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lncRNA: ENSG00000228106

Summary for RP11-452F19.3

Gene summary

Gene information	Ensembl ID	ENSG00000228106
	Gene symbol	RP11-452F19.3
	Gene name
	HGNC
	Entrez ID
	Gene type	lincRNA
	Synonyms
	UniProtAcc

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Structure and expression level for RP11-452F19.3

AS events and RNA A-to-I editing events of lncRNA in TCGA based on Genvode V22 structure.

Differentially expressed gene analysis between cancer and normal samples.

Ensembl ID	Base mean	log2FC(AD/control)	lfcSE	Stat	P-value	Adjc.p-value	DEG direction	Cancer type
ENSG00000228106	2.177307e+02	2.126204e+00	3.523068e-01	6.035094e+00	1.590000e-09	2.470000e-08	UP	GBM
ENSG00000228106	1.839117e+02	-1.392657e+00	1.547706e-01	-8.998199e+00	2.290000e-19	3.540000e-18	DOWN	KICH
ENSG00000228106	1.448852e+02	1.062130e+00	1.606139e-01	6.612941e+00	3.770000e-11	2.690000e-10	UP	UCEC

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000228106	4.712373e-01	1.085571e-03	CHOL	1.825930e-03
ENSG00000228106	3.199449e-01	5.541331e-05	ESCA	2.093392e-03
ENSG00000228106	-5.893021e-01	1.237548e-09	KICH	9.590998e-09
ENSG00000228106	3.207902e-01	5.025982e-11	LIHC	2.051044e-10

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lncRNA-Protein interaction for RP11-452F19.3

lncRNA-epigenetic factor interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID

LncRNA ENST ID

LncRNA Name

Protein Ensembl ID

Protein Name

CatRAPID Score

Lncpro Score

UniPortID

Gene Subtype

Public source

lncRNA-transcript factor interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000228106	ENST00000441676	RP11-452F19.3	ENSG00000166526	ZNF3	9.84	90.8106	P17036	TF	NA
ENSG00000228106	ENST00000441676	RP11-452F19.3	ENSG00000176946	THAP4	6.18	90.1034	Q8WY91	TF	NA
ENSG00000228106	ENST00000441676	RP11-452F19.3	ENSG00000154957	ZNF18	4.01	91.2633	P17022	TF	NA
ENSG00000228106	ENST00000450784	RP11-452F19.3	ENSG00000154957	ZNF18	4.01	90.5986	P17022	TF	NA

lncRNA-RNA binding protein interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000228106	ENST00000450784	RP11-452F19.3	ENSG00000004534	RBM6	65.66	93.2938	P78332	RBP	NA
ENSG00000228106	ENST00000441676	RP11-452F19.3	ENSG00000004534	RBM6	52.69	94.0664	P78332	RBP	NA
ENSG00000228106	ENST00000450784	RP11-452F19.3	ENSG00000162775	RBM15	47.92	92.7318	Q96T37	RBP	NA
ENSG00000228106	ENST00000441676	RP11-452F19.3	ENSG00000162775	RBM15	42.32	92.8221	Q96T37	RBP	NA
ENSG00000228106	ENST00000450784	RP11-452F19.3	ENSG00000204356	NELFE	7.6	91.4988	P18615	RBP	NA
ENSG00000228106	ENST00000435378	RP11-452F19.3	ENSG00000004534	RBM6	62.73	90.972	P78332	RBP	NA

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lncRNA-DNA interaction for RP11-452F19.3

lncRNA targets the enhancer region and positively regulates the gene expression.

Only predicted by TDF

SLIRP,ISG20,THAP4,IRF3,JMJD6,OVOL2,RPP25,SNRPA,THOC1,LSM3,CHTOP,LSM5,EIF3G,CENPT,PCBP2,LSM4,CSTF3,CWC15,DHX34,CPSF4,RBM15,PPIE,SF3B6,NELFE,USF1,ZNF22,THYN1,THOC6,ILF2,CENPA,ATF4,SF3B4,REXO4,TIGD1,ELK4,MBD4,THAP3,MESP1,SRSF2,ZNF3,ZNF18,EIF2D,CREM,HMGN3,CPSF3,E2F1,LSM2,NFYB,PIN1,THOC5,TRA2A,RBM8A,RRP7A,SMYD3,XPA,THOC7,NR1H2,SRSF7

Exist in public source

lncRNA targets the promoter region and positively regulates the gene expression.

lncRNA targets the promoter region and negatively regulates the gene expression.

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lncRNA-RNA interaction for RP11-452F19.3

lncRNA targets the 3'UTR region and negatively regulates the mRNA.

Only predicted by lncTar

UBR5,PRDM4,CIC,GLIS2,SON,RFX1,GTF2I,BAZ2A,FUBP3,STAU1,MNT,PHAX,MBD1,NACC2,MAFG,FOXJ2,MECP2,RREB1,FOXN3,NOP9,ZNF41,STAT6,AGO2,EEA1,NFKB1,AGO1,KLF7,MAFK,NCOA2,FOXK1,KMT2B,NFIC,IRF2,PUM1,SYNJ1,G3BP2,KLF13,NCOA1

Exist in public source

lncRNA targets the skipped exon region.

-lncRNA and exonskipping events are positively correlated.

lncRNA and exonskipping events positive correlated

LncRNA Ensembl ID	LncRNA ENST ID	Exon ID	Skipped Exon	dG	ndG	Gene name with skipped exon	TransID with skipped exon	ORF mutation
ENSG00000228106	ENST00000448808	exon_skip_99856	chr13:39042104-39042305	-10.79	-0.1300	NHLRC3	ENST00000379600	In-frame

-lncRNA and exonskipping events are negatively correlated.

lncRNA and exonskipping events negative correlated

LncRNA Ensembl ID	LncRNA ENST ID	Exon ID	Skipped Exon	dG	ndG	Gene name with skipped exon	TransID with skipped exon	LOF
ENSG00000228106	ENST00000448808	exon_skip_3490	chr1:28742402-28743986	-16.20	-0.1296	YTHDF2	ENST00000373812,ENST00000542507	In-frame
ENSG00000228106	ENST00000439440	exon_skip_143728	chr16:29993905-29994843	-16.68	-0.1030	HIRIP3	ENST00000279392	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_358606	chr20:63202286-63203807	-52.05	-0.1071	YTHDF1	ENST00000370339	In-frame
ENSG00000228106	ENST00000434872	exon_skip_390412	chr3:183833723-183833825	-9.88	-0.1251	PARL	ENST00000317096	In-frame
ENSG00000228106	ENST00000439440	exon_skip_445390	chr5:150403120-150403312	-16.22	-0.1053	CD74	ENST00000009530	In-frame
ENSG00000228106	ENST00000434872	exon_skip_61261	chr11:65713347-65713503	-17.22	-0.1179	KAT5	ENST00000377046	In-frame
ENSG00000228106	ENST00000434872	exon_skip_123601	chr15:74897010-74897219	-21.30	-0.1411	MPI	ENST00000352410	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_283774	chr17:78171509-78171649	-13.79	-0.1029	SYNGR2	ENST00000225777,ENST00000585591	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_430434	chr4:82356536-82356683	-13.49	-0.1046	HNRNPD	ENST00000313899	In-frame
ENSG00000228106	ENST00000434872	exon_skip_446758	chr5:178212972-178213103	-17.02	-0.1773	PHYKPL	ENST00000308158	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_446770	chr5:178215275-178215430	-14.33	-0.1024	PHYKPL	ENST00000308158	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_41813	chr10:68337857-68337996	-12.79	-0.1332	HNRNPH3	ENST00000265866	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_99811	chr13:37002272-37002309	-6.23	-0.2596	EXOSC8	ENST00000389704	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_129468	chr15:74906277-74906365	-13.07	-0.1676	FAM219B	ENST00000563119	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_140339	chr16:635611-635774	-18.49	-0.1193	METTL26	ENST00000301686	Frame-shift
ENSG00000228106	ENST00000439440	exon_skip_303345	chr19:17227839-17228005	-16.06	-0.1316	OCEL1	ENST00000215061	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_361954	chr21:39179923-39179986	-8.77	-0.1993	PSMG1	ENST00000331573	In-frame
ENSG00000228106	ENST00000448808	exon_skip_5818	chr1:45568484-45568684	-14.22	-0.1129	AKR1A1	ENST00000351829,ENST00000372070	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_52712	chr10:97476834-97476963	-12.85	-0.1412	MMS19	ENST00000370782,ENST00000438925	In-frame
ENSG00000228106	ENST00000434872	exon_skip_153767	chr17:48057031-48057121	-14.60	-0.1738	NFE2L1	ENST00000362042	In-frame
ENSG00000228106	ENST00000434872	exon_skip_11029	chr1:154989559-154989707	-15.01	-0.2001	FLAD1	ENST00000292180	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_52891	chr10:98429790-98429889	-13.11	-0.3277	HPS1	ENST00000325103,ENST00000361490	In-frame
ENSG00000228106	ENST00000420335	exon_skip_348333	chr20:409880-410025	-14.44	-0.1017	RBCK1	ENST00000356286	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_382356	chr3:37091466-37091538	-8.81	-0.1377	LRRFIP2	ENST00000336686	In-frame
ENSG00000228106	ENST00000434872	exon_skip_324294	chr2:27774423-27774530	-11.23	-0.1070	MRPL33	ENST00000296102	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_78771	chr11:134248808-134248959	-13.28	-0.1006	THYN1	ENST00000341541,ENST00000392594,ENST00000392595	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_128982	chr15:72250844-72250954	-12.85	-0.1179	PARP6	ENST00000287196,ENST00000569795	Frame-shift
ENSG00000228106	ENST00000434872	exon_skip_52895	chr10:98431130-98431291	-16.42	-0.1087	HPS1	ENST00000325103,ENST00000361490	Frame-shift

lncRNA targets by miRNA.

LncRNA Ensembl ID

miRNA ID

LncRNA ENST ID

Binding site in lncRNA

Score

Energy

Align Len

Public source

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Variants for RP11-452F19.3

RNA A-to-I editing events in lncRNA.

LncRNAediting ID

LncRNA Ensembl ID

Chromosome

Editing Position

Strand

Gene Type

Gene Name

Transcript ID

Transcript Type

Transcript Name

Edited-associated DElncRNAs in cancer.

LncRNA Ensembl ID

LncRNA Index

Cancer Type

Chr_Postion_Strand

AVE1

AVE2

log2FC

W-value

P-value

Adjc.p-value

Change

Correlation between RNA A-to-I editing events's frequecy and lncRNA expression.

LncRNA Ensembl ID

LncRNA Index

Correlation

P-value

Adjc.p-value

Cis-expression quantitative trait loci(cis-eQTL) of lncRNA.

LncRNA Ensembl ID

LncRNA Name

SNP info

Number of Positive corelated Cancer

Positive corelated Cancer

Number of Negative corelated Cancer

Negative corelated Cancer

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lncRNAs regulate the target genes through functioning as enhancers

lncRNA regulates differentially expressed genes by function as enhancer.

LncRNA Ensembl ID

PC Gene ID

PC Gene Name

Positive correlated cancers

Cancer with PC gene up-regulation

Cancer with PC gene down-regulation

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lncRNAs regulate the target genes through recruiting transcript factors

LncRNA-TF complex positively regulates the gene expression by target promoter region (#cancer types with positive correlation >= 5).

lncRNA ID

TF ID

TF Name

PCgene ID

PCgene Name

Number of Cancer

Canaer Types

LncRNA-TF complex negatively regulates the gene expression by target promoter region (#cancer types with negative correlation >= 5).

lncRNA ID

TF ID

TF Name

PCgene ID

PCgene Name

Number of Cancer

Canaer Types

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lncRNAs regulate the alternative splicing event through interacting with splicing factor

LncRNA-RBP complex positively regulates the exon skippping events by target skipped eoxon region.

LncRNA Ensembl ID

RBP ID

RBP Gene Name

Exon Skipping ID

Skipped Exon

EX Gene Name

EX Affected TransID

ORF_anno

Cancer Type

LncRNA-RBP complex negatively regulates the exon skippping events by target skipped eoxon region.

LncRNA Ensembl ID

RBP ID

RBP Gene Name

Exon Skipping ID

Skipped Exon

EX Gene Name

EX Affected TransID

ORF_anno

Cancer Type

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lncRNAs regulate mRNA through targeting the 3'-UTR region

lncRNA regulates differential expressed mRNA by directly targeting 3' UTR region.

LncRNA Ensembl ID

LncRNA ENST ID

PC Gene Name

PC Gene ID

PC ENST ID

nDG

Cancer with PC gene up-regulation

Cancer with PC gene Down-regulation

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lncRNAs regulate mRNA by competing with miRNA

lncRNA regulates mRNA by competing the miRNA binding site with mRNA.

LncRNA Ensembl ID

lncRNA-miRNA-mRNA

Cancer Types

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lncRNA coding potential

ORFfinder result for the gencode.v22.lncRNA.transcript.fa.

lncRNA Ensembl ID	lncRNA ENST ID	length(AA)	start at transcript	end at transcript
ENSG00000228106.4	ENST00000450784.4	80	204	446
ENSG00000228106.4	ENST00000426045.4	88	464	198
ENSG00000228106.4	ENST00000457955.4	88	522	256
ENSG00000228106.4	ENST00000444858.4	34	84	188
ENSG00000228106.4	ENST00000435378.4	45	165	302
ENSG00000228106.4	ENST00000441676.4	88	691	425
ENSG00000228106.4	ENST00000448808.1	88	498	232
ENSG00000228106.4	ENST00000457636.4	35	24	128
ENSG00000228106.4	ENST00000439440.1	57	171	1
ENSG00000228106.4	ENST00000442171.4	77	417	184
ENSG00000228106.4	ENST00000434872.1	88	469	203

	lncRNA summary
	lncRNA structure and expression level
	lncRNA-Protein interaction
	lncRNA-DNA interaction
	lncRNA-RNA interaction
	Variants in lncRNA
	lncRNAs regulate the target genes through functioning as enhancers
	lncRNAs regulate the target genes through recruiting transcript factors
	lncRNAs regulate the alternative splicing events through interacting with splicing factor
	lncRNAs regulate mRNA through targeting the 3'-UTR region
	lncRNAs regulate mRNA by competing with miRNA
	lncRNA coding potential