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lncRNA: ENSG00000215769

Summary for RP13-104F24.2

Gene summary

Gene information	Ensembl ID	ENSG00000215769
	Gene symbol	RP13-104F24.2
	Gene name
	HGNC
	Entrez ID	109286553
	Gene type	processed_transcript
	Synonyms
	UniProtAcc

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Structure and expression level for RP13-104F24.2

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
ENSG00000215769	1.674614e+02	1.271512e+00	2.445163e-01	5.200111e+00	1.990000e-07	1.490000e-06	UP	CHOL
ENSG00000215769	2.110838e+02	2.052078e+00	1.414001e-01	1.451256e+01	1.010000e-47	2.220000e-46	UP	KIRC
ENSG00000215769	3.346211e+02	1.056886e+00	2.510639e-01	4.209632e+00	2.560000e-05	1.588890e-04	UP	BLCA
ENSG00000215769	2.157870e+02	1.645257e+00	2.038133e-01	8.072373e+00	6.890000e-16	1.070000e-14	UP	KIRP
ENSG00000215769	1.186035e+02	1.019563e+00	2.678277e-01	3.806785e+00	1.407850e-04	1.017433e-03	UP	READ

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000215769	5.223071e-01	2.330396e-04	CHOL	5.615653e-04

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lncRNA-Protein interaction for RP13-104F24.2

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
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000198604	BAZ1A	75.64	96.823	Q9NRL2	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000147854	UHRF2	70.57	94.7273	Q96PU4	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000181555	SETD2	60.1	97.4521	Q9BYW2	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000145241	CENPC	59.45	91.3694	Q03188	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000129292	PHF20L1	58.15	94.3096	A8MW92	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000204227	RING1	51.78	92.1652	Q06587	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000170322	NFRKB	51.0	90.6444	Q6P4R8	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000127483	HP1BP3	50.28	94.0922	Q5SSJ5	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000115524	SF3B1	43.71	91.959	O75533	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000005302	MSL3	39.36	91.4649	Q8N5Y2	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000171456	ASXL1	25.19	94.023	Q8IXJ9	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000156860	FBRS	15.23	92.1712	Q9HAH7	Epi	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000132780	NASP	6.95	91.8394	P49321	Epi	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000185658	BRWD1	4.08	90.8996	Q9NSI6	Epi	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000104885	DOT1L	2.91	92.3436	Q8TEK3	TF,Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000132780	NASP	63.24	94.339	P49321	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000196199	MPHOSPH8	60.03	95.0738	Q99549	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000182979	MTA1	57.98	92.0658	Q13330	Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000104885	DOT1L	47.72	93.2175	Q8TEK3	TF,Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000083544	TDRD3	35.28	92.3655	Q9H7E2	RBP,Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000280789	PAGR1	8.3	91.6298	Q9BTK6	Epi	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000129292	PHF20L1	5.89	93.0571	A8MW92	Epi	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000198604	BAZ1A	5.61	90.156	Q9NRL2	Epi	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000123636	BAZ2B	5.14	92.2049	Q9UIF8	TF,Epi	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000147854	UHRF2	4.16	90.6995	Q96PU4	Epi	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000005483	KMT2E	3.85	90.8132	Q8IZD2	Epi	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000115524	SF3B1	2.98	92.7017	O75533	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
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000135164	DMTF1	61.24	91.5575	Q9Y222	TF	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000104885	DOT1L	47.72	92.6412	Q8TEK3	TF,Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000126804	ZBTB1	47.69	91.9064	Q9Y2K1	TF	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000070476	ZXDC	45.75	91.4126	Q2QGD7	TF	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000168661	ZNF30	36.87	91.7994	P17039	TF	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000102878	HSF4	27.77	90.5828	Q9ULV5	TF	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000256223	ZNF10	23.62	94.1182	P21506	TF	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000278129	ZNF8	12.63	90.3178	P17098	TF	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000144161	ZC3H8	9.76	92.0399	Q8N5P1	TF,RBP	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000256223	ZNF10	17.4	90.8535	P21506	TF	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000197857	ZNF44	12.08	90.4551	P15621	TF	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000186272	ZNF17	8.91	90.5048	P17021	TF	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000123636	BAZ2B	5.14	92.3537	Q9UIF8	TF,Epi	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000167232	ZNF91	5.1	92.7134	Q05481	TF	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000198521	ZNF43	3.83	90.9968	P17038	TF	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000104885	DOT1L	2.91	92.7953	Q8TEK3	TF,Epi	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
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000124193	SRSF6	26.18	91.4164	Q13247	RBP	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000133226	SRRM1	8.94	92.5077	Q8IYB3	RBP	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000083544	TDRD3	5.84	90.3936	Q9H7E2	RBP,Epi	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000013573	DDX11	3.86	92.5278	Q96FC9	RBP	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000139746	RBM26	3.05	93.192	Q5T8P6	RBP	NA
ENSG00000215769	ENST00000579125	RP13-104F24.2	ENSG00000167978	SRRM2	1.47	95.1229	Q9UQ35	RBP	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000013573	DDX11	64.49	94.2763	Q96FC9	RBP	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000124193	SRSF6	57.44	91.3587	Q13247	RBP	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000198000	NOL8	54.58	90.2641	Q76FK4	RBP	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000139746	RBM26	48.36	94.7777	Q5T8P6	RBP	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000083544	TDRD3	35.28	92.2367	Q9H7E2	RBP,Epi	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000133226	SRRM1	34.6	92.9903	Q8IYB3	RBP	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000167978	SRRM2	17.82	94.6954	Q9UQ35	RBP	NA
ENSG00000215769	ENST00000578492	RP13-104F24.2	ENSG00000144161	ZC3H8	9.76	91.5833	Q8N5P1	TF,RBP	NA

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lncRNA-DNA interaction for RP13-104F24.2

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 RP13-104F24.2

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

Only predicted by lncTar

AKR7A2,RNH1,SDHC,MRPL37,SMIM12,DCTPP1,EIF2B3,PSMD2,PSMD8,PRPS1,ATP6V0D1,HSPA8,TXN2,ATP5F1A,ADCK2,FIS1,CHP1,CDK4,FH,UQCRC1,SAMM50,TUFM,ACO2,MRPL15,SLC25A11,CCT7,MAIP1,PCCB,ATP5F1B,PSMA7,CYC1,TMX2,TMED1,SARS1,MDH2,ATG101,TMBIM6,ACAT1,ATP5PB,ST13,SLC25A3,SNX17

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
ENSG00000215769	ENST00000579125	exon_skip_1234	chr1:11658532-11658628	-17.59	-0.2665	FBXO44	ENST00000251547,ENST00000376770	In-frame
ENSG00000215769	ENST00000579125	exon_skip_470077	chr7:102397619-102397698	-12.72	-0.4711	PRKRIP1	ENST00000397912,ENST00000496391	Frame-shift

-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
ENSG00000215769	ENST00000579125	exon_skip_41813	chr10:68337857-68337996	-18.00	-0.1513	HNRNPH3	ENST00000265866	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_133217	chr16:8635038-8635079	-11.03	-0.3803	METTL22	ENST00000381920	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_370518	chr22:50247691-50247776	-17.46	-0.2297	HDAC10	ENST00000216271	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_380242	chr3:186784961-186785101	-14.46	-0.1157	EIF4A2	ENST00000323963	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_382458	chr3:38131595-38131638	-10.07	-0.3873	ACAA1	ENST00000333167	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_4796	chr1:41007448-41007545	-18.22	-0.1938	CTPS1	ENST00000372616,ENST00000372621	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_9446	chr1:147270931-147271005	-10.14	-0.1878	CHD1L	ENST00000369258	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_41841	chr10:68756272-68756483	-28.62	-0.1396	CCAR1	ENST00000265872	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_53559	chr10:101793912-101793998	-17.06	-0.2031	OGA	ENST00000361464	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_74009	chr11:64773429-64773505	-17.06	-0.2585	SF1	ENST00000377390	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_127618	chr15:58890280-58890461	-23.42	-0.1521	SLTM	ENST00000380516	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_290158	chr17:42953723-42953778	-10.55	-0.7536	AARSD1	ENST00000427569	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_302168	chr19:10680345-10680443	-13.93	-0.1620	ILF3	ENST00000590261	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_365497	chr22:38067703-38067770	-14.84	-0.2968	PICK1	ENST00000356976,ENST00000404072	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_374497	chr3:49999439-49999513	-13.77	-0.4918	RBM6	ENST00000266022	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_377198	chr3:123130479-123130616	-25.36	-0.1851	PDIA5	ENST00000316218	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_387016	chr3:121788283-121788432	-15.61	-0.1069	IQCB1	ENST00000310864	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_442657	chr5:74730259-74730398	-15.25	-0.2033	GFM2	ENST00000296805,ENST00000509430	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_444499	chr5:138164086-138164133	-8.73	-0.3796	BRD8	ENST00000254900	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_470226	chr7:103307595-103307708	-17.16	-0.1682	PMPCB	ENST00000249269	Frame-shift
ENSG00000215769	ENST00000579125	exon_skip_340759	chr2:85552415-85552567	-19.57	-0.1428	GGCX	ENST00000233838	Frame-shift

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 RP13-104F24.2

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_333761	ENSG00000215769.7	chr17	64766609	-	processed_transcript	RP13-104F24.2	ENST00000579125.1	processed_transcript	RP13-104F24.2-002

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
ENSG00000215769	LncEditing_333761	ESCA	chr17_64766609_-	3.593597e+00	1.822634e+00	1.021029e+00	5.911350e+00	3.393149e-09	8.072691e-09	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

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
ENSG00000215769	ENST00000578492	ATP5F1A	ENSG00000152234	ENST00000585650	-0.1113	76	-	KIRC,READ
ENSG00000215769	ENST00000578492	UQCRC1	ENSG00000010256	ENST00000203407	-0.2314	252	-	CHOL,KIRC
ENSG00000215769	ENST00000578492	PCCB	ENSG00000114054	ENST00000484181	-0.1349	1	-	CHOL,KIRC
ENSG00000215769	ENST00000578492	MAIP1	ENSG00000162972	ENST00000435773	-0.9908	503	-	CHOL
ENSG00000215769	ENST00000579125	FH	ENSG00000091483	ENST00000366560	-0.1153	841	-	CHOL
ENSG00000215769	ENST00000579125	ATP5F1A	ENSG00000152234	ENST00000585650	-0.1345	1	-	KIRC,READ
ENSG00000215769	ENST00000579125	UQCRC1	ENSG00000010256	ENST00000203407	-0.2246	1045	-	CHOL,KIRC
ENSG00000215769	ENST00000579125	ACAT1	ENSG00000075239	ENST00000528370	-0.1195	976	-	CHOL,KIRC,BLCA,READ
ENSG00000215769	ENST00000579125	PCCB	ENSG00000114054	ENST00000484181	-0.1071	1	-	CHOL,KIRC
ENSG00000215769	ENST00000579125	MAIP1	ENSG00000162972	ENST00000392290	-0.1239	1	-	CHOL
ENSG00000215769	ENST00000579125	MAIP1	ENSG00000162972	ENST00000435773	-0.9908	584	-	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

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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
ENSG00000215769.7	ENST00000578492.4	63	10	201
ENSG00000215769.7	ENST00000579125.1	266	35	835

	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