TBRG4

General Information

Gene Name : TBRG4
Gene ID : ENSG00000136270.13
Essential Gene : Yes

Functions

Novel RBP

Localization(RBPImage: TBRG4)

Cytoplasm
Compartment/Organelle
Mitochondria

Domains (AlphaFold: TBRG4)

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

Antibody Validation

Bethyl Labs: A301-392A

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	TBRG4	ENSG00000136270.13	37.10	80.85	58.97	ENCSR000AEF
HepG2	TBRG4	ENSG00000136270.13	74.54	53.09	63.82	ENCSR985KAT
K562	TBRG4	ENSG00000136270.13	213.41	216.88	215.14	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: 584	ENCSR506OTC	TBRG4	K562	Released	ENCAB890JXZ	ENCSR512EZA
eCLIP	eCLIP: 617	ENCSR916SRV	TBRG4	HepG2	Released	ENCAB890JXZ	ENCSR081WUU
knockdown followed by RNA-seq	TBRG4-BGKLV08-K562	ENCSR079IPT	TBRG4	K562	Released		ENCSR344XID	shRNA	KD% = 60.6,59.9
knockdown followed by RNA-seq	TBRG4-BGHLV27-HepG2	ENCSR741YCA	TBRG4	HepG2	Released		ENCSR246RRQ	shRNA	KD% = 82.5,83.4

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
TBRG4	584	K562	ENCSR506OTC	ENCSR512EZA	ENCAB890JXZ	A301-392A	1	Released	ENCODE3
TBRG4	617	HepG2	ENCSR916SRV	ENCSR081WUU	ENCAB890JXZ	A301-392A	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
TBRG4	ENCAB890JXZ	A301-392A	1		Released, ENCODE3	Released, ENCODE3	BGHLV27-55, Released, ENCODE3	BGKLV08_59, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
TBRG4	K562	shRNA	ENCSR079IPT	ENCSR344XID	TBRG4-LV08-59,TBRG4-LV08-60	Nontarget-LV08-1_00003531,nontarget-LV08-2_00003531	60.6,59.9	Released	ENCODE3
TBRG4	HepG2	shRNA			BGHLV12-85,BGHLV12-86	BGHLV12-1,BGHLV12-2		NotSatisfied	ENCODE3
TBRG4	HepG2	shRNA	ENCSR741YCA	ENCSR246RRQ	TBRG4_BGHLV27-55,TBRG4_BGHLV27-56	non-target_BGHLV27-1,non-target_BGHLV27-2	82.5,83.4	Released	ENCODE3

RNA Bind-n-Seqn

No RBNS experiment available

Localization Image in HepG2

TBRG4: Click to RBP Image Database

Cytoplasm

Compartment/Organelle

Mitochondria

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
TBRG4	Product_ID: A301-392A Lot_ID: 1 Source: Bethyl Labs Target Name: TBRG4-human

RNA Targets

TBRG4 protein binds to 445 RNA regions.

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Proteins bound to RNA

TBRG4 RNA is bound by 38 proteins.

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TBRG4 protein has 445 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
TBRG4	chrM	8537	8540	+	7.59199	400.00000	HepG2	MT-ATP6, MT-ATP8	CDS
TBRG4	chrM	6635	6661	+	4.47818	400.00000	HepG2	MT-CO1	CDS
TBRG4	chrM	11571	11621	+	4.22978	400.00000	HepG2	MT-ND4	CDS
TBRG4	chrM	10272	10306	+	4.57014	400.00000	K562	MT-ND3	CDS
TBRG4	chrM	9754	9774	+	3.72062	400.00000	HepG2	MT-CO3	CDS
TBRG4	chrM	6539	6575	+	4.84445	400.00000	HepG2	MT-CO1	CDS
TBRG4	chrM	9902	9928	+	4.59794	400.00000	HepG2	MT-CO3	CDS
TBRG4	chrM	4684	4723	+	4.78312	400.00000	HepG2	MT-ND2	CDS
TBRG4	chrM	9133	9182	+	4.34848	400.00000	HepG2	MT-ATP6	CDS
TBRG4	chrM	15808	15827	+	5.03022	400.00000	HepG2	MT-CYB	CDS

Showing 1 to 10 of 100 entries

38 proteins are bound to TBRG4 RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr7	45144199	45144329	-	CDS,intron-Distal,intron-Proximal	5.43249	400.00000	K562	AATF
chr7	45144633	45144641	-	intron-Distal	4.31241	400.00000	HepG2	DKC1
chr7	45144566	45144571	-	intron-Distal	5.64792	400.00000	HepG2	DKC1
chr7	45144571	45144574	-	intron-Distal	5.41219	400.00000	HepG2	DKC1
chr7	45144042	45144077	-	intron-Distal,intron-Proximal	4.08155	400.00000	HepG2	DKC1
chr7	45143988	45144001	-	intron-Distal	3.43191	400.00000	HepG2	DKC1
chr7	45144001	45144005	-	intron-Distal	3.49206	400.00000	HepG2	DKC1
chr7	45144033	45144042	-	intron-Distal,intron-Proximal	4.20897	400.00000	HepG2	DKC1
chr7	45143952	45143979	-	intron-Distal,intron-Proximal	3.09605	400.00000	HepG2	DKC1
chr7	45144013	45144019	-	intron-Distal	4.11915	400.00000	HepG2	DKC1
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 172 entries

No autoregularoty interactions between protein TBRG4 and its RNA.

Diffrential Expression

3,109 differentially expressed genes after Knockdown/Knockout TBRG4 protein.

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112 RBPs can affect the levels of TBRG4.

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3,109 differentially expressed genes after Knockdown/Knockout TBRG4 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
RNASET2	ENSG00000026297.11	1583.08210	7593.67400	-2.26210	28.33690	25.50260	HepG2	TBRG4
VCAN	ENSG00000038427.11	284.53450	1102.67890	-1.95430	16.31780	14.01140	HepG2	TBRG4
SLC7A2	ENSG00000003989.12	3624.46450	11401.19170	-1.65330	16.13490	13.85000	HepG2	TBRG4
RNF19A	ENSG00000034677.7	1142.45160	3852.47030	-1.75370	15.50680	13.25880	HepG2	TBRG4
HIVEP2	ENSG00000010818.4	1076.21020	3402.38060	-1.66060	15.44620	13.20460	HepG2	TBRG4
EHD2	ENSG00000024422.7	11.55770	118.20810	-3.35440	14.10600	11.94260	HepG2	TBRG4
FAS	ENSG00000026103.15	376.80700	93.36610	2.01280	13.91390	11.76090	HepG2	TBRG4
ITGA3	ENSG00000005884.13	312.94350	50.06040	2.64410	12.95600	10.85640	HepG2	TBRG4
USP2	ENSG00000036672.11	504.07390	166.61880	1.59700	10.46840	8.56440	HepG2	TBRG4
CYP3A43	ENSG00000021461.12	213.40850	54.86410	1.95960	10.17720	8.29440	HepG2	TBRG4
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".

112 RBPs can affect the gene expression of TBRG4 :

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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
TBRG4	ENSG00000136270.9	1055.73510	1969.64680	-0.89970	26.12250	24.80370	HepG2	NELFE
TBRG4	ENSG00000136270.9	877.80440	1728.72790	-0.97770	25.37810	23.91230	HepG2	TAF15
TBRG4	ENSG00000136270.9	2346.77010	3635.76170	-0.63160	20.60940	18.86730	K562	UPF1
TBRG4	ENSG00000136270.9	398.20570	955.00110	-1.26200	21.75150	18.34840	K562	TBRG4
TBRG4	ENSG00000136270.9	1314.18000	2398.31860	-0.86790	18.19550	16.75050	K562	HNRNPC
TBRG4	ENSG00000136270.9	1156.86100	1864.00260	-0.68820	17.69740	16.63750	HepG2	SSB
TBRG4	ENSG00000136270.9	1073.66040	1769.82480	-0.72110	17.59240	16.44130	HepG2	PTBP1
TBRG4	ENSG00000136270.9	973.77280	1564.70130	-0.68420	16.38940	15.24780	HepG2	SRSF9
TBRG4	ENSG00000136270.9	3353.50660	5539.26720	-0.72400	13.88950	11.80560	K562	ZC3H8
TBRG4	ENSG00000136270.9	1223.48490	1834.45510	-0.58440	12.22940	11.07300	HepG2	RECQL
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 136 entries

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

872 alternative splicing events after Knockdown/Knockout TBRG4 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	TEX22	ENSG00000226174.2	chr14	+	105915695	105915746	105911754	105911848	105916394	105916443	0.28000	0.00008	included	HepG2	TBRG4
SE	SNRNP70	ENSG00000104852.10	chr19	+	49605370	49606844	49604646	49604728	49607890	49607992	0.16600	0.00000	included	HepG2	TBRG4
SE	MRPS18C	ENSG00000163319.6	chr4	+	84379498	84379582	84378061	84378111	84380892	84380950	0.20200	0.00072	included	HepG2	TBRG4
SE	ITFG3	ENSG00000167930.11	chr16	+	298242	298396	284842	284856	299547	299653	0.06800	0.00035	included	HepG2	TBRG4
SE	SREBF1	ENSG00000072310.12	chr17	-	17726831	17726921	17723403	17723835	17740040	17740301	0.30700	0.00018	included	HepG2	TBRG4
SE	PKP4	ENSG00000144283.17	chr2	+	159433782	159433895	159389691	159389828	159459581	159459616	0.18400	0.00072	included	HepG2	TBRG4
SE	MGRN1	ENSG00000102858.8	chr16	+	4736259	4736304	4733843	4733933	4738796	4739040	0.20500	0.00027	included	HepG2	TBRG4
SE	GPBP1	ENSG00000062194.11	chr5	+	56532939	56532999	56531792	56531859	56542126	56542311	0.26800	0.00000	included	HepG2	TBRG4
SE	IL17RB	ENSG00000056736.5	chr3	+	53889320	53889368	53886897	53887024	53890870	53891004	0.18200	0.00001	included	HepG2	TBRG4
SE	ACADSB	ENSG00000196177.8	chr10	+	124797262	124797363	124793870	124794031	124799981	124800173	0.05200	0.00003	included	HepG2	TBRG4

Showing 1 to 10 of 100 entries

24 RBPs can affect the splicing of TBRG4 :

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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	TBRG4	ENSG00000136270.9	chr7	-	45143697	45143855			45142931	45143042	45145039	45145363	-0.49700	0.00000	0.00000	excluded	HepG2	U2AF1
SE	TBRG4	ENSG00000136270.9	chr7	-	45143697	45143855			45142931	45143042	45145039	45145363	-0.33200	0.00000	0.00053	excluded	HepG2	DKC1
SE	TBRG4	ENSG00000136270.9	chr7	-	45143697	45143855			45142931	45143042	45145039	45145268	-0.27900	0.00000	0.00000	excluded	K562	AQR
A3SS	TBRG4	ENSG00000136270.9	chr7	-	45144136	45144364			45144136	45144308	45145039	45145363	0.08500	0.00000	0.00000	longer	K562	AQR
A3SS	TBRG4	ENSG00000136270.9	chr7	-	45143697	45143938			45143697	45143855	45144136	45144364	0.17500	0.00000	0.00000	longer	K562	AQR
A3SS	TBRG4	ENSG00000136270.9	chr7	-	45142030	45142183			45142030	45142090	45142931	45143042	0.09100	0.00000	0.00000	longer	K562	AQR
MXE	TBRG4	ENSG00000136270.9	chr7	-	45142030	45142090	45142090	45142137	45141451	45141669	45142931	45143042	0.09300	0.00000	0.00000	1included	K562	AQR
MXE	TBRG4	ENSG00000136270.9	chr7	-	45141879	45142090	45142090	45142137	45141451	45141669	45142931	45143042	0.07200	0.00000	0.00001	1included	K562	AQR
SE	TBRG4	ENSG00000136270.9	chr7	-	45143697	45143855			45142931	45143042	45145039	45145363	-0.23300	0.00001	0.00095	excluded	K562	PRPF8
SE	TBRG4	ENSG00000136270.9	chr7	-	45147333	45147377			45144884	45145363	45148425	45148886	0.05400	0.00001	0.00619	included	K562	EIF3G

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".

The TBRG4 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
MXE	TBRG4	ENSG00000136270.9	chr7	-	45143697	45143855	45144136	45144345	45142931	45143042	45145039	45147063	0.15000	0.00083	0.05259	1included	HepG2	TBRG4

Showing 1 to 1 of 1 entries