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Center for Computational Systems Medicine
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lncRNA summary

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lncRNA structure and expression level

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lncRNA-Protein interaction

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lncRNA-DNA interaction

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lncRNA-RNA interaction

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Variants in lncRNA

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lncRNAs regulate the target genes through functioning as enhancers

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lncRNAs regulate the target genes through recruiting transcript factors

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lncRNAs regulate the alternative splicing events through interacting with splicing factor

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lncRNAs regulate mRNA through targeting the 3'-UTR region

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lncRNAs regulate mRNA by competing with miRNA

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lncRNA coding potential

lncRNA: ENSG00000279382

Summary for RP11-449J21.3

check button Gene summary

Gene informationEnsembl ID

ENSG00000279382

Gene symbol

RP11-449J21.3

Gene name
HGNC
Entrez ID
Gene typeTEC
Synonyms
UniProtAcc

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Structure and expression level for RP11-449J21.3

check buttonDifferentially expressed gene analysis between cancer and normal samples.
DEG result
Ensembl IDBase meanlog2FC(AD/control)lfcSEStatP-valueAdjc.p-valueDEG direction Cancer type
ENSG000002793821.329531e+021.294580e+003.506457e-013.691990e+002.225060e-049.008470e-04UPCHOL
ENSG000002793821.187913e+021.286971e+001.469457e-018.758136e+001.990000e-181.090000e-17UPKIRC
ENSG000002793822.665727e+021.068589e+001.554338e-016.874882e+006.200000e-125.560000e-11UPPRAD
ENSG000002793828.817510e+011.059619e+002.798065e-013.786969e+001.524960e-041.090984e-03UPREAD

check buttonCorrelation between lncRNAs and cancer stages.
LncRNA Ensembl IDCorrelationP-valueCancer TypeAdjc.p-value
ENSG000002793825.261079e-012.057687e-04CHOL5.189281e-04

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lncRNA-Protein interaction for RP11-449J21.3

lncrna_protein
check buttonlncRNA-epigenetic factor interaction (#cancer types with positive correlation >= 5).
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source

check buttonlncRNA-transcript factor interaction (#cancer types with positive correlation >= 5).
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source

check buttonlncRNA-RNA binding protein interaction (#cancer types with positive correlation >= 5).
LncRNA Ensembl IDLncRNA ENST IDLncRNA NameProtein Ensembl IDProtein NameCatRAPID ScoreLncpro ScoreUniPortIDGene SubtypePublic source

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lncRNA-DNA interaction for RP11-449J21.3

lncrna_DNA
check buttonlncRNA targets the enhancer region and positively regulates the gene expression.

check buttonlncRNA targets the promoter region and positively regulates the gene expression.

check buttonlncRNA targets the promoter region and negatively regulates the gene expression.

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lncRNA-RNA interaction for RP11-449J21.3

lncrna_RNA
check buttonlncRNA targets the 3'UTR region and negatively regulates the mRNA.
Only predicted by lncTar
TMEM147,SMIM12,DNAJC8,DDT,RNF181,GET3,NDUFA13,LAMTOR2,ATOX1,NEDD8,FTL,AURKAIP1,ALDOA,BLOC1S1,UCHL3,ZNHIT1,SLC25A11,PET100,ATP5PO,CIB1,MPDU1,SURF1,ATP6V0B,COX6A1,NDUFS5,NME1,ARPC4,SELENOW,AVEN,CLPP,SRA1,COMMD9,DYNLRB1,SERF2,ATP5ME,LGALS1,ENO1,MRPL27,COX4I1,PSMD13,VAMP8,NDUFA2,SH3BGRL3,EIF2B3,RPL35,YIF1A,SMPD1,GPX4,GYG1,POLR2J,ELOC,MICOS13,TSR3,RPL36,COX6B1,UQCRC1,MYDGF,PSMC3,DHRS4L2,RHOG,COPE,RPS17,MRPS12,POLR2L,NDUFB10,PFN1,NDUFB9,APRT,PSENEN,CCDC124,PARK7,NDUFA12,SQOR,ATP5PB,GPX1,DYNLL1,RPS8,MCTS1,UQCR11,SOD1,MRPL37,TYROBP,NDUFB4,COX17,ELOB,HSD17B10,EIF6,UQCRQ,AKR1A1,TXN2,MRPL47,SNRPB,EMC3,HIGD2A,GSTO1,MRPL54,RPL32,TXNDC17,SURF2,RABAC1,AP2S1,ATP5MJ,POP7,NDUFB11,NDUFS6,CTSB,VKORC1,NDUFS3,SSBP1,ATP5MC3,NDUFV2,OAZ1,RPS13,ATP6V1F,STX8,DGCR6L,MRPL20,ORMDL2,TRMT112,APOO,SRM,ATP5PF,TRAPPC1,CFL1,LSM2,HINT1,FKBP1A,RHOC,PSMD8,EMC7,TMEM258,BRMS1,UBE2F,ABRACL,RPS27,RPL27,PSMB7,MYL6,PSMB1,COX8A,COX7C,C19orf53,RGS10,NDUFB3,NTMT1,COX5A,COX7A2,KARS1,UBA52,EIF3K,TRAPPC2L,MRPS15,TXNL4A,ARL2,ATP5MF,PRR13,PPIA,PSMB6,MRPL34,NSMCE1,PSMB3,MTLN,NDUFA6,NDUFA1,ECHS1,CARD16,SEM1,TMSB10
Exist in public source
NA

check buttonlncRNA targets the skipped exon region.
-lncRNA and exonskipping events are positively correlated.
lncRNA and exonskipping events positive correlated
LncRNA Ensembl IDLncRNA ENST IDExon IDSkipped ExondGndGGene name with skipped exonTransID with skipped exonORF mutation
ENSG00000279382ENST00000622927exon_skip_430434chr4:82356536-82356683-14.21-0.1128HNRNPDENST00000313899In-frame
ENSG00000279382ENST00000622927exon_skip_326009chr2:64581189-64581273-12.01-0.1430AFTPHENST00000238855,ENST00000409933In-frame
ENSG00000279382ENST00000622927exon_skip_334374chr2:227347225-227347384-20.61-0.1356MFFENST00000353339In-frame
ENSG00000279382ENST00000622927exon_skip_423795chr4:55888887-55888932-7.75-0.2672EXOC1ENST00000346134,ENST00000381295In-frame
ENSG00000279382ENST00000622927exon_skip_111672chr14:23089981-23090101-22.29-0.2164ACIN1ENST00000262710In-frame

-lncRNA and exonskipping events are negatively correlated.
lncRNA and exonskipping events negative correlated
LncRNA Ensembl IDLncRNA ENST IDExon IDSkipped ExondGndGGene name with skipped exonTransID with skipped exonLOF
ENSG00000279382ENST00000622927exon_skip_95407chr12:95040475-95040597-16.36-0.1461NR2C1ENST00000333003Frame-shift
ENSG00000279382ENST00000622927exon_skip_133217chr16:8635038-8635079-13.04-0.3726METTL22ENST00000381920Frame-shift
ENSG00000279382ENST00000622927exon_skip_340759chr2:85552415-85552567-17.90-0.1705GGCXENST00000233838Frame-shift
ENSG00000279382ENST00000622927exon_skip_382458chr3:38131595-38131638-14.52-0.3924ACAA1ENST00000333167Frame-shift
ENSG00000279382ENST00000622927exon_skip_436035chr5:79656957-79657001-10.89-0.2593TENT2ENST00000296783,ENST00000428308,ENST00000453514Frame-shift
ENSG00000279382ENST00000622927exon_skip_9446chr1:147270931-147271005-13.37-0.1910CHD1LENST00000369258Frame-shift
ENSG00000279382ENST00000622927exon_skip_41841chr10:68756272-68756483-23.27-0.1152CCAR1ENST00000265872Frame-shift
ENSG00000279382ENST00000622927exon_skip_62623chr11:69079833-69079883-12.22-0.3133TPCN2ENST00000294309Frame-shift
ENSG00000279382ENST00000622927exon_skip_66482chr11:126274926-126275021-15.25-0.1713FOXRED1ENST00000263578Frame-shift
ENSG00000279382ENST00000622927exon_skip_111863chr14:23565815-23565892-23.74-0.4024AP1G2ENST00000308724,ENST00000397120Frame-shift
ENSG00000279382ENST00000622927exon_skip_114365chr14:74290026-74290118-18.26-0.2501ABCD4ENST00000356924Frame-shift
ENSG00000279382ENST00000622927exon_skip_139933chr16:90035632-90035687-11.09-0.2411GAS8ENST00000268699Frame-shift
ENSG00000279382ENST00000622927exon_skip_290158chr17:42953723-42953778-9.11-0.2603AARSD1ENST00000427569Frame-shift
ENSG00000279382ENST00000622927exon_skip_300663chr19:1425877-1425960-13.02-0.3028DAZAP1ENST00000233078Frame-shift
ENSG00000279382ENST00000622927exon_skip_302168chr19:10680345-10680443-12.10-0.1274ILF3ENST00000590261Frame-shift
ENSG00000279382ENST00000622927exon_skip_370518chr22:50247691-50247776-17.32-0.2112HDAC10ENST00000216271Frame-shift
ENSG00000279382ENST00000622927exon_skip_374497chr3:49999439-49999513-11.52-0.1800RBM6ENST00000266022Frame-shift
ENSG00000279382ENST00000622927exon_skip_470226chr7:103307595-103307708-16.52-0.2708PMPCBENST00000249269Frame-shift
ENSG00000279382ENST00000622927exon_skip_511212chrX:71555189-71555385-19.97-0.1305OGTENST00000373719Frame-shift

check buttonlncRNA targets by miRNA.
LncRNA Ensembl IDmiRNA IDLncRNA ENST IDBinding site in lncRNAScoreEnergyAlign LenPublic source

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Variants for RP11-449J21.3

check buttonRNA A-to-I editing events in lncRNA.
LncRNAediting IDLncRNA Ensembl IDChromosomeEditing PositionStrandGene TypeGene NameTranscript IDTranscript TypeTranscript Name

check buttonEdited-associated DElncRNAs in cancer.
LncRNA Ensembl IDLncRNA IndexCancer TypeChr_Postion_StrandAVE1AVE2log2FCW-valueP-valueAdjc.p-valueChange

check buttonCorrelation between RNA A-to-I editing events's frequecy and lncRNA expression.
LncRNA Ensembl IDLncRNA IndexCorrelationP-valueAdjc.p-value

check buttonCis-expression quantitative trait loci(cis-eQTL) of lncRNA.
LncRNA Ensembl IDLncRNA NameSNP infoNumber of Positive corelated CancerPositive corelated CancerNumber of Negative corelated CancerNegative corelated Cancer

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lncRNAs regulate the target genes through functioning as enhancers

lncrna_enhancer
check buttonlncRNA regulates differentially expressed genes by function as enhancer.
LncRNA Ensembl IDPC Gene IDPC Gene NamePositive correlated cancersCancer with PC gene up-regulationCancer with PC gene down-regulation

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lncRNAs regulate the target genes through recruiting transcript factors

lncrna_TF
check buttonLncRNA-TF complex positively regulates the gene expression by target promoter region (#cancer types with positive correlation >= 5).
lncRNA IDTF IDTF NamePCgene IDPCgene NameNumber of CancerCanaer Types

check buttonLncRNA-TF complex negatively regulates the gene expression by target promoter region (#cancer types with negative correlation >= 5).
lncRNA IDTF IDTF NamePCgene IDPCgene NameNumber of CancerCanaer Types

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lncRNAs regulate the alternative splicing event through interacting with splicing factor

lncrna_AS
check buttonLncRNA-RBP complex positively regulates the exon skippping events by target skipped eoxon region.
LncRNA Ensembl IDRBP IDRBP Gene NameExon Skipping IDSkipped ExonEX Gene NameEX Affected TransIDORF_annoCancer Type

check buttonLncRNA-RBP complex negatively regulates the exon skippping events by target skipped eoxon region.
LncRNA Ensembl IDRBP IDRBP Gene NameExon Skipping IDSkipped ExonEX Gene NameEX Affected TransIDORF_annoCancer Type

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lncRNAs regulate mRNA through targeting the 3'-UTR region

lncrna_mRNA
check buttonlncRNA regulates differential expressed mRNA by directly targeting 3' UTR region.
LncRNA Ensembl IDLncRNA ENST IDPC Gene NamePC Gene IDPC ENST IDdGnDGCancer with PC gene up-regulationCancer with PC gene Down-regulation
ENSG00000279382ENST00000622927CTSBENSG00000164733ENST00000526481-0.12411-CHOL
ENSG00000279382ENST00000622927CTSBENSG00000164733ENST00000530640-0.148394-CHOL
ENSG00000279382ENST00000622927CTSBENSG00000164733ENST00000531089-0.1569135-CHOL
ENSG00000279382ENST00000622927SQORENSG00000137767ENST00000565997-0.1183412-READ
ENSG00000279382ENST00000622927GSTO1ENSG00000148834ENST00000539281-0.2550343-CHOL
ENSG00000279382ENST00000622927GSTO1ENSG00000148834ENST00000369710-0.2550343-CHOL
ENSG00000279382ENST00000622927GSTO1ENSG00000148834ENST00000369713-0.3506345-CHOL
ENSG00000279382ENST00000622927UQCRC1ENSG00000010256ENST00000203407-0.2681909-CHOL,KIRC
ENSG00000279382ENST00000622927HSD17B10ENSG00000072506ENST00000375304-0.1281699-CHOL
ENSG00000279382ENST00000622927HSD17B10ENSG00000072506ENST00000168216-0.1281699-CHOL
ENSG00000279382ENST00000622927HSD17B10ENSG00000072506ENST00000375298-0.1008180-CHOL
ENSG00000279382ENST00000622927FTLENSG00000087086ENST00000331825-0.175981-CHOL
ENSG00000279382ENST00000622927DDTENSG00000099977ENST00000398344-0.174823-CHOL
ENSG00000279382ENST00000622927DDTENSG00000099977ENST00000350608-0.174823-CHOL
ENSG00000279382ENST00000622927DDTENSG00000099977ENST00000428792-0.174828-CHOL
ENSG00000279382ENST00000622927DDTENSG00000099977ENST00000404092-0.174836-CHOL
ENSG00000279382ENST00000622927DDTENSG00000099977ENST00000403754-0.6378393-CHOL
ENSG00000279382ENST00000622927DDTENSG00000099977ENST00000430101-0.1406474-CHOL
ENSG00000279382ENST00000622927ZNHIT1ENSG00000106400ENST00000305105-0.136299-CHOL
ENSG00000279382ENST00000622927PARK7ENSG00000116288ENST00000377488-0.6529487-CHOL
ENSG00000279382ENST00000622927AKR1A1ENSG00000117448ENST00000372070-0.2356565-CHOL
ENSG00000279382ENST00000622927AKR1A1ENSG00000117448ENST00000621846-0.2356566-CHOL
ENSG00000279382ENST00000622927AKR1A1ENSG00000117448ENST00000351829-0.2356565-CHOL
ENSG00000279382ENST00000622927ECHS1ENSG00000127884ENST00000368547-0.1287550-CHOL,KIRC
ENSG00000279382ENST00000622927DGCR6LENSG00000128185ENST00000248879-0.1051141-CHOL
ENSG00000279382ENST00000622927DGCR6LENSG00000128185ENST00000405465-0.1060114-CHOL
ENSG00000279382ENST00000622927DGCR6LENSG00000128185ENST00000443409-0.1182307-CHOL
ENSG00000279382ENST00000622927COX17ENSG00000138495ENST00000468918-0.1678603-CHOL
ENSG00000279382ENST00000622927COX17ENSG00000138495ENST00000486606-0.15361171-CHOL
ENSG00000279382ENST00000622927COX17ENSG00000138495ENST00000497116-0.10291-CHOL
ENSG00000279382ENST00000622927SOD1ENSG00000142168ENST00000270142-0.10571-CHOL
ENSG00000279382ENST00000622927SOD1ENSG00000142168ENST00000389995-0.10571-CHOL
ENSG00000279382ENST00000622927SURF1ENSG00000148290ENST00000371974-0.10221-CHOL
ENSG00000279382ENST00000622927SURF1ENSG00000148290ENST00000615505-0.148846-CHOL
ENSG00000279382ENST00000622927ATP5PFENSG00000154723ENST00000400099-0.1858761-CHOL,READ
ENSG00000279382ENST00000622927ATP5PFENSG00000154723ENST00000400094-0.1533505-CHOL,READ
ENSG00000279382ENST00000622927ATP5PFENSG00000154723ENST00000284971-0.1533505-CHOL,READ
ENSG00000279382ENST00000622927ATP5PFENSG00000154723ENST00000457143-0.1533505-CHOL,READ
ENSG00000279382ENST00000622927ATP5PFENSG00000154723ENST00000400090-0.1533505-CHOL,READ
ENSG00000279382ENST00000622927ATP5PFENSG00000154723ENST00000400087-0.1533505-CHOL,READ
ENSG00000279382ENST00000622927ATP5PFENSG00000154723ENST00000400093-0.1533505-CHOL,READ
ENSG00000279382ENST00000622927SMPD1ENSG00000166311ENST00000342245-0.104266-CHOL,READ
ENSG00000279382ENST00000622927SMPD1ENSG00000166311ENST00000527275-0.1926283-CHOL,READ
ENSG00000279382ENST00000622927SMPD1ENSG00000166311ENST00000526280-0.11781-CHOL,READ
ENSG00000279382ENST00000622927VKORC1ENSG00000167397ENST00000394971-0.1476601-CHOL
ENSG00000279382ENST00000622927VKORC1ENSG00000167397ENST00000498155-0.19851225-CHOL
ENSG00000279382ENST00000622927YIF1AENSG00000174851ENST00000496746-0.3105460-CHOL
ENSG00000279382ENST00000622927YIF1AENSG00000174851ENST00000471387-0.1717948-CHOL
ENSG00000279382ENST00000622927YIF1AENSG00000174851ENST00000359461-0.3105460-CHOL
ENSG00000279382ENST00000622927YIF1AENSG00000174851ENST00000376901-0.3105460-CHOL
ENSG00000279382ENST00000622927YIF1AENSG00000174851ENST00000484814-0.1854406-CHOL
ENSG00000279382ENST00000622927AURKAIP1ENSG00000175756ENST00000338370-0.2113755-CHOL
ENSG00000279382ENST00000622927AURKAIP1ENSG00000175756ENST00000338338-0.2113755-CHOL
ENSG00000279382ENST00000622927AURKAIP1ENSG00000175756ENST00000321751-0.2113757-CHOL
ENSG00000279382ENST00000622927AURKAIP1ENSG00000175756ENST00000378853-0.348880-CHOL
ENSG00000279382ENST00000622927DHRS4L2ENSG00000187630ENST00000558753-0.7544482-CHOL
ENSG00000279382ENST00000622927DHRS4L2ENSG00000187630ENST00000560276-0.19431-CHOL
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000550697-0.1419454-READ
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000548580-0.1296453-READ
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000293422-0.1296454-READ
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000348108-0.1419441-READ
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000549017-0.1296454-READ
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000549566-0.2517563-READ
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000536128-0.11411-READ
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000547649-0.1296454-READ
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000547408-0.1411703-READ
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000548400-0.1419453-READ
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000548293-0.1497205-READ
ENSG00000279382ENST00000622927MYL6ENSG00000092841ENST00000546845-0.1286641-READ

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lncRNAs regulate mRNA by competing with miRNA

lncrna_miRNA
check buttonlncRNA regulates mRNA by competing the miRNA binding site with mRNA.
LncRNA Ensembl IDlncRNA-miRNA-mRNACancer Types

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lncRNA coding potential

check buttonORFfinder result for the gencode.v22.lncRNA.transcript.fa.
lncRNA Ensembl IDlncRNA ENST IDlength(AA)start at transcriptend at transcript
ENSG00000279382.1ENST00000622927.138114227