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lncRNA: ENSG00000224081

Summary for SLC44A3-AS1

Gene summary

Gene information	Ensembl ID	ENSG00000224081
	Gene symbol	SLC44A3-AS1
	Gene name	SLC44A3 antisense RNA 1
	HGNC	49057
	Entrez ID	101928079
	Gene type	lincRNA
	Synonyms	SLC44A3-AS1\|01p21.3\|LINC01057
	UniProtAcc

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Structure and expression level for SLC44A3-AS1

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
ENSG00000224081	1.289975e+02	1.482649e+00	3.735868e-01	3.968687e+00	7.230000e-05	3.724880e-04	UP	GBM
ENSG00000224081	2.207230e+02	3.600978e+00	4.250757e-01	8.471380e+00	2.430000e-17	8.370000e-16	UP	CHOL
ENSG00000224081	1.768480e+02	1.119027e+00	2.656436e-01	4.212510e+00	2.530000e-05	1.571320e-04	UP	BLCA
ENSG00000224081	1.626540e+02	1.603478e+00	1.091572e-01	1.468962e+01	7.510000e-49	4.020000e-47	UP	LUAD
ENSG00000224081	2.067234e+02	1.002832e+00	1.678875e-01	5.973238e+00	2.330000e-09	2.580000e-08	UP	STAD

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000224081	4.053788e-01	5.735332e-03	CHOL	7.275134e-03

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lncRNA-Protein interaction for SLC44A3-AS1

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
ENSG00000224081	ENST00000414374	LINC01057	ENSG00000123636	BAZ2B	50.23	90.5478	Q9UIF8	TF,Epi	NA
ENSG00000224081	ENST00000452922	LINC01057	ENSG00000123636	BAZ2B	73.67	95.1502	Q9UIF8	TF,Epi	NA
ENSG00000224081	ENST00000442418	LINC01057	ENSG00000123636	BAZ2B	61.26	92.9607	Q9UIF8	TF,Epi	NA
ENSG00000224081	ENST00000418366	LINC01057	ENSG00000123636	BAZ2B	61.17	92.9225	Q9UIF8	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
ENSG00000224081	ENST00000452922	LINC01057	ENSG00000123636	BAZ2B	73.67	95.0925	Q9UIF8	TF,Epi	NA
ENSG00000224081	ENST00000442418	LINC01057	ENSG00000123636	BAZ2B	61.26	93.4492	Q9UIF8	TF,Epi	NA
ENSG00000224081	ENST00000452922	LINC01057	ENSG00000167232	ZNF91	40.19	94.0636	Q05481	TF	NA
ENSG00000224081	ENST00000442418	LINC01057	ENSG00000167232	ZNF91	32.57	92.1355	Q05481	TF	NA
ENSG00000224081	ENST00000452922	LINC01057	ENSG00000198040	ZNF84	30.38	91.9803	P51523	TF	NA
ENSG00000224081	ENST00000432162	LINC01057	ENSG00000198040	ZNF84	24.92	90.7497	P51523	TF	NA
ENSG00000224081	ENST00000452922	LINC01057	ENSG00000275410	HNF1B	15.62	91.3382	P35680	TF	NA
ENSG00000224081	ENST00000414374	LINC01057	ENSG00000123636	BAZ2B	50.23	90.3697	Q9UIF8	TF,Epi	NA
ENSG00000224081	ENST00000414374	LINC01057	ENSG00000167232	ZNF91	29.21	90.3577	Q05481	TF	NA
ENSG00000224081	ENST00000418366	LINC01057	ENSG00000123636	BAZ2B	61.17	92.8387	Q9UIF8	TF,Epi	NA
ENSG00000224081	ENST00000418366	LINC01057	ENSG00000085276	MECOM	46.92	90.2064	Q03112	TF	NA
ENSG00000224081	ENST00000418366	LINC01057	ENSG00000167232	ZNF91	34.75	93.2175	Q05481	TF	NA
ENSG00000224081	ENST00000418366	LINC01057	ENSG00000198040	ZNF84	26.48	92.5647	P51523	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
ENSG00000224081	ENST00000418366	LINC01057	ENSG00000100201	DDX17	29.74	92.0278	Q92841	RBP	NA
ENSG00000224081	ENST00000418366	LINC01057	ENSG00000135870	RC3H1	28.29	90.6254	Q5TC82	RBP	NA
ENSG00000224081	ENST00000418366	LINC01057	ENSG00000184863	RBM33	15.78	90.1927	Q96EV2	RBP	NA
ENSG00000224081	ENST00000452922	LINC01057	ENSG00000100201	DDX17	35.9	91.7807	Q92841	RBP	NA
ENSG00000224081	ENST00000432162	LINC01057	ENSG00000135870	RC3H1	33.1	91.5876	Q5TC82	RBP	NA
ENSG00000224081	ENST00000442418	LINC01057	ENSG00000135870	RC3H1	28.59	90.1057	Q5TC82	RBP	NA

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lncRNA-DNA interaction for SLC44A3-AS1

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 SLC44A3-AS1

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 SLC44A3-AS1

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_13386	ENSG00000224081.6	chr1	94657920	-	lincRNA	LINC01057	ENST00000452922.4	lincRNA	LINC01057-001
LncEditing_13528	ENSG00000224081.6	chr1	94742640	-	lincRNA	LINC01057	ENST00000452922.4	lincRNA	LINC01057-001

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
ENSG00000224081	LncEditing_13386	CHOL	chr1_94657920_-	5.199652e+00	2.814691e+00	1.129384e+00	2.843992e+00	4.455222e-03	9.434588e-03	UP
ENSG00000224081	LncEditing_13528	STAD	chr1_94742640_-	2.399586e+00	1.347415e+00	1.201069e+00	7.080972e+00	1.431468e-12	2.773833e-12	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

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
ENSG00000224081.6	ENST00000442418.4	155	1037	1504
ENSG00000224081.6	ENST00000452922.4	103	637	326
ENSG00000224081.6	ENST00000456551.1	113	706	365
ENSG00000224081.6	ENST00000432162.4	57	5	175
ENSG00000224081.6	ENST00000421997.4	107	225	548
ENSG00000224081.6	ENST00000414374.1	134	464	60
ENSG00000224081.6	ENST00000418366.2	124	425	51
ENSG00000224081.6	ENST00000424711.1	96	493	203

	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