ABCF1

General Information

Gene Name : ABCF1
Gene ID : ENSG00000204574.12
Essential Gene : Yes

Functions

Translation regulation

Localization(RBPImage: ABCF1)

Nuclei
Nucleolus
Cytoplasm
Compartment/Organelle
Mitochondria
Cell Cortex

Domains (AlphaFold: ABCF1)

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

Antibody Validation

Bethyl Labs: A301-999A

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	ABCF1	ENSG00000204574.12	43.18	54.14	48.66	ENCSR000AEF
HepG2	ABCF1	ENSG00000204574.12	97.70	82.34	90.02	ENCSR985KAT
K562	ABCF1	ENSG00000204574.12	140.16	129.77	134.97	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: 734	ENCSR089BXO	ABCF1	K562	Released	ENCAB710VED	ENCSR857ORY
knockdown followed by RNA-seq	ABCF1-BGKLV29-K562	ENCSR721MXZ	ABCF1	K562	Released		ENCSR032YMP	shRNA	KD% = 69.0,69.7
knockdown followed by RNA-seq	ABCF1-BGHLV30-HepG2	ENCSR610VTA	ABCF1	HepG2	Released		ENCSR067GHD	shRNA	KD% = 80.3,78.6

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
ABCF1	734	K562	ENCSR089BXO	ENCSR857ORY	ENCAB710VED	A301-999A	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
ABCF1	ENCAB710VED	A301-999A	1			Released, ENCODE3	BGHLV30-3, Released, ENCODE3	BGKLV29-3, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project	Note
ABCF1	K562	shRNA	ENCSR721MXZ	ENCSR032YMP	ABCF1_BGKLV29-3,ABCF1_BGKLV29-4	NT_BGKLV29-1,NT_BGKLV29-2	69.0,69.7	Released	ENCODE3
ABCF1	HepG2	shRNA	ENCSR610VTA	ENCSR067GHD	ABCF1_BGHLV30-3,ABCF1_BGHLV30-4	NT_BGHLV30-1,NT_BGHLV30-2	80.3,78.6	Released	ENCODE3

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

ABCF1: Click to RBP Image Database

Nuclei

Nucleolus

Cytoplasm

Compartment/Organelle

Mitochondria

Cell Cortex

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ABCF1	Product_ID: A301-999A Lot_ID: 1 Source: Bethyl Labs Target Name: ABCF1-human

RNA Targets

ABCF1 protein binds to 55 RNA regions.

CanvasJS.com

Proteins bound to RNA

ABCF1 RNA is bound by 35 proteins.

CanvasJS.com

ABCF1 protein has 55 RNA targets:

Only display 100 entries as example. Please click "View All" button to see all 55 entries.

Show entries

Search:

RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
ABCF1	chr11	93454901	93455012	+	3.20702	47.17521	K562	KIAA1731	intron-Distal
ABCF1	chr8	144940490	144940702	-	3.48339	43.29510	K562	EPPK1	CDS,intron-Distal
ABCF1	chr11	93454678	93454774	+	3.10041	23.24399	K562	KIAA1731	intron-Distal
ABCF1	chr17	27047563	27047625	+	3.39226	19.14606	K562	RPL23A	5'-UTR,intron-Distal
ABCF1	chr7	45144236	45144341	-	3.49698	17.04962	K562	TBRG4	CDS,intron-Distal,intron-Proximal
ABCF1	chr9	136217701	136217737	+	3.19604	16.96102	K562	RPL7A	intron-Distal
ABCF1	chr17	2232459	2232488	-	3.30647	14.86748	K562	TSR1	intron-Distal
ABCF1	chr5	137896766	137896776	-	3.07678	14.64054	K562	HSPA9	intron-Distal
ABCF1	chr5	137896764	137896766	-	3.05040	14.46045	K562	HSPA9	intron-Distal
ABCF1	chr13	92000777	92000858	+	4.00297	14.32157	K562	MIR17HG	intron-Distal

Showing 1 to 10 of 55 entries

35 proteins are bound to ABCF1 RNA:

Show entries

Search:

Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr6	30550182	30550275	+	CDS,intron-Distal	5.52191	53.45525	K562	UCHL5
chr6	30550842	30550938	+	CDS,intron-Distal,intron-Proximal	7.65443	53.15288	K562	UCHL5
chr6	30545892	30545967	+	3'-UTR,CDS,intron-Proximal	5.91323	42.17581	K562	UCHL5
chr6	30553183	30553233	+	intron-Distal,intron-Proximal	6.08775	37.92990	HepG2	PCBP2
chr6	30550193	30550281	+	CDS,intron-Distal	5.74518	35.26909	K562	ZNF622
chr6	30545608	30545690	+	3'-UTR,CDS	4.57988	35.06920	K562	UCHL5
chr6	30548184	30548247	+	CDS,intron-Distal	5.85981	28.12248	K562	UCHL5
chr6	30545942	30545980	+	CDS,intron-Proximal	5.73729	25.79132	K562	ZNF622
chr6	30546258	30546342	+	CDS,intron-Distal	4.66139	24.59039	K562	ZNF622
chr6	30546124	30546161	+	CDS,intron-Distal,intron-Proximal	6.77624	24.58044	K562	UCHL5
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 185 entries

No autoregularoty interactions between protein ABCF1 and its RNA.

Diffrential Expression

5,438 differentially expressed genes after Knockdown/Knockout ABCF1 protein.

CanvasJS.com

94 RBPs can affect the levels of ABCF1.

CanvasJS.com

5,438 differentially expressed genes after Knockdown/Knockout ABCF1 protein :

Only display 100 entries as example. Please click "View All" button to see all 5,438 entries.

Show entries

Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
JHDM1D	ENSG00000006459.6	786.29580	2401.00330	-1.61050	36.66150	34.10640	HepG2	ABCF1
TFPI	ENSG00000003436.10	5849.16610	13750.31620	-1.23320	30.11520	27.73620	HepG2	ABCF1
PLEKHB1	ENSG00000021300.9	924.33920	2446.56410	-1.40430	28.43270	26.12060	HepG2	ABCF1
SLC7A2	ENSG00000003989.12	3215.57640	6526.38560	-1.02120	19.74360	17.64820	HepG2	ABCF1
NR1H4	ENSG00000012504.9	2063.92570	903.63540	1.19150	19.10680	17.03510	HepG2	ABCF1
ACSM3	ENSG00000005187.7	2302.07140	1125.61430	1.03210	17.38070	15.39790	HepG2	ABCF1
MLXIPL	ENSG00000009950.11	10082.77710	5401.18020	0.90040	15.25850	13.35940	HepG2	ABCF1
ZFX	ENSG00000005889.11	2212.88060	1127.21770	0.97310	15.06470	13.17680	HepG2	ABCF1
WWTR1	ENSG00000018408.10	1743.24300	3262.04070	-0.90400	14.91910	13.03660	HepG2	ABCF1
ADIPOR2	ENSG00000006831.9	1727.23020	3141.66580	-0.86310	12.05450	10.32010	HepG2	ABCF1
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".

94 RBPs can affect the gene expression of ABCF1 :

Show entries

Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
ABCF1	ENSG00000204574.8	1668.57840	3472.00610	-1.05720	65.24940	63.51500	HepG2	ZNF622
ABCF1	ENSG00000204574.8	5513.40040	2590.24800	1.08980	50.74040	48.35200	K562	FXR1
ABCF1	ENSG00000204574.8	2928.35830	6080.98830	-1.05420	49.19240	46.44820	K562	SF3A3
ABCF1	ENSG00000204574.8	1387.85330	2977.31770	-1.10120	43.89360	41.60530	HepG2	PRPF4
ABCF1	ENSG00000204574.8	3178.17550	8762.45620	-1.46310	22.23120	19.22200	K562	ABCF1
ABCF1	ENSG00000204574.8	3942.58900	2547.31520	0.63010	16.36050	15.41510	HepG2	SRSF1
ABCF1	ENSG00000204574.8	4698.82740	2360.60390	0.99300	15.83030	14.41430	HepG2	MATR3
ABCF1	ENSG00000204574.8	2278.24420	4058.30960	-0.83300	15.81750	14.32400	HepG2	TARDBP
ABCF1	ENSG00000204574.8	4187.88450	2538.05400	0.72240	16.30010	14.29930	K562	EIF3G
ABCF1	ENSG00000204574.8	7546.41310	4794.45750	0.65430	15.62680	13.70560	K562	SYNCRIP
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 112 entries

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

125 alternative splicing events after Knockdown/Knockout ABCF1 protein :

Only display 100 entries as example. Please click "View All" button to see all 125 entries.

Show entries

Search:

Event Type	Gene Name	Gene ID	chr	Strand	ExonStart	ExonEnd	upstreamES	upstreamEE	downstreamES	downstreamEE	dPSI	FDR	is_included	Cell Line	Affected by RBP
SE	RPS24	ENSG00000138326.14	chr10	+	79799961	79799983	79796951	79797062	79800372	79800455	0.19700	0.00000	included	K562	ABCF1
SE	LRRFIP2	ENSG00000093167.13	chr3	-	37132957	37133029	37125126	37125297	37136282	37136399	0.28300	0.00013	included	K562	ABCF1
SE	SNRNP70	ENSG00000104852.10	chr19	+	49605370	49606844	49604646	49604728	49607890	49607992	0.09000	0.00000	included	K562	ABCF1
SE	ZNF207	ENSG00000010244.12	chr17	+	30693683	30693776	30692348	30692506	30694790	30694962	0.14100	0.00003	included	K562	ABCF1
SE	UAP1	ENSG00000117143.9	chr1	+	162562521	162562572	162560112	162560301	162567581	162567648	0.08800	0.00000	included	K562	ABCF1
SE	ANKHD1	ENSG00000131503.16	chr5	+	139927227	139927425	139921756	139921866	139928490	139928661	0.09200	0.00034	included	K562	ABCF1
SE	MRRF	ENSG00000148187.13	chr9	+	125048317	125048445	125047447	125047566	125054027	125054077	0.18600	0.00465	included	K562	ABCF1
SE	SMIM15	ENSG00000188725.3	chr5	-	60458043	60458186	60456914	60457054	60458272	60458295	0.08900	0.00091	included	K562	ABCF1
SE	C22orf34	ENSG00000188511.8	chr22	-	49810250	49810384	49808175	49809684	49810463	49810577	0.33000	0.00031	included	K562	ABCF1
SE	OXSR1	ENSG00000172939.4	chr3	+	38234772	38234909	38232221	38232330	38240212	38240354	0.07000	0.00265	included	K562	ABCF1

Showing 1 to 10 of 100 entries

7 RBPs can affect the splicing of ABCF1 :

Show entries

Search:

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	ABCF1	ENSG00000204574.8	chr6	+	30545185	30545232			30539209	30539337	30545594	30545690	-0.06300	0.00000	0.00000	excluded	HepG2	U2AF2
A5SS	ABCF1	ENSG00000204574.8	chr6	+	30554417	30554584			30554417	30554488	30557464	30557497	0.05400	0.00000	0.00000	longer	K562	AQR
MXE	ABCF1	ENSG00000204574.8	chr6	+	30548182	30548296	30550170	30550284	30547707	30547782	30550842	30550965	0.05100	0.00000	0.00004	1included	HepG2	FTO
A5SS	ABCF1	ENSG00000204574.8	chr6	+	30551285	30551485			30551285	30551471	30551581	30551667	-0.07000	0.00001	0.00262	shorter	HepG2	SF3A3
SE	ABCF1	ENSG00000204574.8	chr6	+	30545157	30545232			30539209	30539337	30545594	30545690	-0.05200	0.00015	0.00400	excluded	HepG2	U2AF1
A3SS	ABCF1	ENSG00000204574.8	chr6	+	30545849	30545979			30545852	30545979	30545594	30545690	0.19900	0.00019	0.03103	longer	HepG2	PCBP1
SE	ABCF1	ENSG00000204574.8	chr6	+	30545185	30545232			30539209	30539337	30545594	30545690	-0.06300	0.00041	0.00956	excluded	K562	U2AF2
MXE	ABCF1	ENSG00000204574.8	chr6	+	30548182	30548296	30550170	30550284	30547707	30547782	30550842	30550965	0.11300	0.00388	0.07105	1included	HepG2	DDX55
MXE	ABCF1	ENSG00000204574.8	chr6	+	30547707	30547782	30548182	30548296	30546246	30546354	30550170	30550284	-0.08000	0.00756	0.04312	2included	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".

ABCF1

General Information

Functions

Localization(RBPImage: ABCF1)

Domains (AlphaFold: ABCF1)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

ABCF1 protein has 55 RNA targets:

35 proteins are bound to ABCF1 RNA:

No autoregularoty interactions between protein ABCF1 and its RNA.

Diffrential Expression

5,438 differentially expressed genes after Knockdown/Knockout ABCF1 protein :

94 RBPs can affect the gene expression of ABCF1 :

125 alternative splicing events after Knockdown/Knockout ABCF1 protein :

7 RBPs can affect the splicing of ABCF1 :

No autoregularoty alternative splicing events between protein ABCF1 and its RNA.