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lncRNA: ENSG00000273142

Summary for LINC02604

Gene summary

Gene information	Ensembl ID	ENSG00000273142
	Gene symbol	LINC02604
	Gene name	long intergenic non-protein coding RNA 2604
	HGNC	53972
	Entrez ID
	Gene type	lincRNA
	Synonyms	RP11-458F8.4\|LINC02604\|07q11.21
	UniProtAcc

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Structure and expression level for LINC02604

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
ENSG00000273142	4.804664e+02	1.584887e+00	1.419247e-01	1.116710e+01	5.910000e-29	5.740000e-28	UP	KIRC
ENSG00000273142	5.948586e+02	1.106389e+00	2.427782e-01	4.557202e+00	5.180000e-06	3.880000e-05	UP	BLCA
ENSG00000273142	8.727311e+02	1.660974e+00	2.242842e-01	7.405666e+00	1.300000e-13	1.510000e-12	UP	KIRP
ENSG00000273142	2.403637e+02	1.356426e+00	1.663831e-01	8.152425e+00	3.570000e-16	3.560000e-15	UP	COAD
ENSG00000273142	7.886058e+02	1.228548e+00	1.802085e-01	6.817369e+00	9.270000e-12	1.580000e-10	UP	STAD
ENSG00000273142	3.100615e+02	2.310877e+00	2.909569e-01	7.942334e+00	1.980000e-15	1.650000e-13	UP	READ

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000273142	3.952893e-01	7.199166e-03	CHOL	8.825800e-03
ENSG00000273142	3.075433e-01	8.733383e-15	KIRC	3.508948e-14
ENSG00000273142	3.022799e-01	4.177109e-13	PRAD	2.114392e-12

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lncRNA-Protein interaction for LINC02604

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
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000118058	KMT2A	45.97	94.0911	Q03164	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
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000130254	SAFB2	50.77	94.8149	Q14151	TF,RBP	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000118058	KMT2A	45.97	94.1086	Q03164	TF,Epi	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000126804	ZBTB1	42.98	90.1292	Q9Y2K1	TF	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000167232	ZNF91	35.04	93.113	Q05481	TF	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000196378	ZNF34	15.27	91.4629	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
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000124193	SRSF6	54.65	90.0334	Q13247	RBP	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000130254	SAFB2	50.77	94.7642	Q14151	TF,RBP	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000137776	SLTM	46.73	93.1537	Q9NWH9	RBP	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000198000	NOL8	43.89	93.6377	Q76FK4	RBP	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000004534	RBM6	42.2	90.2249	P78332	RBP	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000106344	RBM28	36.42	90.5566	Q9NW13	RBP	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000135870	RC3H1	32.31	90.6984	Q5TC82	RBP	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000116350	SRSF4	32.08	91.5901	Q08170	RBP	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000133226	SRRM1	26.43	92.9416	Q8IYB3	RBP	NA
ENSG00000273142	ENST00000610177	RP11-458F8.4	ENSG00000161547	SRSF2	17.08	90.1635	Q01130	RBP	NA

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lncRNA-DNA interaction for LINC02604

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 LINC02604

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

Only predicted by lncTar

BRF2,SMAD1

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
ENSG00000273142	ENST00000610177	exon_skip_430601	chr4:82842139-82842481	-43.90	-0.1355	SEC31A	ENST00000355196,ENST00000395310,ENST00000448323	In-frame
ENSG00000273142	ENST00000610177	exon_skip_470077	chr7:102397619-102397698	-11.22	-0.1753	PRKRIP1	ENST00000397912,ENST00000496391	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_1234	chr1:11658532-11658628	-21.21	-0.2866	FBXO44	ENST00000251547,ENST00000376770	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
ENSG00000273142	ENST00000610177	exon_skip_290158	chr17:42953723-42953778	-10.36	-0.3837	AARSD1	ENST00000427569	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_382458	chr3:38131595-38131638	-13.44	-0.3537	ACAA1	ENST00000333167	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_41813	chr10:68337857-68337996	-22.34	-0.1655	HNRNPH3	ENST00000265866	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_95407	chr12:95040475-95040597	-17.06	-0.1625	NR2C1	ENST00000333003	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_133217	chr16:8635038-8635079	-13.41	-0.4470	METTL22	ENST00000381920	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_309204	chr19:49181348-49181461	-24.12	-0.2539	TRPM4	ENST00000252826	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_319223	chr19:43526200-43526349	-24.58	-0.2235	ETHE1	ENST00000292147	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_340759	chr2:85552415-85552567	-20.52	-0.1405	GGCX	ENST00000233838	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_370518	chr22:50247691-50247776	-15.12	-0.1844	HDAC10	ENST00000216271	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_380242	chr3:186784961-186785101	-15.28	-0.1273	EIF4A2	ENST00000323963	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_436035	chr5:79656957-79657001	-4.45	-0.1271	TENT2	ENST00000296783,ENST00000428308,ENST00000453514	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_2106	chr1:17648553-17648675	-23.19	-0.2251	ARHGEF10L	ENST00000361221	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_9446	chr1:147270931-147271005	-10.19	-0.1568	CHD1L	ENST00000369258	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_38175	chr1:234398381-234398553	-18.51	-0.1234	TARBP1	ENST00000040877	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_41841	chr10:68756272-68756483	-24.88	-0.1208	CCAR1	ENST00000265872	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_52701	chr10:97468965-97469104	-19.38	-0.1746	MMS19	ENST00000370782,ENST00000438925	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_53559	chr10:101793912-101793998	-11.61	-0.1635	OGA	ENST00000361464	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_66482	chr11:126274926-126275021	-18.13	-0.1929	FOXRED1	ENST00000263578	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_74009	chr11:64773429-64773505	-14.16	-0.1994	SF1	ENST00000377390	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_92074	chr12:50142052-50142110	-6.06	-0.1731	CERS5	ENST00000317551	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_103007	chr13:37025319-37025437	-13.57	-0.1344	SUPT20H	ENST00000350612	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_111863	chr14:23565815-23565892	-15.69	-0.2377	AP1G2	ENST00000308724,ENST00000397120	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_114365	chr14:74290026-74290118	-17.59	-0.2625	ABCD4	ENST00000356924	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_139933	chr16:90035632-90035687	-12.50	-0.2717	GAS8	ENST00000268699	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_296625	chr18:42057882-42058051	-18.51	-0.1108	PIK3C3	ENST00000262039	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_300663	chr19:1425877-1425960	-14.54	-0.2019	DAZAP1	ENST00000233078	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_302168	chr19:10680345-10680443	-18.00	-0.1915	ILF3	ENST00000590261	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_326885	chr2:74490024-74490127	-19.67	-0.2162	TTC31	ENST00000233623	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_327433	chr2:86125794-86125880	-9.22	-0.1676	PTCD3	ENST00000254630	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_340545	chr2:75680192-75680314	-8.97	-0.1165	GCFC2	ENST00000321027	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_353131	chr20:58669290-58669453	-32.88	-0.3073	STX16	ENST00000371141	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_365497	chr22:38067703-38067770	-15.11	-0.2325	PICK1	ENST00000356976,ENST00000404072	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_374497	chr3:49999439-49999513	-18.10	-0.2828	RBM6	ENST00000266022	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_374551	chr3:50100531-50100605	-13.09	-0.1925	RBM5	ENST00000347869	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_377198	chr3:123130479-123130616	-15.94	-0.1317	PDIA5	ENST00000316218	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_378467	chr3:143023974-143024018	-7.43	-0.2064	U2SURP	ENST00000473835	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_384420	chr3:49812647-49812738	-17.30	-0.4553	UBA7	ENST00000333486	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_438188	chr5:141638954-141639021	-15.80	-0.2926	RELL2	ENST00000297164,ENST00000444782	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_442657	chr5:74730259-74730398	-15.67	-0.1205	GFM2	ENST00000296805,ENST00000509430	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_444499	chr5:138164086-138164133	-5.88	-0.1633	BRD8	ENST00000254900	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_446758	chr5:178212972-178213103	-20.47	-0.1796	PHYKPL	ENST00000308158	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_470226	chr7:103307595-103307708	-13.12	-0.1544	PMPCB	ENST00000249269	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_511212	chrX:71555189-71555385	-21.14	-0.1489	OGT	ENST00000373719	Frame-shift
ENSG00000273142	ENST00000610177	exon_skip_374581	chr3:50110378-50110463	-12.31	-0.1448	RBM5	ENST00000347869	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 LINC02604

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
ENSG00000273142	ENSG00000004534	RBM6	exon_skip_290158	ENSG00000266967:chr17:42953723-42953778	AARSD1	ENST00000427569	Frame-shift	READ,PRAD,PCPG,PAAD,TGCT,THCA
ENSG00000273142	ENSG00000004534	RBM6	exon_skip_382458	ENSG00000060971:chr3:38131595-38131638	ACAA1	ENST00000333167	Frame-shift	SARC,STAD,UVM,SKCM,READ,OV,MESO,PRAD,PCPG,PAAD,THCA
ENSG00000273142	ENSG00000130254	SAFB2	exon_skip_382458	ENSG00000060971:chr3:38131595-38131638	ACAA1	ENST00000333167	Frame-shift	SARC,OV,PCPG,PAAD,THCA
ENSG00000273142	ENSG00000124193	SRSF6	exon_skip_382458	ENSG00000060971:chr3:38131595-38131638	ACAA1	ENST00000333167	Frame-shift	STAD,UVM,SKCM,UCS,PAAD,THCA
ENSG00000273142	ENSG00000004534	RBM6	exon_skip_41813	ENSG00000096746:chr10:68337857-68337996	HNRNPH3	ENST00000265866	Frame-shift	STAD,UVM,PCPG,PAAD,THCA
ENSG00000273142	ENSG00000004534	RBM6	exon_skip_370518	ENSG00000100429:chr22:50247691-50247776	HDAC10	ENST00000216271	Frame-shift	STAD,UVM,SKCM,READ,PRAD,PAAD,THCA
ENSG00000273142	ENSG00000004534	RBM6	exon_skip_53559	ENSG00000198408:chr10:101793912-101793998	OGA	ENST00000361464	Frame-shift	UVM,PCPG,PAAD,TGCT,THCA
ENSG00000273142	ENSG00000004534	RBM6	exon_skip_114365	ENSG00000119688:chr14:74290026-74290118	ABCD4	ENST00000356924	Frame-shift	UVM,READ,OV,PCPG,THCA
ENSG00000273142	ENSG00000004534	RBM6	exon_skip_302168	ENSG00000129351:chr19:10680345-10680443	ILF3	ENST00000590261	Frame-shift	OV,MESO,PCPG,PAAD,THCA
ENSG00000273142	ENSG00000004534	RBM6	exon_skip_377198	ENSG00000065485:chr3:123130479-123130616	PDIA5	ENST00000316218	Frame-shift	UVM,READ,OV,PCPG,PAAD
ENSG00000273142	ENSG00000004534	RBM6	exon_skip_470226	ENSG00000105819:chr7:103307595-103307708	PMPCB	ENST00000249269	Frame-shift	UVM,SKCM,PCPG,PAAD,THCA
ENSG00000273142	ENSG00000124193	SRSF6	exon_skip_470226	ENSG00000105819:chr7:103307595-103307708	PMPCB	ENST00000249269	Frame-shift	UVM,SKCM,UCS,PAAD,THCA
ENSG00000273142	ENSG00000004534	RBM6	exon_skip_374581	ENSG00000003756:chr3:50110378-50110463	RBM5	ENST00000347869	Frame-shift	UVM,READ,PCPG,PAAD,THCA

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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
ENSG00000273142.1	ENST00000610177.1	92	343	65

	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