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Editing gene: SMG9 (CAeditome ID:56006)

Gene summary for SMG9

Gene summary

Gene information	Gene symbol	SMG9
	Gene ID	56006
	Gene name	SMG9 nonsense mediated mRNA decay factor
	Synonyms	C19orf61\|F17127_1\|HBMS
	Cytomap	19q13.31
	Type of gene	protein-coding
	Description	protein SMG9protein smg-9 homolog
	Modification date	20210518
	UniProtAcc	Q9H0W8
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene

GO ID

GO term

PubMed ID

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RNA A-to-I events for SMG9

RNA A-to-I editing events across TCGA 33 cancers data sets based on Ensembl gene isoform structure.

RNA editing frequencies across 33 cancers of gene: ENSG00000105771.12

RNA A-to-I editing events in Cancer.

CAediting_1359189(43735406, -), CAediting_1359190(43735571, -), CAediting_1359191(43737031, -), CAediting_1359192(43737062, -), CAediting_1359193(43737094, -), CAediting_1359194(43737141, -), CAediting_1359195(43737161, -), CAediting_1359196(43737164, -), CAediting_1359197(43746087, -), CAediting_1359198(43746868, -), CAediting_1359199(43746874, -), CAediting_1359200(43746884, -), CAediting_1359201(43746898, -), CAediting_1359202(43746905, -), CAediting_1359203(43746906, -), CAediting_1359204(43746914, -), CAediting_1359205(43746932, -), CAediting_1359206(43746937, -), CAediting_1359207(43746946, -), CAediting_1359208(43746978, -), CAediting_1359209(43746982, -), CAediting_1359210(43746993, -), CAediting_1359211(43746994, -), CAediting_1359212(43746995, -), CAediting_1359213(43746996, -), CAediting_1359214(43746997, -), CAediting_1359215(43747000, -), CAediting_1359216(43747017, -), CAediting_1359217(43747045, -), CAediting_1359218(43747050, -), CAediting_1359219(43747051, -), CAediting_1359220(43747055, -), CAediting_1359221(43753528, -), CAediting_1359222(43753533, -), CAediting_1359223(43753598, -), CAediting_1359224(43753599, -),

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RNA editing positional annotations for SMG9 using Annovar

Protein coding RNA editing(s).

CAeditome ID

Position

Variant type

ENST

NTchange

AAchange

SIFT_score

Polyphen2_HVAR_score

PROVEAN_pred

Gene structure information of RNA editing(s).

CAeditome ID	Position	Variant type
CAediting_1359189	chr19_43735406_-	intronic
CAediting_1359190	chr19_43735571_-	intronic
CAediting_1359191	chr19_43737031_-	intronic
CAediting_1359192	chr19_43737062_-	intronic
CAediting_1359193	chr19_43737094_-	intronic
CAediting_1359194	chr19_43737141_-	intronic
CAediting_1359195	chr19_43737161_-	intronic
CAediting_1359196	chr19_43737164_-	intronic
CAediting_1359197	chr19_43746087_-	ncRNA_intronic
CAediting_1359198	chr19_43746868_-	ncRNA_intronic
CAediting_1359199	chr19_43746874_-	ncRNA_intronic
CAediting_1359200	chr19_43746884_-	ncRNA_intronic
CAediting_1359201	chr19_43746898_-	ncRNA_intronic
CAediting_1359202	chr19_43746905_-	ncRNA_intronic
CAediting_1359203	chr19_43746906_-	ncRNA_intronic
CAediting_1359204	chr19_43746914_-	ncRNA_intronic
CAediting_1359205	chr19_43746932_-	ncRNA_intronic
CAediting_1359206	chr19_43746937_-	ncRNA_intronic
CAediting_1359207	chr19_43746946_-	ncRNA_intronic
CAediting_1359208	chr19_43746978_-	ncRNA_intronic
CAediting_1359209	chr19_43746982_-	ncRNA_intronic
CAediting_1359210	chr19_43746993_-	ncRNA_intronic
CAediting_1359211	chr19_43746994_-	ncRNA_intronic
CAediting_1359212	chr19_43746995_-	ncRNA_intronic
CAediting_1359213	chr19_43746996_-	ncRNA_intronic
CAediting_1359214	chr19_43746997_-	ncRNA_intronic
CAediting_1359215	chr19_43747000_-	ncRNA_intronic
CAediting_1359216	chr19_43747017_-	ncRNA_intronic
CAediting_1359217	chr19_43747045_-	ncRNA_intronic
CAediting_1359218	chr19_43747050_-	ncRNA_intronic
CAediting_1359219	chr19_43747051_-	ncRNA_intronic
CAediting_1359220	chr19_43747055_-	ncRNA_intronic
CAediting_1359221	chr19_43753528_-	ncRNA_intronic
CAediting_1359222	chr19_43753533_-	ncRNA_intronic
CAediting_1359223	chr19_43753598_-	ncRNA_intronic
CAediting_1359224	chr19_43753599_-	ncRNA_intronic

Repat-regional RNA editing(s).

CAeditome ID	Position	Repeat family	Repeat sub family	Repeat name
CAediting_1359189	chr19_43735406_-	SINE	Alu	AluSx
CAediting_1359190	chr19_43735571_-	SINE	Alu	AluSx
CAediting_1359191	chr19_43737031_-	SINE	Alu	AluSx1
CAediting_1359192	chr19_43737062_-	SINE	Alu	AluSx1
CAediting_1359193	chr19_43737094_-	SINE	Alu	AluSx1
CAediting_1359194	chr19_43737141_-	SINE	Alu	AluSx1
CAediting_1359195	chr19_43737161_-	SINE	Alu	AluSx1
CAediting_1359196	chr19_43737164_-	SINE	Alu	AluSx1
CAediting_1359197	chr19_43746087_-	SINE	Alu	AluSz
CAediting_1359198	chr19_43746868_-	SINE	Alu	AluJb
CAediting_1359199	chr19_43746874_-	SINE	Alu	AluJb
CAediting_1359200	chr19_43746884_-	SINE	Alu	AluJb
CAediting_1359201	chr19_43746898_-	SINE	Alu	AluJb
CAediting_1359202	chr19_43746905_-	SINE	Alu	AluJb
CAediting_1359203	chr19_43746906_-	SINE	Alu	AluJb
CAediting_1359204	chr19_43746914_-	SINE	Alu	AluJb
CAediting_1359205	chr19_43746932_-	SINE	Alu	AluJb
CAediting_1359206	chr19_43746937_-	SINE	Alu	AluJb
CAediting_1359207	chr19_43746946_-	SINE	Alu	AluJb
CAediting_1359208	chr19_43746978_-	SINE	Alu	AluJb
CAediting_1359209	chr19_43746982_-	SINE	Alu	AluJb
CAediting_1359210	chr19_43746993_-	SINE	Alu	AluJb
CAediting_1359211	chr19_43746994_-	SINE	Alu	AluJb
CAediting_1359212	chr19_43746995_-	SINE	Alu	AluJb
CAediting_1359213	chr19_43746996_-	SINE	Alu	AluJb
CAediting_1359214	chr19_43746997_-	SINE	Alu	AluJb
CAediting_1359215	chr19_43747000_-	SINE	Alu	AluJb
CAediting_1359216	chr19_43747017_-	SINE	Alu	AluJb
CAediting_1359217	chr19_43747045_-	SINE	Alu	AluJb
CAediting_1359218	chr19_43747050_-	SINE	Alu	AluJb
CAediting_1359219	chr19_43747051_-	SINE	Alu	AluJb
CAediting_1359220	chr19_43747055_-	SINE	Alu	AluJb
CAediting_1359221	chr19_43753528_-	SINE	Alu	AluSz
CAediting_1359222	chr19_43753533_-	SINE	Alu	AluSz
CAediting_1359223	chr19_43753598_-	SINE	Alu	AluSz
CAediting_1359224	chr19_43753599_-	SINE	Alu	AluSz

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RNA A-to-I editing events in the alternative splicing sites for SMG9

RNA A-to-I editing(s) in the alternative splicing sites.

AStype

CAeditomID

Editing position

AS position

AS direction

Exonic location

Wildtype sequence

Wildtype splicing strength

RNA edited sequence

RNA edited splicing strength

Differential percent of spliced in (PSI) between RNA A-to-I edited and non-edited samples for ENSG00000105771.12.SMG9.

Correlation between RNA A-to-I editing and PSI for ENSG00000105771.12.SMG9.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for SMG9

Differential gene expressions between RNA A-to-I edited and non-edited tumor samples.
* The grey color means N/A.

Correlation between RNA A-to-I editing and gene expression.

- Differentially expressed gene between RNA A-to-I edited samples versus non-edited samples.
* Click on the image to enlarge it in a new window.

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Protein coding region RNA A-to-I editings for SMG9

- Lollipop plot for RNA A-to-I editings across protein structure.
* Click on the image to enlarge it in a new window.

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The effects of the RNA editing to the miRNA binding sites for SMG9

**If you are searching a miRNA gene with RNA editing events in its seed regions, please see the search pages of miRNA targets to discover the effects of this RNA editing event to miRNA regulations. For more information, please check the files in the Download page.

RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in lncRNA gained miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in lncRNA lost miRNA binding sites.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in miRNAs gained binding to lncRNA.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in miRNAs lost binding to lncRNA.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA.

CAeditom_ID	Position	ENSG	ENST	miRNA	Targetscan start	Targetscan end	Targetscan score	Miranda start	Miranda end	Miranda score	Miranda energy
CAediting_1229415	chr17_67471547_+	ENSG00000105771.12	ENST00000601170	hsa-miR-548aa	43732379	43732385	7mer-m8	43732378	43732402	142	-7.4
CAediting_524911	chr7_5495852_-	ENSG00000105771.12	ENST00000601170	hsa-miR-589-3p	43732343	43732348	6mer	43732342	43732365	143	-27.01
CAediting_414656	chr5_72878640_+	ENSG00000105771.12	ENST00000597598	hsa-miR-4804-3p	43739996	43740002	7mer-m8	43739995	43740015	140	-10.09
CAediting_468389	chr6_31355314_-	ENSG00000105771.12	ENST00000601170	hsa-miR-6891-5p	43732756	43732762	7mer-m8	43732755	43732776	152	-24.75

RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA.

CAeditom_ID

Position

ENSG

ENST

miRNA

Targetscan start

Targetscan end

Targetscan score

Miranda start

Miranda end

Miranda score

Miranda energy

Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for SMG9

- RNA A-to-I editing in mRNA.
* Click on the image to enlarge it in a new window.

ENST

ENST type

RNA structure without RNA A-to-I editing.

RNA structure with RNA A-to-I editing.

RNA A-to-I editing in RNA structures for Minimum free energy (MFE).

CAeditom_ID

ENST

Editing_Position

MFE_withoneAI

MFE_withoutAI

MFE_withmultipleAI

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Relation with ADAR for SMG9

Correlation between ADAR gene expression and RNA editing frequency

Cancer

CAeditomID

position

ADAR1 (p-val)

ADAR1 (coeff.)

ADAR2 (p-val)

ADAR2 (coeff.)

ADAR3 (p-val)

ADAR3 (coeff.)

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Relation with cancer stages for SMG9

Correlation between Cancer stages and RNA editing frequency

Cancer

Stage_type

CAeditomID

position

P-val

Coeff.

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Relation with survival for SMG9

Correlation between RNA editing and survival

Cancer

CAeditomID

position

KMpvalue

Coxpvalue

CoxHR

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RelatedDrugs for SMG9

Approved drugs targeting this gene.
(DrugBank Version 5.1.8 2021-01-03)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for SMG9

Diseases associated with this gene.
(DisGeNet 7.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SMG9	C4310793	HEART AND BRAIN MALFORMATION SYNDROME	2	CTD_human;GENOMICS_ENGLAND

	Gene summary
	RNA A-to-I events
	Differntial gene expression between RNA A-to-I edited tumor samples versus normal samples
	Protein coding region RNA A-to-I editings
	The effects of the RNA editing to the miRNA binding sites
	The effects of the RNA editing to the stability of the RNA structures
	Relation with ADAR
	Relation with cancer stages
	Relation with survival state
	Related drugs with this gene
	Related diseases with this gene