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lncRNA: ENSG00000259933

Summary for RP11-304L19.1

Gene summary

Gene information	Ensembl ID	ENSG00000259933
	Gene symbol	RP11-304L19.1
	Gene name
	HGNC
	Entrez ID	105371049
	Gene type	sense_overlapping
	Synonyms
	UniProtAcc

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Structure and expression level for RP11-304L19.1

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
ENSG00000259933	2.030549e+02	2.893519e+00	6.651616e-01	4.350100e+00	1.360000e-05	4.655021e-03	UP	PAAD
ENSG00000259933	4.699557e+01	1.925223e+00	2.693058e-01	7.148835e+00	8.750000e-13	7.380000e-12	UP	UCEC
ENSG00000259933	9.000189e+01	3.792449e+00	2.427707e-01	1.562152e+01	5.190000e-55	3.650000e-53	UP	LUAD
ENSG00000259933	3.716704e+02	1.024223e+00	1.383153e-01	7.404985e+00	1.310000e-13	1.040000e-12	UP	COAD
ENSG00000259933	4.136277e+02	1.276371e+00	2.851248e-01	4.476534e+00	7.590000e-06	7.740000e-05	UP	READ

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000259933	4.045495e-01	5.845011e-03	CHOL	7.369797e-03

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lncRNA-Protein interaction for RP11-304L19.1

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

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 RP11-304L19.1

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

Only predicted by TDF

GPX2,NDUFB10,MST1R,EEF2KMT,FAM83E,GFPT1,CALML4,SLC29A2,ANTKMT,NMRAL1,NAPRT,SEM1,ZNF598,OVOL2,DAPK3,GAK,ICA1,ACY3,AGR2,RPP25,HAGHL,SLC44A4,TIMM13,ATAD3B,MTX1,GFUS,MRPS12,TRAF7,RDH13,EPCAM,ARFGAP1,CAPN10,SMIM22,WDR24,ZNHIT1,GFER,ADAM15,KDELR2,INF2,DPAGT1,ADAP1,PPP1R16A,SLC52A2,FUT3,CLN3,TP53I11,TPRN,ASL,MMP15,BRI3,GMDS,C9orf152,IMP4,CDK2AP2,OSBPL7,SIGIRR,PTPRH,ECI1,NABP2,ETHE1,UBALD1,LSM4,NPDC1,POLR3K,BAIAP2L2,JTB,CDC42EP5,NR2F6,TBL3,RNPS1,MROH6,AGPAT2,FLAD1,HMOX2,LAD1,CAPN15,FA2H,PLEKHJ1,LLGL2,RBM47,ERN2,MRPL14,PDIA3,IFT172,PGP,DGAT1,ELMO3,CHMP2A,ABHD11,MYDGF,AGR3,THOC6,KLF16,TELO2,FBXL6,PRXL2B,UNC93B1,RASSF7,EFHD2,CCHCR1,ANO9,GPR35,GALNT6,SH2D3A,HDHD3,MICALL2,KRT18,CYBA,MISP,SLC1A5,CRACR2B,TRAF4,MVP,GSS,SLCO4A1,CIAO2B,KIAA2013,SMG9,PAM16,PSMG3,PLPP2,DGKQ,SLC39A11,SPIRE2,NOP2,PLS1,RAB25,PNKP,TSPAN8,COG7,PAQR4,AXIN1,SLC35A2,NTHL1,CIAO3,TRMT61A,ACY1,TUFM,GALNT3,TMEM238,RNF126,CCDC12,KRTCAP3,DECR2,AKAP1,GALE,SLC22A18,SIRT6,TMEM63A,AP1M2,CYB561D2,CCNF,SPDEF,SLC9A3R2

Exist in public source

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

Only predicted by TDF

ECI1,NPDC1,KRT18,SMG9,ETHE1,CBLC,E4F1,ABHD11,MSLN,HMOX2,TSTA3,MISP,SLC39A11,DAPK3,C9orf152,RNF126,COG7,C16orf91,SHFM1,RAB25,AP1M2,NMRAL1,GSTP1,AKAP1,KIAA2013

Exist in public source

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

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lncRNA-RNA interaction for RP11-304L19.1

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

Only predicted by lncTar

TUT4,FRMD6,ZFYVE1,TRIM23,DENND5A,NKIRAS1,QKI,SGTB,ELL2

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
ENSG00000259933	ENST00000563284	exon_skip_11286	chr1:155061903-155061975	-12.78	-0.3873	ADAM15	ENST00000356955	In-frame
ENSG00000259933	ENST00000563284	exon_skip_44998	chr10:110132304-110132400	-9.56	-0.2276	ADD3	ENST00000356080	In-frame
ENSG00000259933	ENST00000563284	exon_skip_59476	chr11:57815914-57816001	-13.54	-0.1907	CTNND1	ENST00000399050	In-frame
ENSG00000259933	ENST00000563284	exon_skip_114200	chr14:73279280-73279424	-23.57	-0.2086	NUMB	ENST00000355058,ENST00000555238	In-frame
ENSG00000259933	ENST00000563284	exon_skip_150188	chr17:27643524-27643620	-15.26	-0.1839	LGALS9	ENST00000395473	In-frame
ENSG00000259933	ENST00000563284	exon_skip_386291	chr3:108050577-108050602	-6.61	-0.3672	CD47	ENST00000361309	Frame-shift
ENSG00000259933	ENST00000563284	exon_skip_423795	chr4:55888887-55888932	-9.61	-0.3432	EXOC1	ENST00000346134,ENST00000381295	In-frame
ENSG00000259933	ENST00000563284	exon_skip_106758	chr14:55663954-55664041	-12.08	-0.1632	KTN1	ENST00000395314	In-frame
ENSG00000259933	ENST00000563284	exon_skip_461111	chr6:90544551-90544632	-9.23	-0.1465	MAP3K7	ENST00000369329	In-frame
ENSG00000259933	ENST00000563284	exon_skip_44853	chr10:104010815-104010908	-12.34	-0.1387	SLK	ENST00000369755	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
ENSG00000259933	ENST00000563284	exon_skip_52231	chr10:93392916-93392955	-7.33	-0.2036	MYOF	ENST00000359263	In-frame
ENSG00000259933	ENST00000563284	exon_skip_96112	chr12:109945259-109945349	-12.15	-0.1599	GIT2	ENST00000355312	In-frame
ENSG00000259933	ENST00000563284	exon_skip_287874	chr17:29085603-29085648	-6.17	-0.8814	MYO18A	ENST00000527372	In-frame
ENSG00000259933	ENST00000563284	exon_skip_337919	chr2:27445744-27445843	-15.30	-0.1681	IFT172	ENST00000260570	In-frame
ENSG00000259933	ENST00000563284	exon_skip_376144	chr3:100311832-100311877	-9.72	-0.2558	TBC1D23	ENST00000394144	In-frame
ENSG00000259933	ENST00000563284	exon_skip_382356	chr3:37091466-37091538	-8.34	-0.1390	LRRFIP2	ENST00000336686	In-frame
ENSG00000259933	ENST00000563284	exon_skip_508298	chr9:136445051-136445111	-9.97	-0.2695	SEC16A	ENST00000313050	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 RP11-304L19.1

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

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
ENSG00000259933	ENSG00000099812	MISP	CESC,CHOL,ESCA,LUAD,PAAD,STAD,THYM	PAAD
ENSG00000259933	ENSG00000101187	SLCO4A1	CESC,CHOL,COAD,ESCA,PAAD	COAD
ENSG00000259933	ENSG00000104522	GFUS	CESC,CHOL,COAD,ESCA,PAAD,READ,STAD,UVM	COAD,READ
ENSG00000259933	ENSG00000105523	FAM83E	CESC,CHOL,ESCA,LUAD,PAAD,STAD	PAAD
ENSG00000259933	ENSG00000106541	AGR2	CESC,CHOL,ESCA,PAAD,STAD	PAAD
ENSG00000259933	ENSG00000117308	GALE	CESC,CHOL,COAD,ESCA,PAAD,UCEC,UVM	UCEC
ENSG00000259933	ENSG00000128298	BAIAP2L2	CESC,ESCA,OV,PAAD,STAD	PAAD
ENSG00000259933	ENSG00000134398	ERN2	CESC,CHOL,ESCA,PAAD,STAD	PAAD
ENSG00000259933	ENSG00000160972	PPP1R16A	CESC,COAD,ESCA,PAAD,READ,STAD,THYM	READ
ENSG00000259933	ENSG00000173467	AGR3	CESC,CHOL,ESCA,PAAD,STAD	PAAD
ENSG00000259933	ENSG00000178623	GPR35	CESC,COAD,ESCA,LUAD,PAAD,READ,STAD	LUAD,READ
ENSG00000259933	ENSG00000196187	TMEM63A	CESC,COAD,ESCA,LAML,PAAD	COAD
ENSG00000259933	ENSG00000198380	GFPT1	CESC,CHOL,ESCA,PAAD,STAD	PAAD
ENSG00000259933	ENSG00000204991	SPIRE2	CESC,CHOL,COAD,ESCA,LUAD,PAAD,PCPG,STAD	LUAD,PAAD
ENSG00000259933	ENSG00000105281	SLC1A5	CHOL,COAD,PAAD,THYM,UVM	COAD
ENSG00000259933	ENSG00000160072	ATAD3B	CHOL,COAD,ESCA,LAML,READ	COAD,READ
ENSG00000259933	ENSG00000162063	CCNF	CHOL,COAD,PAAD,PCPG,READ	COAD,READ
ENSG00000259933	ENSG00000166166	TRMT61A	CHOL,COAD,PAAD,READ,THYM	READ
ENSG00000259933	ENSG00000185803	SLC52A2	CHOL,COAD,ESCA,PAAD,STAD,THYM,UVM	COAD
ENSG00000259933	ENSG00000204839	MROH6	CHOL,COAD,ESCA,READ,STAD,THYM	COAD,READ
ENSG00000259933	ENSG00000065057	NTHL1	COAD,ESCA,LUAD,PAAD,READ,STAD,TGCT,UCEC	COAD,READ
ENSG00000259933	ENSG00000103253	HAGHL	COAD,LUAD,OV,PAAD,READ,STAD,THYM	COAD,LUAD,READ
ENSG00000259933	ENSG00000127580	WDR24	COAD,LAML,READ,STAD,TGCT	READ
ENSG00000259933	ENSG00000128626	MRPS12	COAD,ESCA,PAAD,READ,TGCT,THYM,UVM	READ
ENSG00000259933	ENSG00000132698	RAB25	COAD,LUAD,PAAD,READ,THYM	LUAD
ENSG00000259933	ENSG00000142330	CAPN10	COAD,ESCA,LAML,PCPG,READ	READ
ENSG00000259933	ENSG00000162073	PAQR4	COAD,PAAD,READ,STAD,THYM	COAD,READ
ENSG00000259933	ENSG00000164078	MST1R	COAD,ESCA,OV,PAAD,THYM	PAAD
ENSG00000259933	ENSG00000182325	FBXL6	COAD,PAAD,READ,STAD,THYM	COAD,READ
ENSG00000259933	ENSG00000183751	TBL3	COAD,PAAD,READ,STAD,THYM	READ
ENSG00000259933	ENSG00000184207	PGP	COAD,ESCA,PAAD,READ,STAD,TGCT,UVM	READ
ENSG00000259933	ENSG00000185101	ANO9	COAD,ESCA,LAML,PAAD,UVM	COAD
ENSG00000259933	ENSG00000233493	TMEM238	COAD,ESCA,PAAD,READ,STAD,TGCT	READ

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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
ENSG00000259933	ENST00000570072	FRMD6	ENSG00000139926	ENST00000555197	-0.2497	243	-	UCEC,READ
ENSG00000259933	ENST00000563284	FRMD6	ENSG00000139926	ENST00000557405	-0.1002	119	-	UCEC,READ
ENSG00000259933	ENST00000563284	FRMD6	ENSG00000139926	ENST00000555197	-0.1560	411	-	UCEC,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
ENSG00000259933.5	ENST00000570072.4	118	148	501
ENSG00000259933.5	ENST00000563284.3	112	335	0

	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