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lncRNA: ENSG00000277744

Summary for CTC-435M10.12

Gene summary

Gene information	Ensembl ID	ENSG00000277744
	Gene symbol	CTC-435M10.12
	Gene name
	HGNC
	Entrez ID
	Gene type	sense_intronic
	Synonyms
	UniProtAcc

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Structure and expression level for CTC-435M10.12

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
ENSG00000277744	3.133490e+01	2.709409e+00	4.465364e-01	6.067612e+00	1.300000e-09	1.420000e-08	UP	CHOL
ENSG00000277744	3.844517e+01	2.075200e+00	1.713999e-01	1.210736e+01	9.660000e-34	1.180000e-32	UP	KIRC
ENSG00000277744	2.722345e+01	1.054276e+00	2.822667e-01	3.735037e+00	1.876880e-04	9.033310e-04	UP	BLCA
ENSG00000277744	5.015645e+01	1.101570e+00	2.406557e-01	4.577369e+00	4.710000e-06	1.830000e-05	UP	KIRP
ENSG00000277744	2.606983e+01	1.164380e+00	1.655826e-01	7.032016e+00	2.040000e-12	8.440000e-12	UP	LUSC
ENSG00000277744	2.380478e+01	1.244167e+00	1.655872e-01	7.513669e+00	5.750000e-14	3.710000e-13	UP	LUAD

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000277744	3.187753e-01	4.719142e-03	ACC	1.512769e-02
ENSG00000277744	5.701288e-01	4.343990e-05	CHOL	1.675823e-04

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lncRNA-Protein interaction for CTC-435M10.12

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
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000204371	EHMT2	55.49	91.141	Q96KQ7	Epi	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000185658	BRWD1	42.46	93.6442	Q9NSI6	Epi	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000143442	POGZ	36.16	91.8703	Q7Z3K3	Epi	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000104885	DOT1L	36.0	93.41	Q8TEK3	TF,Epi	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000123636	BAZ2B	59.0	94.0655	Q9UIF8	TF,Epi	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000275023	MLLT6	43.56	93.2922	P55198	Epi	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000149929	HIRIP3	9.05	91.7935	Q9BW71	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
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000123636	BAZ2B	59.0	94.2574	Q9UIF8	TF,Epi	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000167967	E4F1	47.3	90.5344	Q66K89	TF	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000104885	DOT1L	36.0	93.4556	Q8TEK3	TF,Epi	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000141258	SGSM2	33.16	91.036	O43147	TF	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000065029	ZNF76	17.57	90.3066	P36508	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
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000004534	RBM6	45.63	91.0288	P78332	RBP	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000184863	RBM33	14.35	90.2169	Q96EV2	RBP	NA
ENSG00000277744	ENST00000616866	CTC-435M10.12	ENSG00000167978	SRRM2	12.44	97.2676	Q9UQ35	RBP	NA

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lncRNA-DNA interaction for CTC-435M10.12

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 CTC-435M10.12

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

Only predicted by lncTar

CNIH1,COPB2,HSD17B4,MRPL19,SNX2,SH3GLB1,CCDC47,EIF3L,HPS5,EIF4G2,RAB31,HSPA8,M6PR,CSNK1A1,UHRF1BP1L,MYH9,ARSB,TANGO6,CHP1,VAMP7,SCARB2,ILK,CAB39,PDLIM5,SEC31A,YWHAZ,RAB18,CCT5,YME1L1,CYFIP1,SCP2,NRBF2,MAIP1,UGP2,RAP1B,IQGAP1,DYNC1I2,SBDS,HCCS,ATP5F1B,PLAA,PTPN11,FERMT2,OSBPL8,CORO1C,RNF19B,PLEKHB2,SDCBP,NCOA4,EIF4G1,TUBA1C,BZW1,STRAP,RAB7A,SEC23A,TMLHE,STK24,SLAIN2,ABHD5,ATP6V0C,AZI2,ATP5PB,ST13,DNAJC14,SELENOT,PSMC1,ACTR2,SRP72,CAP1,CLTC,NDUFS1,NOMO2,RAB6A

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
ENSG00000277744	ENST00000616866	exon_skip_1234	chr1:11658532-11658628	-14.56	-0.1820	FBXO44	ENST00000251547,ENST00000376770	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
ENSG00000277744	ENST00000616866	exon_skip_9446	chr1:147270931-147271005	-9.34	-0.1483	CHD1L	ENST00000369258	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_132563	chr16:2527560-2527615	-13.29	-0.3091	AMDHD2	ENST00000293971	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_302168	chr19:10680345-10680443	-11.45	-0.1613	ILF3	ENST00000590261	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_319223	chr19:43526200-43526349	-16.14	-0.1113	ETHE1	ENST00000292147	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_377198	chr3:123130479-123130616	-17.10	-0.2192	PDIA5	ENST00000316218	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_382458	chr3:38131595-38131638	-10.02	-0.3131	ACAA1	ENST00000333167	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_11029	chr1:154989559-154989707	-16.89	-0.2194	FLAD1	ENST00000292180	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_16568	chr1:201989382-201989531	-16.40	-0.1390	RNPEP	ENST00000295640	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_41813	chr10:68337857-68337996	-18.63	-0.1620	HNRNPH3	ENST00000265866	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_41841	chr10:68756272-68756483	-25.14	-0.1496	CCAR1	ENST00000265872	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_66185	chr11:124626472-124626609	-20.53	-0.1567	TBRG1	ENST00000441174	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_66482	chr11:126274926-126275021	-14.01	-0.1610	FOXRED1	ENST00000263578	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_92074	chr12:50142052-50142110	-7.36	-0.1389	CERS5	ENST00000317551	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_95407	chr12:95040475-95040597	-12.22	-0.1063	NR2C1	ENST00000333003	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_114365	chr14:74290026-74290118	-12.36	-0.3745	ABCD4	ENST00000356924	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_290158	chr17:42953723-42953778	-7.18	-0.1465	AARSD1	ENST00000427569	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_300663	chr19:1425877-1425960	-9.08	-0.1227	DAZAP1	ENST00000233078	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_327433	chr2:86125794-86125880	-7.12	-0.1295	PTCD3	ENST00000254630	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_339830	chr2:69423581-69423717	-15.42	-0.1307	NFU1	ENST00000410022	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_370518	chr22:50247691-50247776	-15.71	-0.2310	HDAC10	ENST00000216271	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_433210	chr4:177436275-177436351	-8.45	-0.1760	AGA	ENST00000264595	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_442657	chr5:74730259-74730398	-16.55	-0.1357	GFM2	ENST00000296805,ENST00000509430	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_470226	chr7:103307595-103307708	-14.81	-0.1592	PMPCB	ENST00000249269	Frame-shift
ENSG00000277744	ENST00000616866	exon_skip_374581	chr3:50110378-50110463	-16.84	-0.2079	RBM5	ENST00000347869	Frame-shift

lncRNA targets by miRNA.

LncRNA Ensembl ID	miRNA ID	LncRNA ENST ID	Binding site in lncRNA	Score	Energy	Align Len	Public source
ENSG00000277744	hsa-mir-378a	ENST00000616866	chr19:41374153-41374222	203.00	-74.43	69	NA
ENSG00000277744	hsa-mir-378a	ENST00000616866	chr19:41374238-41374311	174.00	-81.88	68	NA
ENSG00000277744	hsa-mir-22	ENST00000616866	chr19:41374148-41374233	163.00	-86.76	85	NA
ENSG00000277744	hsa-mir-22	ENST00000616866	chr19:41374232-41374326	153.00	-96.17	89	NA
ENSG00000277744	hsa-mir-22	ENST00000616866	chr19:41374048-41374138	148.00	-70.14	93	NA

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Variants for CTC-435M10.12

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
ENSG00000277744	ENSG00000184863	RBM33	exon_skip_382458	ENSG00000060971:chr3:38131595-38131638	ACAA1	ENST00000333167	Frame-shift	SARC,OV,UCS,PAAD,THCA
ENSG00000277744	ENSG00000004534	RBM6	exon_skip_382458	ENSG00000060971:chr3:38131595-38131638	ACAA1	ENST00000333167	Frame-shift	SARC,OV,UCS,PCPG,PAAD,TGCT,THCA

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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
ENSG00000277744	ENST00000616866	CNIH1	ENSG00000100528	ENST00000556113	-0.1667	184	-	CHOL
ENSG00000277744	ENST00000616866	CORO1C	ENSG00000110880	ENST00000546705	-0.1362	208	-	BLCA
ENSG00000277744	ENST00000616866	CORO1C	ENSG00000110880	ENST00000421578	-0.7690	190	-	BLCA
ENSG00000277744	ENST00000616866	SBDS	ENSG00000126524	ENST00000617799	-0.7067	351	-	BLCA
ENSG00000277744	ENST00000616866	FERMT2	ENSG00000073712	ENST00000399304	-0.1109	307	-	CHOL,BLCA,LUSC,LUAD
ENSG00000277744	ENST00000616866	SEC23A	ENSG00000100934	ENST00000557280	-0.2064	320	-	CHOL,BLCA
ENSG00000277744	ENST00000616866	SEC23A	ENSG00000100934	ENST00000553970	-0.2064	320	-	CHOL,BLCA
ENSG00000277744	ENST00000616866	TANGO6	ENSG00000103047	ENST00000261778	-0.1559	173	-	CHOL
ENSG00000277744	ENST00000616866	HPS5	ENSG00000110756	ENST00000537258	-0.1265	216	-	CHOL,LUAD
ENSG00000277744	ENST00000616866	SCP2	ENSG00000116171	ENST00000533119	-0.1068	1	-	CHOL
ENSG00000277744	ENST00000616866	HSD17B4	ENSG00000133835	ENST00000513628	-0.1285	200	-	CHOL,LUSC
ENSG00000277744	ENST00000616866	NRBF2	ENSG00000148572	ENST00000611479	-0.1115	93	-	CHOL
ENSG00000277744	ENST00000616866	PDLIM5	ENSG00000163110	ENST00000512274	-0.1014	176	-	CHOL,BLCA
ENSG00000277744	ENST00000616866	PDLIM5	ENSG00000163110	ENST00000504489	-0.1111	302	-	CHOL,BLCA
ENSG00000277744	ENST00000616866	PDLIM5	ENSG00000163110	ENST00000509357	-0.1021	204	-	CHOL,BLCA
ENSG00000277744	ENST00000616866	UGP2	ENSG00000169764	ENST00000497510	-0.1093	109	-	CHOL
ENSG00000277744	ENST00000616866	UGP2	ENSG00000169764	ENST00000467400	-0.1112	109	-	CHOL

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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
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,DENND6B	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,SALL2	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,PRR36	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,BRSK1	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,ABCA2	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,TCTN2	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,EPOR	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,TSPOAP1	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,FIZ1	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,EFHC1	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,PLXNB1	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-378a,CLBA1	TGCT,CHOL,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-22,BRAT1	CHOL,MESO,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-22,ING5	CHOL,MESO,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-22,CEP131	CHOL,MESO,UCS,PAAD,KIRP
ENSG00000277744	CTC-435M10.12,hsa-mir-22,TSEN54	CHOL,MESO,UCS,PAAD,KIRP

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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
ENSG00000277744.1	ENST00000616866.1	70	2	214

	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