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lncRNA: ENSG00000260257

Summary for RP5-1085F17.3

Gene summary

Gene information	Ensembl ID	ENSG00000260257
	Gene symbol	RP5-1085F17.3
	Gene name
	HGNC
	Entrez ID	119746555
	Gene type	lincRNA
	Synonyms
	UniProtAcc

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Structure and expression level for RP5-1085F17.3

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
ENSG00000260257	5.142808e+02	1.486087e+00	2.223682e-01	6.683002e+00	2.340000e-11	1.560000e-10	UP	KICH

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000260257	5.748280e-01	3.630738e-05	CHOL	1.499144e-04
ENSG00000260257	3.303570e-01	1.568003e-03	KICH	2.085495e-03

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lncRNA-Protein interaction for RP5-1085F17.3

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
ENSG00000260257	ENST00000569087	RP5-1085F17.3	ENSG00000130254	SAFB2	75.06	93.192	Q14151	TF,RBP	NA
ENSG00000260257	ENST00000569087	RP5-1085F17.3	ENSG00000166432	ZMAT1	32.66	94.1088	Q5H9K5	TF	NA
ENSG00000260257	ENST00000569087	RP5-1085F17.3	ENSG00000185252	ZNF74	26.86	90.3889	Q16587	TF,RBP	NA
ENSG00000260257	ENST00000569087	RP5-1085F17.3	ENSG00000130522	JUND	21.14	90.9591	P17535	TF	NA
ENSG00000260257	ENST00000569087	RP5-1085F17.3	ENSG00000128272	ATF4	14.72	90.7218	P18848	TF	NA
ENSG00000260257	ENST00000569087	RP5-1085F17.3	ENSG00000179943	FIZ1	13.64	91.8608	Q96SL8	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
ENSG00000260257	ENST00000569087	RP5-1085F17.3	ENSG00000130254	SAFB2	75.06	93.2207	Q14151	TF,RBP	NA
ENSG00000260257	ENST00000569087	RP5-1085F17.3	ENSG00000185252	ZNF74	26.86	90.0831	Q16587	TF,RBP	NA
ENSG00000260257	ENST00000569087	RP5-1085F17.3	ENSG00000111364	DDX55	13.81	94.4047	Q8NHQ9	RBP	ENCODE

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lncRNA-DNA interaction for RP5-1085F17.3

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

Only predicted by TDF

ZNF30,RBM19,SLIRP,GLI4,MYPOP,IRF3,CIRBP,DDX56,IMP3,MZF1,NRF1,HES6,CENPB,RBM28,ZNF74,DDX55,ZFP14,ZFP69,SNRPA,SAFB2,THOC1,LSM3,TFAP4,LSM5,EIF3G,PA2G4,CENPT,TTC14,ZGLP1,PCBP2,SUGP1,LSM4,RBM4B,CSTF3,TCFL5,CPSF1,RNPS1,NR2F6,CWC15,NFYC,DHX34,CPSF4,PPIE,SF3B6,NELFE,USF1,CXXC1,CSTF1,HSF1,ZNF22,PHF1,THYN1,ZC3H8,DEAF1,DDX49,HSF4,THOC6,RBM42,KLF16,ZNF48,SGSM2,ATF4,SF3B4,TIGD1,DDX51,E2F4,MBD3,PCBP4,THAP3,FOXP1,ZGPAT,FIZ1,PBX4,ZMAT1,ZNF83,ZNF3,NXF1,ZNF8,ZNF18,DDX11,SOX12,HMGN3,NOP2,THAP8,LSM2,ZNF84,PIN1,TRA2A,SMYD3,THOC7,USF2,RALY,RBM33,ZNF10

Exist in public source

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

Only predicted by TDF

PA2G4,SF3B4,CENPB,ZNF18,ZMAT1,ZNF3,E2F4,SMYD3,TCFL5,ZNF30,TRA2A,FOXS1,ZFP14,EIF3G,E4F1,THAP7,RBM19,ZNF83,USF1,USF2,THAP3,SRP14,MZF1,LSM2,ZNF22,CXXC1,SRSF5,TFAP4,RBMX2,RBM42,PBX4,CWC15,ZNF48,THOC7,SNRPA,RNPS1,RBM6,PCBP2,CIRBP

Exist in public source

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

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lncRNA-RNA interaction for RP5-1085F17.3

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

Only predicted by lncTar

SMAD1,BAZ2A,HBP1,HELZ2,BRF2,ZNF28,FOXN3,NOP9,GRHL2,AKAP1,STAT3,SF3A1,ADNP2,ATF1,PBX1,ADAT1,DDX3X,GLYR1,PPARA,RBM7

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
ENSG00000260257	ENST00000569087	exon_skip_84780	chr12:57720098-57720263	-19.14	-0.1507	OS9	ENST00000315970	In-frame
ENSG00000260257	ENST00000569087	exon_skip_110959	chr14:20372732-20372857	-18.94	-0.1676	TEP1	ENST00000262715	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_111863	chr14:23565815-23565892	-14.71	-0.1988	AP1G2	ENST00000308724,ENST00000397120	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_111870	chr14:23566561-23566686	-15.25	-0.1540	AP1G2	ENST00000397120	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_114365	chr14:74290026-74290118	-13.76	-0.1938	ABCD4	ENST00000356924	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_114376	chr14:74293153-74293248	-14.54	-0.1598	ABCD4	ENST00000356924	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_309204	chr19:49181348-49181461	-18.18	-0.3081	TRPM4	ENST00000252826	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_319223	chr19:43526200-43526349	-23.71	-0.1796	ETHE1	ENST00000292147	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_326741	chr2:73946718-73946906	-21.52	-0.1151	DGUOK	ENST00000264093	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_370518	chr22:50247691-50247776	-13.25	-0.1656	HDAC10	ENST00000216271	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_382458	chr3:38131595-38131638	-7.93	-0.2266	ACAA1	ENST00000333167	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_384420	chr3:49812647-49812738	-14.86	-0.1670	UBA7	ENST00000333486	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_41813	chr10:68337857-68337996	-23.09	-0.1908	HNRNPH3	ENST00000265866	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_52701	chr10:97468965-97469104	-16.62	-0.1614	MMS19	ENST00000370782,ENST00000438925	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_53559	chr10:101793912-101793998	-13.35	-0.2086	OGA	ENST00000361464	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_66800	chr11:130123611-130123779	-16.32	-0.1525	APLP2	ENST00000263574	In-frame
ENSG00000260257	ENST00000569087	exon_skip_90780	chr12:26979783-26979936	-17.12	-0.1515	TM7SF3	ENST00000343028	In-frame
ENSG00000260257	ENST00000569087	exon_skip_92074	chr12:50142052-50142110	-8.33	-0.1700	CERS5	ENST00000317551	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_100646	chr13:52661474-52661570	-12.17	-0.1323	SUGT1	ENST00000343788	In-frame
ENSG00000260257	ENST00000569087	exon_skip_290158	chr17:42953723-42953778	-7.19	-0.2479	AARSD1	ENST00000427569	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_324294	chr2:27774423-27774530	-15.46	-0.1594	MRPL33	ENST00000296102	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_363747	chr22:23877720-23877869	-20.36	-0.1683	SLC2A11	ENST00000345044	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_377198	chr3:123130479-123130616	-16.03	-0.2196	PDIA5	ENST00000316218	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_380242	chr3:186784961-186785101	-15.76	-0.1420	EIF4A2	ENST00000323963	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_445390	chr5:150403120-150403312	-20.80	-0.1083	CD74	ENST00000009530	In-frame
ENSG00000260257	ENST00000569087	exon_skip_470226	chr7:103307595-103307708	-13.53	-0.1471	PMPCB	ENST00000249269	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_509943	chrX:47175018-47175092	-11.29	-0.1792	RBM10	ENST00000377604	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_52895	chr10:98431130-98431291	-20.74	-0.1304	HPS1	ENST00000325103,ENST00000361490	Frame-shift
ENSG00000260257	ENST00000569087	exon_skip_75223	chr11:72012400-72012442	-9.28	-0.2994	NUMA1	ENST00000393695	In-frame
ENSG00000260257	ENST00000569087	exon_skip_476061	chr7:65979726-65979911	-26.24	-0.1715	GUSB	ENST00000304895	Frame-shift

lncRNA targets by miRNA.

LncRNA Ensembl ID	miRNA ID	LncRNA ENST ID	Binding site in lncRNA	Score	Energy	Align Len	Public source
ENSG00000260257	hsa-mir-152	ENST00000569087	chr20:32857378-32857463	172.00	-80.20	87	NA
ENSG00000260257	hsa-mir-152	ENST00000569087	chr20:32857245-32857331	168.00	-69.29	79	NA
ENSG00000260257	hsa-mir-152	ENST00000569087	chr20:32856661-32856751	160.00	-74.34	89	NA
ENSG00000260257	hsa-mir-152	ENST00000569087	chr20:32858206-32858295	154.00	-74.72	90	NA
ENSG00000260257	hsa-mir-152	ENST00000569087	chr20:32857625-32857709	143.00	-88.13	82	NA
ENSG00000260257	hsa-mir-152	ENST00000569087	chr20:32856769-32856853	141.00	-82.87	82	NA
ENSG00000260257	hsa-mir-152	ENST00000569087	chr20:32857054-32857132	141.00	-72.83	84	NA

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Variants for RP5-1085F17.3

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
LncEditing_365529	ENSG00000260257.2	chr20	32857625	+	lincRNA	RP5-1085F17.3	ENST00000569087.2	lincRNA	RP5-1085F17.3-001

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
ENSG00000260257	LncEditing_365529	TGCT	chr20_32857625_+	1.161909e+01	8.899481e+00	2.599399e+00	2.069064e+00	3.854012e-02	3.872951e-02	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
ENSG00000260257	LncEditing_365529	-4.891388e-01	3.939096e-02	4.176857e-02

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
ENSG00000260257	ENSG00000128272	ATF4	ENSG00000143368	SF3B4	5	CHOL,KIRC,KIRP,LGG,LIHC
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000143368	SF3B4	6	CHOL,KIRC,KIRP,LGG,LIHC,THCA
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000125817	CENPB	10	CHOL,KICH,KIRP,LGG,LIHC,MESO,PAAD,PCPG,PRAD,THCA
ENSG00000260257	ENSG00000130254	SAFB2	ENSG00000154957	ZNF18	5	CHOL,KIRC,KIRP,PAAD,THCA
ENSG00000260257	ENSG00000130254	SAFB2	ENSG00000166432	ZMAT1	5	CHOL,KIRC,KIRP,PAAD,TGCT
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000205250	E2F4	5	CHOL,KICH,KIRP,LGG,LIHC
ENSG00000260257	ENSG00000130254	SAFB2	ENSG00000168661	ZNF30	6	CHOL,GBM,KIRP,LIHC,PAAD,TGCT
ENSG00000260257	ENSG00000130254	SAFB2	ENSG00000164548	TRA2A	9	CHOL,KIRC,KIRP,LGG,LIHC,PCPG,STAD,TGCT,THCA
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000130811	EIF3G	5	CHOL,LGG,LIHC,PRAD,THCA
ENSG00000260257	ENSG00000128272	ATF4	ENSG00000167967	E4F1	7	CHOL,HNSC,KIRC,KIRP,LGG,PRAD,THYM
ENSG00000260257	ENSG00000130254	SAFB2	ENSG00000167967	E4F1	9	CHOL,GBM,HNSC,KIRC,KIRP,LGG,PCPG,TGCT,THCA
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000167967	E4F1	12	CHOL,GBM,HNSC,KICH,KIRC,KIRP,LGG,MESO,PCPG,PRAD,SKCM,THCA
ENSG00000260257	ENSG00000128272	ATF4	ENSG00000184436	THAP7	6	CHOL,KIRC,KIRP,LGG,LIHC,PRAD
ENSG00000260257	ENSG00000130254	SAFB2	ENSG00000184436	THAP7	6	CHOL,KIRP,LIHC,PAAD,PCPG,THCA
ENSG00000260257	ENSG00000130522	JUND	ENSG00000184436	THAP7	5	KIRC,KIRP,LGG,PAAD,PRAD
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000184436	THAP7	9	CHOL,KICH,KIRC,KIRP,LIHC,PAAD,PCPG,PRAD,THCA
ENSG00000260257	ENSG00000128272	ATF4	ENSG00000158773	USF1	5	CHOL,KIRC,KIRP,LGG,LIHC
ENSG00000260257	ENSG00000128272	ATF4	ENSG00000105698	USF2	5	CHOL,KIRC,LIHC,PRAD,THYM
ENSG00000260257	ENSG00000130254	SAFB2	ENSG00000105698	USF2	5	CHOL,LIHC,PAAD,PCPG,THCA
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000105698	USF2	9	CHOL,KICH,KIRC,LIHC,MESO,PAAD,PCPG,PRAD,THCA
ENSG00000260257	ENSG00000128272	ATF4	ENSG00000041988	THAP3	5	CHOL,KIRP,LIHC,PRAD,THYM
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000041988	THAP3	7	CHOL,KIRP,LGG,LIHC,PAAD,PRAD,THCA
ENSG00000260257	ENSG00000130254	SAFB2	ENSG00000099326	MZF1	11	CHOL,GBM,HNSC,KIRC,KIRP,LGG,LIHC,LUAD,PAAD,STAD,THCA
ENSG00000260257	ENSG00000166432	ZMAT1	ENSG00000099326	MZF1	5	CHOL,KIRC,KIRP,LUAD,PAAD
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000099326	MZF1	12	CHOL,DLBC,GBM,HNSC,KIRC,KIRP,LGG,LIHC,MESO,PAAD,SKCM,THCA
ENSG00000260257	ENSG00000128272	ATF4	ENSG00000204392	LSM2	5	CHOL,HNSC,LGG,LIHC,THYM
ENSG00000260257	ENSG00000130254	SAFB2	ENSG00000154832	CXXC1	7	CHOL,GBM,KIRP,LGG,LIHC,PAAD,THCA
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000154832	CXXC1	7	CHOL,GBM,KIRP,LGG,LIHC,PAAD,THCA
ENSG00000260257	ENSG00000128272	ATF4	ENSG00000134597	RBMX2	5	CHOL,KIRP,LGG,LIHC,PRAD
ENSG00000260257	ENSG00000128272	ATF4	ENSG00000126254	RBM42	6	CHOL,KIRC,KIRP,LIHC,PRAD,THYM
ENSG00000260257	ENSG00000130522	JUND	ENSG00000126254	RBM42	6	KIRC,KIRP,LGG,PCPG,PRAD,THCA
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000126254	RBM42	9	CHOL,KICH,KIRC,KIRP,LGG,LIHC,PCPG,PRAD,THCA
ENSG00000260257	ENSG00000128272	ATF4	ENSG00000150316	CWC15	7	CHOL,KIRC,KIRP,LGG,LIHC,PRAD,THYM
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000180035	ZNF48	5	CHOL,KICH,KIRP,LIHC,PAAD
ENSG00000260257	ENSG00000128272	ATF4	ENSG00000077312	SNRPA	8	CHOL,HNSC,KIRC,KIRP,LGG,LIHC,PRAD,THYM
ENSG00000260257	ENSG00000130522	JUND	ENSG00000077312	SNRPA	7	KIRC,KIRP,LGG,MESO,PCPG,TGCT,UCS
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000077312	SNRPA	11	CHOL,HNSC,KIRC,KIRP,LGG,LIHC,MESO,PCPG,PRAD,SKCM,THCA
ENSG00000260257	ENSG00000130254	SAFB2	ENSG00000004534	RBM6	13	CHOL,GBM,HNSC,KIRC,KIRP,LGG,LIHC,LUAD,LUSC,PAAD,READ,TGCT,THCA
ENSG00000260257	ENSG00000166432	ZMAT1	ENSG00000004534	RBM6	5	CHOL,KIRC,KIRP,LUAD,PAAD
ENSG00000260257	ENSG00000130254	SAFB2	ENSG00000099622	CIRBP	9	CHOL,GBM,HNSC,KIRP,LGG,LIHC,LUAD,PAAD,THCA
ENSG00000260257	ENSG00000179943	FIZ1	ENSG00000099622	CIRBP	10	CHOL,DLBC,GBM,HNSC,KIRP,LIHC,PAAD,PCPG,PRAD,THCA

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
ENSG00000260257.2	ENST00000569087.2	82	413	165

	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