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lncRNA: ENSG00000261338

Summary for RP11-378A13.1

Gene summary

Gene information	Ensembl ID	ENSG00000261338
	Gene symbol	RP11-378A13.1
	Gene name
	HGNC
	Entrez ID
	Gene type	sense_overlapping
	Synonyms
	UniProtAcc

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Structure and expression level for RP11-378A13.1

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
ENSG00000261338	1.060392e+02	-1.534462e+00	2.455744e-01	-6.248461e+00	4.150000e-10	7.310000e-09	DOWN	GBM
ENSG00000261338	1.061308e+02	-1.593896e+00	1.004027e-01	-1.587503e+01	9.440000e-57	7.280000e-55	DOWN	LUAD

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000261338	-3.647581e-01	7.019842e-20	LUAD	3.309942e-18

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lncRNA-Protein interaction for RP11-378A13.1

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
ENSG00000261338	ENST00000562328	RP11-378A13.1	ENSG00000073584	SMARCE1	2.0	91.974	Q969G3	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

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

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lncRNA-DNA interaction for RP11-378A13.1

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

Only predicted by TDF

C2orf42,IFFO1,ADD1,MAP2K4,IDS,PIP5K1C,VAMP1,CLN5,MTMR10,PPP3CB,ZBTB4,CLIP3,C3orf62,VAMP2,GNAI2,EID1,LPCAT4,CBX7,HSPB8,NLRP1,RILPL2,LDB2,N4BP2L1,DENND6B,PRICKLE2,MAP1A,LARGE1,BORCS7,SMARCE1,IGIP,ANXA11,PAFAH1B1,AP3S2,PPP1R21,BMERB1,ISCU,SSBP3,PPM1M,YPEL5,RAI2,SERP2,PTPRN2,CLK1,CTDSP1,LIMS2,ZNF25,GNB5,WDR47

Exist in public source

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

Only predicted by TDF

HSPB8,VAMP2,PAFAH1B1,ZBTB4,CNTNAP1,RILPL2,CRTC1,MAP1A

Exist in public source

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

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lncRNA-RNA interaction for RP11-378A13.1

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

Only predicted by lncTar

RAD54L,GMPS,SGO1,PSMD2,ALG3,CDCA5,CENPN,NDC80,DLGAP5,NCAPH,BUB1,TROAP,SPAG5,ORC1,CENPI,ECE2,EIF4G1,TUBA1C,HDGF,CHEK1,POLD1,CSTF2,STIL,FANCA,CENPL,CDC20,RFC4

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 Ensembl ID

LncRNA ENST ID

Exon ID

Skipped Exon

ndG

Gene name with skipped exon

TransID with skipped exon

LOF

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 RP11-378A13.1

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
LncEditing_99663	ENSG00000261338.2	chr2	218256306	+	sense_overlapping	RP11-378A13.1	ENST00000562328.2	sense_overlapping	RP11-378A13.1-001

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
ENSG00000261338	LncEditing_99663	KIRC	chr2_218256306_+	1.470097e+00	1.043984e+00	2.025059e+00	7.714335e+00	1.216147e-14	2.276064e-14	UP
ENSG00000261338	LncEditing_99663	DLBC	chr2_218256306_+	2.762101e+00	1.393852e+00	1.013491e+00	3.397964e+00	6.788928e-04	2.657046e-03	UP
ENSG00000261338	LncEditing_99663	MESO	chr2_218256306_+	1.984935e+00	1.164244e+00	1.299211e+00	4.105895e+00	4.027523e-05	1.063241e-04	UP
ENSG00000261338	LncEditing_99663	LGG	chr2_218256306_+	1.992744e+00	1.317781e+00	1.676035e+00	1.090006e+01	1.151763e-27	5.457349e-27	UP
ENSG00000261338	LncEditing_99663	PCPG	chr2_218256306_+	1.926571e+00	1.510923e+00	2.852211e+00	3.291746e+00	9.956765e-04	1.260153e-03	UP
ENSG00000261338	LncEditing_99663	KIRP	chr2_218256306_+	2.554267e+00	1.636184e+00	1.556239e+00	5.686349e+00	1.297844e-08	2.438209e-08	UP
ENSG00000261338	LncEditing_99663	THCA	chr2_218256306_+	1.459495e+00	1.137371e+00	2.779585e+00	6.169525e+00	6.849524e-10	1.283761e-09	UP
ENSG00000261338	LncEditing_99663	THYM	chr2_218256306_+	2.068078e+00	1.534636e+00	2.323453e+00	4.408002e+00	1.043287e-05	2.235025e-05	UP
ENSG00000261338	LncEditing_99663	BRCA	chr2_218256306_+	1.562631e+00	9.278137e-01	1.329663e+00	1.222590e+01	2.260763e-34	4.906194e-34	UP
ENSG00000261338	LncEditing_99663	PAAD	chr2_218256306_+	1.769221e+00	1.236147e+00	1.933246e+00	5.054132e+00	4.323515e-07	9.312187e-07	UP

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

LncRNA Ensembl ID	LncRNA Index	Correlation	P-value	Adjc.p-value
ENSG00000261338	LncEditing_99663	-4.510754e-01	6.188499e-04	1.663077e-03

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
ENSG00000261338	ENSG00000176454	LPCAT4	BLCA,GBM,LGG,PRAD,THCA,UVM		GBM
ENSG00000261338	ENSG00000010404	IDS	BRCA,GBM,LGG,PAAD,UVM		GBM
ENSG00000261338	ENSG00000069966	GNB5	BRCA,DLBC,GBM,LGG,PAAD,PRAD,UVM		GBM
ENSG00000261338	ENSG00000100307	CBX7	BRCA,DLBC,GBM,LGG,LUAD,PAAD,PRAD		GBM,LUAD
ENSG00000261338	ENSG00000150977	RILPL2	BRCA,KIRP,LUAD,PRAD,UVM		LUAD
ENSG00000261338	ENSG00000182700	IGIP	BRCA,GBM,KIRP,LGG,PAAD,UCEC,UVM		GBM
ENSG00000261338	ENSG00000220205	VAMP2	BRCA,DLBC,GBM,LGG,LUAD,PAAD		GBM,LUAD
ENSG00000261338	ENSG00000072163	LIMS2	DLBC,KIRP,LUAD,PAAD,PRAD,THCA		LUAD
ENSG00000261338	ENSG00000105270	CLIP3	DLBC,GBM,LGG,PAAD,PRAD		GBM
ENSG00000261338	ENSG00000131831	RAI2	DLBC,GBM,KIRP,LUAD,PAAD,PRAD		GBM,LUAD
ENSG00000261338	ENSG00000139597	N4BP2L1	DLBC,GBM,KIRP,LUAD,PAAD		GBM,LUAD
ENSG00000261338	ENSG00000152137	HSPB8	DLBC,LUAD,PAAD,PRAD,UVM		LUAD
ENSG00000261338	ENSG00000155093	PTPRN2	DLBC,GBM,KIRP,PAAD,SARC		GBM
ENSG00000261338	ENSG00000166912	MTMR10	DLBC,KIRC,LAML,LUAD,PAAD,UVM		LUAD
ENSG00000261338	ENSG00000007168	PAFAH1B1	GBM,LGG,LUAD,PAAD,UVM		GBM
ENSG00000261338	ENSG00000065559	MAP2K4	GBM,KIRP,LGG,PAAD,UVM		GBM
ENSG00000261338	ENSG00000085433	WDR47	GBM,LGG,LUAD,PAAD,UVM		GBM
ENSG00000261338	ENSG00000107758	PPP3CB	GBM,KIRC,LGG,PAAD,UVM		GBM
ENSG00000261338	ENSG00000122359	ANXA11	GBM,KIRC,KIRP,LGG,SARC		GBM
ENSG00000261338	ENSG00000133424	LARGE1	GBM,LGG,MESO,PAAD,PRAD		GBM
ENSG00000261338	ENSG00000139190	VAMP1	GBM,KIRP,LGG,PAAD,UVM		GBM
ENSG00000261338	ENSG00000151778	SERP2	GBM,KIRP,PAAD,PRAD,THCA		GBM
ENSG00000261338	ENSG00000162869	PPP1R21	GBM,LAML,LGG,PAAD,UVM		GBM
ENSG00000261338	ENSG00000163637	PRICKLE2	GBM,LGG,LUAD,PAAD,PRAD		GBM,LUAD
ENSG00000261338	ENSG00000166780	BMERB1	GBM,LGG,PAAD,PRAD,UVM		GBM
ENSG00000261338	ENSG00000166963	MAP1A	GBM,LGG,PAAD,PRAD,UVM		GBM
ENSG00000261338	ENSG00000169744	LDB2	GBM,LGG,LUAD,PAAD,UVM		GBM,LUAD
ENSG00000261338	ENSG00000186111	PIP5K1C	GBM,LGG,MESO,PAAD,PRAD		GBM
ENSG00000261338	ENSG00000205593	DENND6B	GBM,KIRP,LGG,PAAD,THCA		GBM

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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
ENSG00000261338	ENST00000562328	POLD1	ENSG00000062822	ENST00000600859	-0.1269	1079	GBM	-
ENSG00000261338	ENST00000562328	POLD1	ENSG00000062822	ENST00000613923	-0.1661	1877	GBM	-
ENSG00000261338	ENST00000562328	POLD1	ENSG00000062822	ENST00000440232	-0.3594	1881	GBM	-
ENSG00000261338	ENST00000562328	POLD1	ENSG00000062822	ENST00000599857	-0.3594	1881	GBM	-
ENSG00000261338	ENST00000562328	SPAG5	ENSG00000076382	ENST00000321765	-0.1348	1775	GBM,LUAD	-
ENSG00000261338	ENST00000562328	SPAG5	ENSG00000076382	ENST00000582076	-0.1021	1188	GBM,LUAD	-
ENSG00000261338	ENST00000562328	SPAG5	ENSG00000076382	ENST00000578230	-0.1185	1652	GBM,LUAD	-
ENSG00000261338	ENST00000562328	NDC80	ENSG00000080986	ENST00000261597	-0.1206	1850	GBM,LUAD	-
ENSG00000261338	ENST00000562328	NDC80	ENSG00000080986	ENST00000576274	-0.1058	600	GBM,LUAD	-
ENSG00000261338	ENST00000562328	ORC1	ENSG00000085840	ENST00000371568	-0.2071	1078	GBM,LUAD	-
ENSG00000261338	ENST00000562328	ORC1	ENSG00000085840	ENST00000371566	-0.2149	1080	GBM,LUAD	-
ENSG00000261338	ENST00000562328	RAD54L	ENSG00000085999	ENST00000488942	-0.1505	1698	GBM,LUAD	-
ENSG00000261338	ENST00000562328	CENPI	ENSG00000102384	ENST00000423383	-1.0083	820	GBM,LUAD	-
ENSG00000261338	ENST00000562328	CDC20	ENSG00000117399	ENST00000310955	-0.1985	1728	GBM,LUAD	-
ENSG00000261338	ENST00000562328	CDC20	ENSG00000117399	ENST00000372462	-0.1985	1728	GBM,LUAD	-
ENSG00000261338	ENST00000562328	CENPL	ENSG00000120334	ENST00000345664	-0.1052	956	GBM,LUAD	-
ENSG00000261338	ENST00000562328	CENPL	ENSG00000120334	ENST00000367710	-0.1052	956	GBM,LUAD	-
ENSG00000261338	ENST00000562328	NCAPH	ENSG00000121152	ENST00000435349	-0.1055	1270	GBM,LUAD	-
ENSG00000261338	ENST00000562328	STIL	ENSG00000123473	ENST00000396221	-0.1736	1185	GBM,LUAD	-
ENSG00000261338	ENST00000562328	DLGAP5	ENSG00000126787	ENST00000247191	-0.2303	1993	GBM,LUAD	-
ENSG00000261338	ENST00000562328	DLGAP5	ENSG00000126787	ENST00000554067	-0.3050	1530	GBM,LUAD	-
ENSG00000261338	ENST00000562328	SGO1	ENSG00000129810	ENST00000425061	-0.1766	157	GBM,LUAD	-
ENSG00000261338	ENST00000562328	SGO1	ENSG00000129810	ENST00000443724	-0.1766	157	GBM,LUAD	-
ENSG00000261338	ENST00000562328	SGO1	ENSG00000129810	ENST00000421451	-0.1766	157	GBM,LUAD	-
ENSG00000261338	ENST00000562328	SGO1	ENSG00000129810	ENST00000452020	-0.1766	157	GBM,LUAD	-
ENSG00000261338	ENST00000562328	SGO1	ENSG00000129810	ENST00000412997	-0.1190	1039	GBM,LUAD	-
ENSG00000261338	ENST00000562328	SGO1	ENSG00000129810	ENST00000417364	-0.2661	1148	GBM,LUAD	-
ENSG00000261338	ENST00000562328	TROAP	ENSG00000135451	ENST00000549275	-1.4829	676	GBM,LUAD	-
ENSG00000261338	ENST00000562328	TROAP	ENSG00000135451	ENST00000551245	-0.2781	1234	GBM,LUAD	-
ENSG00000261338	ENST00000562328	TROAP	ENSG00000135451	ENST00000380327	-0.1962	592	GBM,LUAD	-
ENSG00000261338	ENST00000562328	TROAP	ENSG00000135451	ENST00000548311	-0.1781	568	GBM,LUAD	-
ENSG00000261338	ENST00000562328	TROAP	ENSG00000135451	ENST00000550709	-0.1101	604	GBM,LUAD	-
ENSG00000261338	ENST00000562328	TROAP	ENSG00000135451	ENST00000257909	-0.1345	1234	GBM,LUAD	-
ENSG00000261338	ENST00000562328	TROAP	ENSG00000135451	ENST00000547923	-0.2534	1234	GBM,LUAD	-
ENSG00000261338	ENST00000562328	HDGF	ENSG00000143321	ENST00000368206	-0.1516	1249	LUAD	-
ENSG00000261338	ENST00000562328	ECE2	ENSG00000145194	ENST00000357474	-0.1975	1449	LUAD	-
ENSG00000261338	ENST00000562328	CHEK1	ENSG00000149554	ENST00000427383	-0.2773	1961	GBM,LUAD	-
ENSG00000261338	ENST00000562328	CHEK1	ENSG00000149554	ENST00000428830	-0.3477	1055	GBM,LUAD	-
ENSG00000261338	ENST00000562328	CHEK1	ENSG00000149554	ENST00000524737	-0.1927	604	GBM,LUAD	-
ENSG00000261338	ENST00000562328	CHEK1	ENSG00000149554	ENST00000498122	-0.2634	1055	GBM,LUAD	-
ENSG00000261338	ENST00000562328	CENPN	ENSG00000166451	ENST00000299572	-0.2578	343	LUAD	-
ENSG00000261338	ENST00000562328	CENPN	ENSG00000166451	ENST00000428963	-0.8860	1107	LUAD	-
ENSG00000261338	ENST00000562328	CENPN	ENSG00000166451	ENST00000568445	-0.2328	1103	LUAD	-
ENSG00000261338	ENST00000562328	CENPN	ENSG00000166451	ENST00000562943	-0.1341	1425	LUAD	-
ENSG00000261338	ENST00000562328	BUB1	ENSG00000169679	ENST00000409311	-0.1109	1733	GBM,LUAD	-
ENSG00000261338	ENST00000562328	BUB1	ENSG00000169679	ENST00000302759	-0.1109	1733	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000561722	-0.2048	977	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000567879	-0.2163	1265	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000564475	-3.2550	1159	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000568626	-0.1048	1079	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000561660	-0.1235	1122	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000567510	-0.1144	1146	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000567621	-0.1154	1192	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000566409	-0.1024	899	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000543736	-0.1446	1332	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000534992	-0.1538	1332	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000565582	-0.1134	1232	GBM,LUAD	-
ENSG00000261338	ENST00000562328	FANCA	ENSG00000187741	ENST00000563513	-0.1128	300	GBM,LUAD	-
ENSG00000261338	ENST00000562328	RFC4	ENSG00000163918	ENST00000433496	-0.1350	1179	GBM,LUAD	-
ENSG00000261338	ENST00000562328	RFC4	ENSG00000163918	ENST00000392481	-0.1781	1179	GBM,LUAD	-
ENSG00000261338	ENST00000562328	RFC4	ENSG00000163918	ENST00000296273	-0.1840	1164	GBM,LUAD	-
ENSG00000261338	ENST00000562328	RFC4	ENSG00000163918	ENST00000417876	-0.1119	1167	GBM,LUAD	-
ENSG00000261338	ENST00000562328	ALG3	ENSG00000214160	ENST00000397676	-0.1315	1194	GBM,LUAD	-
ENSG00000261338	ENST00000562328	ALG3	ENSG00000214160	ENST00000445626	-0.1414	1732	GBM,LUAD	-
ENSG00000261338	ENST00000562328	ALG3	ENSG00000214160	ENST00000455059	-0.3031	1776	GBM,LUAD	-

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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
ENSG00000261338.2	ENST00000562328.2	103	64	375

	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