Home

Download

Statistics

Landscape

Help

Contact

lncRNA: ENSG00000260317

Summary for RP11-48B3.4

Gene summary

Gene information	Ensembl ID	ENSG00000260317
	Gene symbol	RP11-48B3.4
	Gene name
	HGNC
	Entrez ID
	Gene type	lincRNA
	Synonyms
	UniProtAcc

Top

Structure and expression level for RP11-48B3.4

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
ENSG00000260317	1.683093e+02	1.809428e+00	2.158322e-01	8.383492e+00	5.140000e-17	6.370000e-16	UP	KICH
ENSG00000260317	1.460737e+02	1.186486e+00	1.625188e-01	7.300608e+00	2.860000e-13	3.180000e-12	UP	KIRP
ENSG00000260317	2.660423e+02	1.263203e+00	1.173275e-01	1.076647e+01	4.960000e-27	3.130000e-25	UP	PRAD

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000260317	3.974822e-01	1.147825e-04	KICH	1.919391e-04
ENSG00000260317	3.861923e-01	4.854998e-21	PRAD	1.288543e-19

Top

lncRNA-Protein interaction for RP11-48B3.4

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
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000084093	REST	51.82	93.0412	Q13127	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
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000167967	E4F1	73.99	92.3745	Q66K89	TF	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000130254	SAFB2	70.23	94.7358	Q14151	TF,RBP	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000099326	MZF1	67.83	93.2949	P28698	TF	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000084093	REST	51.82	94.3502	Q13127	TF,Epi	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000198521	ZNF43	48.03	92.1912	P17038	TF	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000170631	ZNF16	39.16	92.5695	P17020	TF	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000147789	ZNF7	38.94	92.5286	P17097	TF	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000198040	ZNF84	38.07	93.757	P51523	TF	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000146587	RBAK	36.7	91.9771	Q9NYW8	TF	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000164631	ZNF12	25.98	92.5692	P17014	TF	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000167766	ZNF83	7.86	92.7703	P51522	TF	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000178177	LCORL	2.0	93.1833	Q8N3X6	TF	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000196378	ZNF34	1.47	92.572	Q8IZ26	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
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000111641	NOP2	77.7	94.3247	P46087	RBP	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000130254	SAFB2	70.23	94.8616	Q14151	TF,RBP	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000079134	THOC1	44.97	90.6261	Q96FV9	RBP	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000135870	RC3H1	44.13	94.2437	Q5TC82	RBP	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000129351	ILF3	32.85	95.1587	Q12906	RBP	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000184863	RBM33	18.88	93.399	Q96EV2	RBP	NA
ENSG00000260317	ENST00000569134	RP11-48B3.4	ENSG00000164548	TRA2A	3.92	93.5707	Q13595	RBP	NA

Top

lncRNA-DNA interaction for RP11-48B3.4

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

Only predicted by TDF

HSF1,LSM5,ZNF16,NOP2,ILF3,GLI4,THOC6,RC3H1,LCORL,PUF60,TIGD5,MZF1,ZNF43,NRF1,AKAP8,ZNF84,AGO2,CSTF3,CPSF1,RNPS1,DDX51,NR2F6,TRA2A,PURB,MYEF2,ZNF24,NFYC,FOXP1,ZNF83,RALY,USF1,ZNF34,SAFB2,THOC1,RBM33,E2F5

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.

Top

lncRNA-RNA interaction for RP11-48B3.4

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 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
ENSG00000260317	ENST00000569134	exon_skip_23423	chr1:26294204-26294331	-13.09	-0.1487	UBXN11	ENST00000374221,ENST00000374222	Frame-shift
ENSG00000260317	ENST00000569134	exon_skip_41813	chr10:68337857-68337996	-13.00	-0.1066	HNRNPH3	ENST00000265866	Frame-shift
ENSG00000260317	ENST00000569134	exon_skip_382458	chr3:38131595-38131638	-6.96	-0.1933	ACAA1	ENST00000333167	Frame-shift

lncRNA targets by miRNA.

LncRNA Ensembl ID

miRNA ID

LncRNA ENST ID

Binding site in lncRNA

Score

Energy

Align Len

Public source

Top

Variants for RP11-48B3.4

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

Top

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

Top

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

Top

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

Top

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

Top

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

Top

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
ENSG00000260317.1	ENST00000569134.1	123	3735	3364

	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