LIN28B

General Information

Gene Name : LIN28B
Gene ID : ENSG00000187772.7
Essential Gene : No

Functions

RNA modification
RNA stability & decay
microRNA processing

Localization(RBPImage: LIN28B)

Nuclei
Nucleoplasm
Nucleolus
Cytoplasm
Cytosolic

Domains (AlphaFold: LIN28B)

ZNF

Antibody Validation

View validation images for all LIN28B antibodies

Expression Level in Cell lines

Cell Line	Gene Name	Ensembl ID	Rep1 TPM	Rep2 TPM	Average TPM	Experiment ID
Gm12878	LIN28B	ENSG00000187772.7	0.00	0.01	0.01	ENCSR000AEF
HepG2	LIN28B	ENSG00000187772.7	18.23	34.17	26.20	ENCSR985KAT
K562	LIN28B	ENSG00000187772.7	32.54	37.95	35.25	ENCSR000AEO

Assays

7 Released experiments are available on ENCORE database.

Assay Type	Exp_Name	ENCODE ID	Target label	Biosample	Status	Linked Antibody	Controls	Method	Note
eCLIP	eCLIP: 325	ENCSR970NKP	LIN28B	K562	Released	ENCAB006PLV	ENCSR399CBP
eCLIP	eCLIP: 387	ENCSR861GYE	LIN28B	HepG2	Released	ENCAB006PLV	ENCSR746ZSV
knockdown followed by RNA-seq	LIN28B-BGKLV21-K562	ENCSR598YQX	LIN28B	K562	Released		ENCSR572FFX	shRNA	KD% = 79.9,79.4
knockdown followed by RNA-seq	LIN28B-BGHLV18-HepG2	ENCSR927SLP	LIN28B	HepG2	Released		ENCSR674KEK	shRNA	KD% = 79.3,74.6
knockdown followed by RNA-seq	LIN28B-BGRSDLV02-RSD293RBP		LIN28B	Ribo-STAMP-293T	Released			shRNA	KD% =
knockdown followed by RNA-seq	LIN28B-BGRSDLV02-RSD293RBP		LIN28B	Ribo-STAMP-293T	Released			shRNA	KD% = ,
RNA Bind-n-Seq	RBNS: LIN28B	ENCSR369RLA	LIN28B	cell-free sample	Released

eCLIP

RBP	Exp_UID	Cell_Line	ENCODE_ACCESSION	Control_ENCODE_ACCESSION	ENCODE_Antibody_ID	Antibody	Lot_num	Status	Project
LIN28B	325	K562	ENCSR970NKP	ENCSR399CBP	ENCAB006PLV	A303-558A	1	Released	ENCODE3
LIN28B	387	HepG2	ENCSR861GYE	ENCSR746ZSV	ENCAB006PLV	A303-588A	1	Released	ENCODE3

Antibody Validation

GeneName	Antibody_DCC_ID	Product_ID	Lot_ID	HepG2 Primary Validation	K562 Primary Validation	HepG2 Secondary Validation	K562 Secondary Validation
LIN28B	ENCAB006PLV	A303-588A	1	Released, ENCODE3	Released, ENCODE3	BGHLV18-21, Released, ENCODE3	BGKLV21-27, Released, ENCODE3
LIN28B		1965S	1	Released, ENCODE3		BGHLV18-21, Released, ENCODE3	BGKLV21-27, Submitted, ENCORE2
LIN28B		11965S	1	Released, ENCODE3	Submitted, ENCORE2	BGHLV18-21, Released, ENCODE3

KD RNA-Seq

GeneName	Cell_Line	Method	Exp_ID	Control_ID	Sample_reps	Control_reps	KD%	Status	Project
LIN28B	K562	shRNA	ENCSR598YQX	ENCSR572FFX	LIN28B_BGKLV21_27_17573,LIN28B_BGKLV21_28_17574	non-target_BGKLV21_1,non-target_BGKLV21_2	79.9,79.4	Released	ENCODE3
LIN28B	HepG2	shRNA	ENCSR927SLP	ENCSR674KEK	LIN28B_BGHLV18_21,LIN28B_BGHLV18_22	NT_BGHLV18_1,NT_BGHLV18_2	79.3,74.6	Released	ENCODE3
LIN28B	Ribo-STAMP-293T	shRNA			BGRSLV01-9,BGRSLV01-10	BGRSLV01-1,BGRSLV01-2		NotSatisfied	ENCORE2
LIN28B	Ribo-STAMP-293T	shRNA			BGRSLV02-5,BGRSLV02-6	BGRSLV02-1,BGRSLV02-2		NotSatisfied	ENCORE2
LIN28B	Ribo-STAMP-293T	shRNA			BGRSLV09-23,BGRSLV09-24	BGRSLV09-1,BGRSLV09-2		NotSatisfied	ENCORE2
LIN28B	Ribo-STAMP-293T	shRNA			BGRSLV09-25,BGRSLV09-26	BGRSLV09-1,BGRSLV09-2		NotSatisfied	ENCORE2
LIN28B	Ribo-STAMP-293T	shRNA			BGRSDLV02-41,BGRSDLV02-42	BGRSDLV02-1,BGRSDLV02-2		Released	ENCORE2
LIN28B	Ribo-STAMP-293T	shRNA			LIN28B-BGRSDLV02-43dox,LIN28B-BGRSDLV02-44dox	LIN28B-BGRSDLV02-41,LIN28B-BGRSDLV02-42	,	Released	ENCORE2

RNA Bind-n-Seqn

GeneName	gene_aliases	Status	Project	Note
LIN28B	LIN28B		Released	ENCODE4

Localization Image in HepG2

LIN28B: Click to RBP Image Database

Nuclei

Nucleoplasm

Nucleolus

Cytoplasm

Cytosolic

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LIN28B	Product_ID: A303-588A Lot_ID: 1 Source: Bethyl Labs Target Name: LIN28B-human
LIN28B	Product_ID: 11965S Lot_ID: 1 Source: Cell Signaling Technology Target Name: LIN28B-human
LIN28B	Product_ID: 1965S Lot_ID: 1 Source: Cell Signaling Target Name: LIN28B-human

RNA Targets

LIN28B protein binds to 10,548 RNA regions.

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The binding motifs of LIN28B

Proteins bound to RNA

LIN28B RNA is bound by 15 proteins.

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LIN28B protein has 10,548 RNA targets:

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RBP	Chr	Start	End	Strand	log2(fold change)	-log(p-value)	Cell Line	Matched Gene	Matched Area
LIN28B	chr2	216296627	216296643	-	3.40311	400.00000	HepG2	FN1	CDS,intron-Distal
LIN28B	chr2	216248872	216248878	-	4.01989	400.00000	HepG2	FN1	CDS,intron-Distal,intron-Proximal
LIN28B	chr11	17098714	17098719	-	7.92443	400.00000	HepG2	RPS13	CDS,intron-Distal,intron-Proximal
LIN28B	chr9	96941171	96941197	+	8.14411	154.68965	K562	RP11-2B6.3	intron-Distal
LIN28B	chr1	32381518	32381564	-	6.97998	132.83955	K562	PTP4A2, RP11-84A19.4	CDS,intron-Distal
LIN28B	chr11	82550312	82550352	-	8.09185	85.18310	K562	PRCP	CDS,intron-Distal,intron-Proximal
LIN28B	chr17	57737885	57737925	+	5.73637	58.14196	K562	CLTC	3'-UTR,CDS,intron-Distal
LIN28B	chr2	21231049	21231062	-	3.32649	53.66065	HepG2	APOB	CDS,intron-Distal
LIN28B	chr12	65640406	65640442	+	7.37663	52.82500	K562	LEMD3	3'-UTR
LIN28B	chr17	73839239	73839241	-	5.70314	46.56567	K562	UNC13D	CDS,intron-Distal,intron-Proximal

Showing 1 to 10 of 100 entries

15 proteins are bound to LIN28B RNA:

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Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name
chr6	105423266	105423369	+	intron-Distal	4.27962	17.14122	HepG2	QKI
chr6	105406849	105406960	+	intron-Distal	3.77605	12.29548	K562	KHSRP
chr6	105407008	105407068	+	intron-Distal	4.81253	11.62651	HepG2	U2AF2
chr6	105405969	105406041	+	CDS,intron-Proximal	3.39922	9.71090	HepG2	PPIG
chr6	105406172	105406243	+	intron-Proximal	3.36762	9.57775	HepG2	U2AF2
chr6	105517838	105517909	+	intron-Distal	4.20110	8.85307	HepG2	PCBP2
chr6	105405964	105406039	+	CDS,intron-Proximal	3.22086	8.37988	HepG2	BUD13
chr6	105429200	105429389	+	intron-Distal	5.30277	8.32953	HepG2	QKI
chr6	105406384	105406451	+	intron-Distal	4.79226	8.06346	K562	KHSRP
chr6	105408866	105408970	+	intron-Distal	4.80335	7.58902	K562	KHSRP
Chr	Start	End	Strand	Matched Area	log2(fold change)	-log(p-value)	Cell Line	Binding Protein Name

Showing 1 to 10 of 51 entries

No autoregularoty interactions between protein LIN28B and its RNA.

Diffrential Expression

2,557 differentially expressed genes after Knockdown/Knockout LIN28B protein.

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145 RBPs can affect the levels of LIN28B.

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2,557 differentially expressed genes after Knockdown/Knockout LIN28B 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
CSDE1	ENSG00000009307.11	5251.45400	9730.04870	-0.88970	19.16700	16.33960	HepG2	LIN28B
C6	ENSG00000039537.9	125.84990	15.11150	3.05790	16.24600	13.57350	HepG2	LIN28B
CX3CL1	ENSG00000006210.6	2846.07850	1541.93000	0.88410	13.31610	10.81970	HepG2	LIN28B
USP13	ENSG00000058056.4	800.85600	1438.08650	-0.84450	12.29500	9.90120	HepG2	LIN28B
SEC61A1	ENSG00000058262.5	2996.55650	4738.63470	-0.66120	11.25740	8.95420	HepG2	LIN28B
DEPDC1B	ENSG00000035499.8	478.55930	870.40860	-0.86300	10.29060	8.08050	HepG2	LIN28B
CP	ENSG00000047457.9	13892.49980	31161.65070	-1.16550	10.12690	7.93720	HepG2	LIN28B
RNASET2	ENSG00000026297.11	1897.53620	3012.51650	-0.66680	9.86880	7.70950	HepG2	LIN28B
HIVEP2	ENSG00000010818.4	536.19060	949.14740	-0.82390	9.55010	7.41170	HepG2	LIN28B
MLXIPL	ENSG00000009950.11	3696.59430	2041.50590	0.85650	9.30160	7.18780	HepG2	LIN28B
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".

145 RBPs can affect the gene expression of LIN28B :

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Search:

Gene Name	Gene ID	KDMean	CNMean	log2(fold change) *	-log(pval) **	-log(padj) **	Cell Line	Affected by RBP	Bound by RBP
LIN28B	ENSG00000187772.6	674.50080	2177.07400	-1.69050	66.59380	64.75630	HepG2	TIAL1
LIN28B	ENSG00000187772.6	1252.29830	3177.76260	-1.34340	58.07630	56.47780	HepG2	SSB
LIN28B	ENSG00000187772.6	1900.04620	3436.52490	-0.85490	48.88230	46.43810	K562	NSUN2
LIN28B	ENSG00000187772.6	1140.01970	2288.42040	-1.00530	48.77250	46.27750	HepG2	ILF2
LIN28B	ENSG00000187772.6	741.89420	2255.22580	-1.60400	47.26900	44.85770	HepG2	HNRNPC
LIN28B	ENSG00000187772.6	821.65930	1950.18570	-1.24700	42.85640	40.87320	HepG2	ZC3H8
LIN28B	ENSG00000187772.6	737.98040	2027.55060	-1.45810	40.08780	38.19740	HepG2	HNRNPA1
LIN28B	ENSG00000187772.6	3110.30900	1656.14960	0.90910	36.53240	35.24450	HepG2	SRSF1
LIN28B	ENSG00000187772.6	2955.96240	1523.99340	0.95570	36.32900	34.80420	HepG2	PTBP1
LIN28B	ENSG00000187772.6	993.11150	2928.31480	-1.56000	35.49450	33.50280	HepG2	GPKOW
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 183 entries

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

349 alternative splicing events after Knockdown/Knockout LIN28B 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	YBX3	ENSG00000060138.8	chr12	-	10862506	10862713	10856649	10856747	10865809	10865932	0.18500	0.01560	included	K562	LIN28B
SE	DDX5	ENSG00000108654.7	chr17	-	62496792	62496891	62495733	62496444	62498127	62498187	-0.12000	0.00126	excluded	K562	LIN28B
SE	PICALM	ENSG00000073921.13	chr11	-	85689112	85689136	85687665	85687725	85692171	85692271	-0.13000	0.00128	excluded	K562	LIN28B
SE	LEF1	ENSG00000138795.5	chr4	-	109002741	109002825	109000647	109000770	109004511	109004602	-0.23700	0.00000	excluded	K562	LIN28B
SE	PRAME	ENSG00000185686.13	chr22	-	22899231	22899350	22893273	22893511	22899964	22900174	-0.05600	0.00637	excluded	K562	LIN28B
SE	MYL6	ENSG00000092841.14	chr12	+	56554409	56554454	56554026	56554104	56555170	56555371	0.12800	0.00015	included	HepG2	LIN28B
SE	APOC1	ENSG00000130208.5	chr19	+	45417928	45417990	45417503	45417746	45418128	45418206	0.09700	0.00026	included	HepG2	LIN28B
SE	EIF4H	ENSG00000106682.10	chr7	+	73604576	73604636	73604151	73604248	73609070	73609208	0.13900	0.00004	included	HepG2	LIN28B
SE	TRIM33	ENSG00000197323.6	chr1	-	114963001	114963073	114952805	114952938	114964057	114964258	0.30000	0.00142	included	HepG2	LIN28B
SE	SON	ENSG00000159140.13	chr21	+	34944856	34944936	34941276	34941393	34945613	34945761	0.11800	0.00191	included	HepG2	LIN28B

Showing 1 to 10 of 100 entries

LIN28B

General Information

Functions

Localization(RBPImage: LIN28B)

Domains (AlphaFold: LIN28B)

Antibody Validation

Expression Level in Cell lines

Assays

RNA Targets

Proteins bound to RNA

LIN28B protein has 10,548 RNA targets:

15 proteins are bound to LIN28B RNA:

No autoregularoty interactions between protein LIN28B and its RNA.

Diffrential Expression

2,557 differentially expressed genes after Knockdown/Knockout LIN28B protein :

145 RBPs can affect the gene expression of LIN28B :

349 alternative splicing events after Knockdown/Knockout LIN28B protein :

No RBPs affect the alternative splcing events of LIN28B on ENCORE database.

No autoregularoty alternative splicing events between protein LIN28B and its RNA.