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lncRNA: ENSG00000250899

Summary for RP11-253E3.3

Gene summary

Gene information	Ensembl ID	ENSG00000250899
	Gene symbol	RP11-253E3.3
	Gene name
	HGNC
	Entrez ID
	Gene type	lincRNA
	Synonyms
	UniProtAcc

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Structure and expression level for RP11-253E3.3

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
ENSG00000250899	2.684285e+02	-1.192504e+00	1.458619e-01	-8.175568e+00	2.940000e-16	1.550000e-15	DOWN	LUSC
ENSG00000250899	1.753576e+02	1.140019e+00	1.342664e-01	8.490725e+00	2.050000e-17	2.250000e-16	UP	COAD
ENSG00000250899	3.325937e+02	1.093902e+00	1.486301e-01	7.359898e+00	1.840000e-13	4.230000e-12	UP	STAD
ENSG00000250899	1.957767e+02	1.152985e+00	2.740229e-01	4.207622e+00	2.580000e-05	2.290670e-04	UP	READ

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID

Correlation

P-value

Cancer Type

Adjc.p-value

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lncRNA-Protein interaction for RP11-253E3.3

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
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000110851	PRDM4	82.03	96.51	Q9UKN5	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000263001	GTF2I	70.39	96.3715	P78347	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000104885	DOT1L	68.06	97.9659	Q8TEK3	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000118058	KMT2A	66.47	98.534	Q03164	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000101126	ADNP	63.54	96.9377	Q9H2P0	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000187605	TET3	53.24	96.396	O43151	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000076108	BAZ2A	73.37	96.4496	Q9UIF9	TF,RBP,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000116560	SFPQ	55.49	96.884	P23246	RBP,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000169016	E2F6	37.21	93.9089	O75461	TF,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
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000115816	CEBPZ	86.93	90.386	Q03701	TF	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000164916	FOXK1	84.2	92.2686	P85037	TF	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000110851	PRDM4	82.03	96.4637	Q9UKN5	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000100207	TCF20	80.16	97.8225	Q9UGU0	TF	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000159140	SON	76.87	97.6222	P18583	TF,RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000079432	CIC	76.86	95.6729	Q96RK0	TF	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000076108	BAZ2A	73.37	96.3242	Q9UIF9	TF,RBP,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000263001	GTF2I	70.39	96.0322	P78347	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000104885	DOT1L	68.06	97.8362	Q8TEK3	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000118058	KMT2A	66.47	98.4832	Q03164	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000101126	ADNP	63.54	96.8058	Q9H2P0	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000117000	RLF	58.04	97.9286	Q13129	TF	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000188786	MTF1	54.59	96.8015	Q14872	TF	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000187605	TET3	53.24	96.2732	O43151	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000126464	PRR12	44.15	97.3766	Q9ULL5	TF	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000169926	KLF13	40.22	93.0394	Q9Y2Y9	TF	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000169016	E2F6	37.21	93.8491	O75461	TF,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000167182	SP2	32.99	94.5423	Q02086	TF	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000181472	ZBTB2	29.56	95.7195	Q8N680	TF	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000065970	FOXJ2	26.92	96.4948	Q9P0K8	TF	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000196233	LCOR	16.3	93.9035	Q96JN0	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
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000111641	NOP2	91.72	95.7805	P46087	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000213079	SCAF8	84.36	97.9871	Q9UPN6	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000159140	SON	76.87	97.6775	P18583	TF,RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000076108	BAZ2A	73.37	96.4124	Q9UIF9	TF,RBP,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000122965	RBM19	72.72	96.532	Q9Y4C8	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000156304	SCAF4	70.19	97.9409	O95104	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000123908	AGO2	63.98	94.2368	Q9UKV8	RBP	GSE67990
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000085872	CHERP	62.85	96.9293	Q8IWX8	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000116560	SFPQ	55.49	96.5912	P23246	RBP,Epi	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000161813	LARP4	53.05	95.3046	Q71RC2	RBP	ENCODE
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000129351	ILF3	50.82	96.9121	Q12906	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000239306	RBM14	47.62	94.9923	Q96PK6	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000148840	PPRC1	46.81	98.0275	Q5VV67	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000162613	FUBP1	38.51	95.9446	Q96AE4	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000111605	CPSF6	36.86	97.2305	Q16630	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000167978	SRRM2	31.9	98.657	Q9UQ35	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000184863	RBM33	31.87	91.1927	Q96EV2	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000111364	DDX55	19.76	95.4601	Q8NHQ9	RBP	NA
ENSG00000250899	ENST00000513358	RP11-253E3.3	ENSG00000145907	G3BP1	13.21	95.7995	Q13283	RBP	NA

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lncRNA-DNA interaction for RP11-253E3.3

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

Only predicted by TDF

PUS7,E2F6,CEBPZ,SON,RBM19,PRR12,SP2,LCOR,KDM2B,DNMT1,NOP2,ILF3,SCAF4,TEAD4,SART3,XPO1,STAT3,FOXM1,MTF1,DOT1L,MAFG,AGO2,CELF1,KRR1,RBM14,ADNP,BAZ2A,KMT2A,FUBP1,SF3A1,ZBED4,DDX55,TFCP2,TET3,PRDM4,TCF20,UBR5,SFPQ,XPO5,ZFR,NOP9,RBM33,NAF1,NR2C2,ZBTB2,SRRM2

Exist in public source

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 RP11-253E3.3

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

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 RP11-253E3.3

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

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

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
ENSG00000250899.3	ENST00000513358.3	75	168	395

	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