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lncRNA: ENSG00000235501

Summary for CNN3-DT

Gene summary

Gene information	Ensembl ID	ENSG00000235501
	Gene symbol	CNN3-DT
	Gene name	CNN3 divergent transcript
	HGNC	54176
	Entrez ID
	Gene type	antisense
	Synonyms	CNN3-DT\|RP4-639F20.1\|01p21.3
	UniProtAcc

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Structure and expression level for CNN3-DT

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
ENSG00000235501	2.612182e+02	-2.235103e+00	3.385663e-01	-6.601669e+00	4.070000e-11	5.640000e-10	DOWN	CHOL
ENSG00000235501	1.664064e+02	-1.324286e+00	2.806568e-01	-4.718523e+00	2.380000e-06	1.930000e-05	DOWN	BLCA
ENSG00000235501	1.455079e+02	-2.487707e+00	7.398638e-01	-3.362386e+00	7.727210e-04	6.436820e-03	DOWN	CESC
ENSG00000235501	1.087611e+02	-1.208599e+00	1.528674e-01	-7.906190e+00	2.650000e-15	2.880000e-14	DOWN	UCEC
ENSG00000235501	1.692974e+02	-1.907162e+00	4.786021e-01	-3.984858e+00	6.750000e-05	1.309122e-03	DOWN	PCPG
ENSG00000235501	2.201708e+02	-1.394770e+00	1.790680e-01	-7.789049e+00	6.750000e-15	3.280000e-14	DOWN	LUSC
ENSG00000235501	2.398907e+02	-1.102754e+00	1.155280e-01	-9.545342e+00	1.360000e-21	1.540000e-20	DOWN	LUAD
ENSG00000235501	9.929327e+01	-1.231862e+00	1.398617e-01	-8.807712e+00	1.280000e-18	1.540000e-17	DOWN	COAD
ENSG00000235501	1.890745e+02	-1.187319e+00	2.013318e-01	-5.897323e+00	3.690000e-09	3.940000e-08	DOWN	STAD
ENSG00000235501	1.120291e+02	-1.091813e+00	2.758033e-01	-3.958664e+00	7.540000e-05	5.880680e-04	DOWN	READ

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000235501	-4.871318e-01	6.897916e-04	CHOL	1.274977e-03
ENSG00000235501	3.139374e-01	2.735977e-03	KICH	3.483724e-03
ENSG00000235501	-3.250935e-01	6.471211e-16	UCEC	7.806541e-15

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lncRNA-Protein interaction for CNN3-DT

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
ENSG00000235501	ENST00000438509	RP4-639F20.1	ENSG00000106624	AEBP1	48.01	90.0464	Q8IUX7	TF	NA
ENSG00000235501	ENST00000456582	RP4-639F20.1	ENSG00000106624	AEBP1	32.72	90.2878	Q8IUX7	TF	NA
ENSG00000235501	ENST00000456582	RP4-639F20.1	ENSG00000106571	GLI3	24.85	92.0429	P10071	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

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lncRNA-DNA interaction for CNN3-DT

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 CNN3-DT

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

Only predicted by lncTar

MMS19,MCU,RABGGTA,GTF3C2,CNOT3,CASP8,YWHAZ,FAM222B,FAM83H,CNOT11,GMPPA,SLC35A2,CAPN15,PKP3,KCTD5,SLC52A2,ATP13A1,GFUS,CNOT9,NOP16

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
ENSG00000235501	ENST00000456582	exon_skip_7558	chr1:81952986-81953025	-7.15	-0.2234	ADGRL2	ENST00000370717,ENST00000370728	In-frame
ENSG00000235501	ENST00000456582	exon_skip_104174	chr13:79353152-79353224	-7.20	-0.1714	RBM26	ENST00000438737	In-frame
ENSG00000235501	ENST00000456582	exon_skip_335378	chr2:237751199-237751271	-7.24	-0.3620	LRRFIP1	ENST00000392000	In-frame
ENSG00000235501	ENST00000456582	exon_skip_43507	chr10:84499874-84499959	-11.39	-0.1700	CCSER2	ENST00000224756	Frame-shift
ENSG00000235501	ENST00000456582	exon_skip_82144	chr12:50087362-50087485	-12.54	-0.1206	SMARCD1	ENST00000394963	In-frame
ENSG00000235501	ENST00000456582	exon_skip_301850	chr19:8483157-8483211	-7.71	-0.1713	HNRNPM	ENST00000325495	In-frame
ENSG00000235501	ENST00000456582	exon_skip_357772	chr20:47659398-47659452	-7.80	-0.1696	SULF2	ENST00000359930,ENST00000484875	In-frame
ENSG00000235501	ENST00000456582	exon_skip_444483	chr5:138159554-138159599	-5.34	-0.1369	BRD8	ENST00000254900	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
ENSG00000235501	ENST00000456582	exon_skip_11286	chr1:155061903-155061975	-10.54	-0.2395	ADAM15	ENST00000356955	In-frame
ENSG00000235501	ENST00000456582	exon_skip_350485	chr20:34073818-34073866	-5.34	-0.1369	RALY	ENST00000246194	In-frame
ENSG00000235501	ENST00000456582	exon_skip_302276	chr19:10808568-10808580	-5.03	-0.4573	DNM2	ENST00000355667	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 CNN3-DT

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
ENSG00000235501	ENST00000452846	PKP3	ENSG00000184363	ENST00000331563	-0.1074	1	CHOL,CESC,UCEC,LUSC,LUAD	-
ENSG00000235501	ENST00000452846	PKP3	ENSG00000184363	ENST00000525642	-0.1722	16	CHOL,CESC,UCEC,LUSC,LUAD	-
ENSG00000235501	ENST00000452846	SLC52A2	ENSG00000185803	ENST00000527078	-1.7750	171	CHOL,BLCA,CESC,UCEC,LUSC,LUAD,COAD,STAD,READ	-
ENSG00000235501	ENST00000438509	PKP3	ENSG00000184363	ENST00000331563	-0.1139	241	CHOL,CESC,UCEC,LUSC,LUAD	-
ENSG00000235501	ENST00000438509	PKP3	ENSG00000184363	ENST00000525642	-0.1231	567	CHOL,CESC,UCEC,LUSC,LUAD	-
ENSG00000235501	ENST00000438509	SLC52A2	ENSG00000185803	ENST00000527078	-1.7750	434	CHOL,BLCA,CESC,UCEC,LUSC,LUAD,COAD,STAD,READ	-
ENSG00000235501	ENST00000438509	SLC52A2	ENSG00000185803	ENST00000526752	-0.1027	1	CHOL,BLCA,CESC,UCEC,LUSC,LUAD,COAD,STAD,READ	-
ENSG00000235501	ENST00000456582	FAM83H	ENSG00000180921	ENST00000395103	-0.1076	1	CHOL,CESC,UCEC,LUSC,LUAD,READ	-
ENSG00000235501	ENST00000456582	PKP3	ENSG00000184363	ENST00000331563	-0.1192	1	CHOL,CESC,UCEC,LUSC,LUAD	-
ENSG00000235501	ENST00000456582	PKP3	ENSG00000184363	ENST00000525642	-0.1031	70	CHOL,CESC,UCEC,LUSC,LUAD	-
ENSG00000235501	ENST00000456582	GFUS	ENSG00000104522	ENST00000529064	-0.1196	1	BLCA,CESC,UCEC,LUAD,COAD,READ	-
ENSG00000235501	ENST00000456582	GFUS	ENSG00000104522	ENST00000425753	-0.1196	1	BLCA,CESC,UCEC,LUAD,COAD,READ	-
ENSG00000235501	ENST00000456582	SLC52A2	ENSG00000185803	ENST00000530047	-0.1027	12	CHOL,BLCA,CESC,UCEC,LUSC,LUAD,COAD,STAD,READ	-
ENSG00000235501	ENST00000456582	SLC52A2	ENSG00000185803	ENST00000527078	-1.7650	167	CHOL,BLCA,CESC,UCEC,LUSC,LUAD,COAD,STAD,READ	-
ENSG00000235501	ENST00000456582	SLC52A2	ENSG00000185803	ENST00000402965	-0.1027	12	CHOL,BLCA,CESC,UCEC,LUSC,LUAD,COAD,STAD,READ	-
ENSG00000235501	ENST00000456582	SLC52A2	ENSG00000185803	ENST00000532887	-0.1190	41	CHOL,BLCA,CESC,UCEC,LUSC,LUAD,COAD,STAD,READ	-
ENSG00000235501	ENST00000456582	SLC52A2	ENSG00000185803	ENST00000329994	-0.1027	10	CHOL,BLCA,CESC,UCEC,LUSC,LUAD,COAD,STAD,READ	-
ENSG00000235501	ENST00000456582	SLC52A2	ENSG00000185803	ENST00000526779	-0.1267	122	CHOL,BLCA,CESC,UCEC,LUSC,LUAD,COAD,STAD,READ	-
ENSG00000235501	ENST00000456582	SLC52A2	ENSG00000185803	ENST00000526752	-0.1202	10	CHOL,BLCA,CESC,UCEC,LUSC,LUAD,COAD,STAD,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
ENSG00000235501.4	ENST00000452846.4	59	293	114
ENSG00000235501.4	ENST00000438509.1	128	385	2
ENSG00000235501.4	ENST00000456582.1	128	523	909

	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