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lncRNA: ENSG00000225177

Summary for RP11-390P2.4

Gene summary

Gene information	Ensembl ID	ENSG00000225177
	Gene symbol	RP11-390P2.4
	Gene name
	HGNC
	Entrez ID
	Gene type	antisense
	Synonyms
	UniProtAcc

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Structure and expression level for RP11-390P2.4

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
ENSG00000225177	4.411208e+02	1.080054e+00	3.108546e-01	3.474468e+00	5.118680e-04	2.093319e-03	UP	GBM
ENSG00000225177	1.088119e+02	-1.384821e+00	2.843564e-01	-4.870018e+00	1.120000e-06	7.260000e-06	DOWN	CHOL
ENSG00000225177	1.567860e+02	1.027135e+00	2.334781e-01	4.399278e+00	1.090000e-05	7.460000e-05	UP	BLCA
ENSG00000225177	1.040973e+02	1.028000e+00	1.767999e-01	5.814485e+00	6.080000e-09	3.760000e-08	UP	KIRP
ENSG00000225177	9.519169e+01	1.713644e+00	1.674674e-01	1.023270e+01	1.420000e-24	3.300000e-23	UP	UCEC
ENSG00000225177	8.669159e+01	1.046026e+00	1.407069e-01	7.434075e+00	1.050000e-13	1.170000e-12	UP	PRAD
ENSG00000225177	2.294833e+02	2.162131e+00	1.511761e-01	1.430206e+01	2.120000e-46	4.510000e-45	UP	LUSC
ENSG00000225177	4.841182e+01	1.040540e+00	1.306217e-01	7.966058e+00	1.640000e-15	1.550000e-14	UP	COAD
ENSG00000225177	6.083887e+01	1.482263e+00	2.790235e-01	5.312324e+00	1.080000e-07	1.730000e-06	UP	READ

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000225177	3.272650e-01	2.100168e-03	MESO	3.080133e-02
ENSG00000225177	3.351558e-01	7.094633e-17	UCEC	1.232634e-15

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lncRNA-Protein interaction for RP11-390P2.4

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
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000204371	EHMT2	70.06	93.9881	Q96KQ7	Epi	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000154832	CXXC1	38.77	91.3867	Q9P0U4	TF,Epi	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000078487	ZCWPW1	33.33	92.3159	Q9H0M4	Epi	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000071655	MBD3	14.09	90.5932	O95983	TF,Epi	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000204227	RING1	18.94	91.4344	Q06587	Epi	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000178028	DMAP1	9.97	90.3692	Q9NPF5	Epi	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000077463	SIRT6	8.3	90.6682	Q8N6T7	Epi	NA
ENSG00000225177	ENST00000447494	RP11-390P2.4	ENSG00000119403	PHF19	5.49	90.1231	Q5T6S3	TF,Epi	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000119403	PHF19	3.95	90.1334	Q5T6S3	TF,Epi	NA

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
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000167967	E4F1	60.58	90.8066	Q66K89	TF	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000099326	MZF1	48.39	94.3426	P28698	TF	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000154832	CXXC1	38.77	91.6715	Q9P0U4	TF,Epi	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000071655	MBD3	14.09	91.117	O95983	TF,Epi	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000148300	REXO4	9.05	90.0414	Q9GZR2	TF	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000125817	CENPB	7.88	90.5526	P07199	TF	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000154957	ZNF18	7.26	93.0301	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
ENSG00000225177	ENST00000447494	RP11-390P2.4	ENSG00000134815	DHX34	63.95	90.9082	Q14147	RBP	NA
ENSG00000225177	ENST00000447494	RP11-390P2.4	ENSG00000071894	CPSF1	54.97	91.4793	Q10570	RBP	NA
ENSG00000225177	ENST00000432673	RP11-390P2.4	ENSG00000204356	NELFE	12.05	92.6851	P18615	RBP	NA

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lncRNA-DNA interaction for RP11-390P2.4

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

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 RP11-390P2.4

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

Only predicted by lncTar

CNOT1,ASB8,FAM53C,VPS26C,TMED5,SLC30A6,VPS4B,UHRF1BP1L,NT5C2,NAF1,MAP4K3,HIPK1,TCF20,KPNA6,TAPT1,SECISBP2L,UBR1,STX17,SCP2,GNL3L,TAOK3,TRIP11,PTPN11,KIAA0100,MAT2B,SUCLG2,SLAIN2,PDXDC1,ERBIN,CDV3,PCBP1,ARIH1,DNAJC11,NR2C2,RAD21,SEC24B,SEC24A,DHX8,NBR1,TRAPPC8,CCDC47,PDPK1,ACBD5,PHF3,RNF111,TP53BP1,VPS37A,CCT5,CDC42SE2,CCPG1,USP32,UBE2D3,SEC24D,IQGAP1,G3BP1,SLMAP,EEA1,CLCN3,CIPC,PIAS1,FBXO11,RUNDC1,RIOK2,NCOA2,TWF1,MKLN1,SNAP23,NOLC1,DDX3X,MFSD9,CCSER2,ASXL2,MFSD14A,ROCK1,KLF13,POLR2B,AGFG1,FAM102B,IMPA1,LPCAT3,SNRNP200,NIPA2,HSPA9,NSD1,SRFBP1,RHBDD1,EIF3A,RREB1,CERT1,XRN1,SF3A1,KAT7,EPS15,AZI2,LYSMD3,GFM2,TRIP12,MTHFD1,SNX2,TNPO1,PRKAA1,SEC23B,KIF2A,PPIG,GTF2I,REST,PLS1,SNX4,EIF4G2,MORC3,SLC30A5,NDFIP2,CDC23,SMG8,CSNK1G3,CAB39,ACADM,SEC31A,BRF2,YME1L1,IL6ST,GOLM2,AFF1,ZNF28,CLINT1,TMEM184C,USP8,BCOR,RAD17,BDP1,DPP8,CPSF2,CANX,EFL1,RLF,HDHD2,CCNK,ARFGAP3,GLYR1,RALGAPA1,NDUFS1,SDAD1,RAB6A

Exist in public source

lncRNA targets the skipped exon region.

-lncRNA and exonskipping events are positively correlated.

LncRNA Ensembl ID

LncRNA ENST ID

Exon ID

Skipped Exon

ndG

Gene name with skipped exon

TransID with skipped exon

ORF mutation

-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
ENSG00000225177	ENST00000447494	exon_skip_110809	chr14:105449358-105449409	-10.96	-0.2383	MTA1	ENST00000331320	In-frame
ENSG00000225177	ENST00000432673	exon_skip_291980	chr17:59119318-59119495	-13.23	-0.1042	SKA2	ENST00000330137	In-frame
ENSG00000225177	ENST00000447494	exon_skip_370525	chr22:50250426-50250523	-20.16	-0.3600	HDAC10	ENST00000216271	Frame-shift
ENSG00000225177	ENST00000447494	exon_skip_319223	chr19:43526200-43526349	-26.09	-0.2192	ETHE1	ENST00000292147	Frame-shift
ENSG00000225177	ENST00000447494	exon_skip_326741	chr2:73946718-73946906	-16.36	-0.1239	DGUOK	ENST00000264093	Frame-shift
ENSG00000225177	ENST00000432673	exon_skip_430434	chr4:82356536-82356683	-11.89	-0.1062	HNRNPD	ENST00000313899	In-frame
ENSG00000225177	ENST00000447494	exon_skip_476535	chr7:76000889-76001002	-12.65	-0.1304	STYXL1	ENST00000248600,ENST00000359697,ENST00000431581	Frame-shift
ENSG00000225177	ENST00000447494	exon_skip_98384	chr12:124327408-124327633	-22.46	-0.1291	NCOR2	ENST00000405201	In-frame
ENSG00000225177	ENST00000447494	exon_skip_423795	chr4:55888887-55888932	-9.93	-0.4965	EXOC1	ENST00000346134,ENST00000381295	In-frame

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 RP11-390P2.4

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	dG	nDG	Cancer with PC gene up-regulation	Cancer with PC gene Down-regulation
ENSG00000225177	ENST00000432673	SLMAP	ENSG00000163681	ENST00000495364	-0.2107	270	-	BLCA,UCEC,PRAD,COAD,READ
ENSG00000225177	ENST00000432673	DNAJC11	ENSG00000007923	ENST00000451196	-0.1160	1	-	KIRP
ENSG00000225177	ENST00000428044	SLMAP	ENSG00000163681	ENST00000495364	-0.2107	274	-	BLCA,UCEC,PRAD,COAD,READ
ENSG00000225177	ENST00000458733	SLMAP	ENSG00000163681	ENST00000495364	-0.2107	203	-	BLCA,UCEC,PRAD,COAD,READ
ENSG00000225177	ENST00000447494	SLMAP	ENSG00000163681	ENST00000495364	-0.2107	274	-	BLCA,UCEC,PRAD,COAD,READ
ENSG00000225177	ENST00000428044	MORC3	ENSG00000159256	ENST00000549948	-0.1021	165	-	UCEC
ENSG00000225177	ENST00000432673	SUCLG2	ENSG00000172340	ENST00000493112	-0.1083	182	-	COAD,READ
ENSG00000225177	ENST00000432673	AFF1	ENSG00000172493	ENST00000544085	-0.6514	352	-	READ
ENSG00000225177	ENST00000432673	CIPC	ENSG00000198894	ENST00000555437	-0.1511	306	-	GBM,BLCA,KIRP,COAD,READ
ENSG00000225177	ENST00000432673	CIPC	ENSG00000198894	ENST00000555611	-0.1320	286	-	GBM,BLCA,KIRP,COAD,READ
ENSG00000225177	ENST00000432673	IL6ST	ENSG00000134352	ENST00000502326	-0.2041	109	-	BLCA,UCEC,LUSC,COAD,READ
ENSG00000225177	ENST00000432673	CDC42SE2	ENSG00000158985	ENST00000502582	-0.1155	675	-	READ
ENSG00000225177	ENST00000432673	PLS1	ENSG00000120756	ENST00000497002	-0.2558	1	-	COAD,READ
ENSG00000225177	ENST00000428044	SUCLG2	ENSG00000172340	ENST00000493112	-0.1083	186	-	COAD,READ
ENSG00000225177	ENST00000428044	AFF1	ENSG00000172493	ENST00000544085	-0.6514	356	-	READ
ENSG00000225177	ENST00000428044	CIPC	ENSG00000198894	ENST00000555437	-0.1224	310	-	GBM,BLCA,KIRP,COAD,READ
ENSG00000225177	ENST00000428044	CIPC	ENSG00000198894	ENST00000555611	-0.1248	269	-	GBM,BLCA,KIRP,COAD,READ
ENSG00000225177	ENST00000428044	IL6ST	ENSG00000134352	ENST00000502326	-0.2041	113	-	BLCA,UCEC,LUSC,COAD,READ
ENSG00000225177	ENST00000428044	CDC42SE2	ENSG00000158985	ENST00000505065	-0.1021	1	-	READ
ENSG00000225177	ENST00000428044	PLS1	ENSG00000120756	ENST00000497002	-0.1474	303	-	COAD,READ
ENSG00000225177	ENST00000458733	SUCLG2	ENSG00000172340	ENST00000493112	-0.1083	115	-	COAD,READ
ENSG00000225177	ENST00000458733	AFF1	ENSG00000172493	ENST00000544085	-0.6514	285	-	READ
ENSG00000225177	ENST00000458733	CIPC	ENSG00000198894	ENST00000555437	-0.1919	253	-	GBM,BLCA,KIRP,COAD,READ
ENSG00000225177	ENST00000458733	CIPC	ENSG00000198894	ENST00000555611	-0.1412	1	-	GBM,BLCA,KIRP,COAD,READ
ENSG00000225177	ENST00000458733	IL6ST	ENSG00000134352	ENST00000502326	-0.2041	42	-	BLCA,UCEC,LUSC,COAD,READ
ENSG00000225177	ENST00000458733	CDC42SE2	ENSG00000158985	ENST00000502582	-0.1155	461	-	READ
ENSG00000225177	ENST00000458733	PLS1	ENSG00000120756	ENST00000497002	-0.1474	232	-	COAD,READ
ENSG00000225177	ENST00000447494	AFF1	ENSG00000172493	ENST00000544085	-0.6514	356	-	READ
ENSG00000225177	ENST00000447494	CIPC	ENSG00000198894	ENST00000555437	-0.1919	324	-	GBM,BLCA,KIRP,COAD,READ
ENSG00000225177	ENST00000447494	IL6ST	ENSG00000134352	ENST00000502326	-0.6080	355	-	BLCA,UCEC,LUSC,COAD,READ
ENSG00000225177	ENST00000447494	CDC42SE2	ENSG00000158985	ENST00000502582	-0.1155	532	-	READ
ENSG00000225177	ENST00000447494	PLS1	ENSG00000120756	ENST00000497002	-0.1474	303	-	COAD,READ
ENSG00000225177	ENST00000432673	MAP4K3	ENSG00000011566	ENST00000414968	-0.2080	773	CHOL	-
ENSG00000225177	ENST00000432673	MAP4K3	ENSG00000011566	ENST00000484274	-0.1349	347	CHOL	-
ENSG00000225177	ENST00000432673	SECISBP2L	ENSG00000138593	ENST00000561428	-0.1411	375	-	GBM,LUSC,READ
ENSG00000225177	ENST00000428044	MAP4K3	ENSG00000011566	ENST00000414968	-0.1083	304	CHOL	-
ENSG00000225177	ENST00000428044	MAP4K3	ENSG00000011566	ENST00000437968	-0.1037	35	CHOL	-
ENSG00000225177	ENST00000428044	MAP4K3	ENSG00000011566	ENST00000484274	-0.1722	104	CHOL	-
ENSG00000225177	ENST00000428044	SECISBP2L	ENSG00000138593	ENST00000561428	-0.1030	214	-	GBM,LUSC,READ
ENSG00000225177	ENST00000458733	MAP4K3	ENSG00000011566	ENST00000414968	-0.2080	559	CHOL	-
ENSG00000225177	ENST00000458733	MAP4K3	ENSG00000011566	ENST00000484274	-0.1722	33	CHOL	-
ENSG00000225177	ENST00000458733	SECISBP2L	ENSG00000138593	ENST00000561428	-0.1030	143	-	GBM,LUSC,READ
ENSG00000225177	ENST00000447494	MAP4K3	ENSG00000011566	ENST00000414968	-0.2080	630	CHOL	-
ENSG00000225177	ENST00000447494	MAP4K3	ENSG00000011566	ENST00000484274	-0.3564	312	CHOL	-
ENSG00000225177	ENST00000447494	SECISBP2L	ENSG00000138593	ENST00000561428	-0.2057	308	-	GBM,LUSC,READ
ENSG00000225177	ENST00000432673	ACADM	ENSG00000117054	ENST00000420607	-0.4530	822	-	KIRP,COAD,READ
ENSG00000225177	ENST00000432673	VPS4B	ENSG00000119541	ENST00000591519	-0.2405	621	-	COAD,READ
ENSG00000225177	ENST00000432673	IMPA1	ENSG00000133731	ENST00000449740	-0.1303	680	-	COAD,READ
ENSG00000225177	ENST00000428044	SCP2	ENSG00000116171	ENST00000478274	-0.1062	1	-	COAD,READ
ENSG00000225177	ENST00000428044	SCP2	ENSG00000116171	ENST00000488965	-0.1062	1	-	COAD,READ
ENSG00000225177	ENST00000428044	ACADM	ENSG00000117054	ENST00000420607	-0.1531	378	-	KIRP,COAD,READ
ENSG00000225177	ENST00000428044	ACADM	ENSG00000117054	ENST00000528016	-0.1236	1	-	KIRP,COAD,READ
ENSG00000225177	ENST00000428044	VPS4B	ENSG00000119541	ENST00000591519	-0.2405	386	-	COAD,READ
ENSG00000225177	ENST00000428044	IMPA1	ENSG00000133731	ENST00000449740	-0.1259	318	-	COAD,READ
ENSG00000225177	ENST00000428044	TRAPPC8	ENSG00000153339	ENST00000582539	-0.2753	337	-	READ
ENSG00000225177	ENST00000458733	ACADM	ENSG00000117054	ENST00000420607	-0.4530	608	-	KIRP,COAD,READ
ENSG00000225177	ENST00000458733	VPS4B	ENSG00000119541	ENST00000591519	-0.2405	407	-	COAD,READ
ENSG00000225177	ENST00000458733	IMPA1	ENSG00000133731	ENST00000449740	-0.1303	466	-	COAD,READ
ENSG00000225177	ENST00000458733	IMPA1	ENSG00000133731	ENST00000519816	-0.1184	278	-	COAD,READ
ENSG00000225177	ENST00000447494	ACADM	ENSG00000117054	ENST00000420607	-0.4530	679	-	KIRP,COAD,READ
ENSG00000225177	ENST00000447494	VPS4B	ENSG00000119541	ENST00000591519	-0.2405	478	-	COAD,READ
ENSG00000225177	ENST00000447494	IMPA1	ENSG00000133731	ENST00000449740	-0.1303	537	-	COAD,READ
ENSG00000225177	ENST00000447494	IMPA1	ENSG00000133731	ENST00000519816	-0.1184	349	-	COAD,READ

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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
ENSG00000225177.4	ENST00000432673.1	168	120	626
ENSG00000225177.4	ENST00000428044.4	104	605	916
ENSG00000225177.4	ENST00000458733.4	69	214	420
ENSG00000225177.4	ENST00000447494.1	104	391	702

	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