

Showing 1 to 10 of 26 entries

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

PHF6

General Information

Functions

Localization(RBPImage: PHF6)

Domains (AlphaFold: PHF6)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

PHF6 protein has 643 RNA targets:

14 proteins are bound to PHF6 RNA:

No autoregularoty interactions between protein PHF6 and its RNA.

Diffrential Expression

1,315 differentially expressed genes after Knockdown/Knockout PHF6 protein :

95 RBPs can affect the gene expression of PHF6 :

245 alternative splicing events after Knockdown/Knockout PHF6 protein :

19 RBPs can affect the splicing of PHF6 :

No autoregularoty alternative splicing events between protein PHF6 and its RNA.