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Editing gene: FRMD3 (CAeditome ID:257019)

Gene summary for FRMD3

Gene summary

Gene information	Gene symbol	FRMD3
	Gene ID	257019
	Gene name	FERM domain containing 3
	Synonyms	4.1O\|EPB41L4O\|EPB41LO\|P410
	Cytomap	9q21.32
	Type of gene	protein-coding
	Description	FERM domain-containing protein 3band 4.1-like protein 4band 4.1-like protein 4Oovary type protein 4.1protein 4.1O
	Modification date	20210518
	UniProtAcc	A2A2Y4
	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 FRMD3

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: ENSG00000172159.14

RNA A-to-I editing events in Cancer.

CAediting_692013(83245786, -), CAediting_692014(83246394, -), CAediting_692015(83246429, -), CAediting_692016(83246450, -), CAediting_692017(83340038, -), CAediting_692018(83340043, -), CAediting_692019(83370796, -), CAediting_692020(83423693, -), CAediting_692021(83423708, -), CAediting_692022(83423712, -), CAediting_692023(83423721, -), CAediting_692024(83423742, -), CAediting_692025(83423809, -), CAediting_692026(83423823, -), CAediting_692027(83442418, -), CAediting_692028(83442437, -), CAediting_692029(83442451, -), CAediting_692030(83442452, -), CAediting_692031(83442471, -), CAediting_692032(83445179, -), CAediting_692033(83445210, -), CAediting_692034(83452965, -), CAediting_692035(83453974, -), CAediting_692036(83461756, -), CAediting_692037(83461764, -), CAediting_692038(83461799, -), CAediting_692039(83461803, -), CAediting_692040(83461852, -), CAediting_692041(83461867, -), CAediting_692042(83461870, -), CAediting_692043(83461918, -), CAediting_692044(83461919, -), CAediting_692045(83461924, -), CAediting_692046(83461968, -), CAediting_692047(83467079, -), CAediting_692048(83467098, -), CAediting_692049(83483656, -), CAediting_692050(83483738, -), CAediting_692051(83484555, -), CAediting_692052(83484655, -), CAediting_692053(83520942, -),

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RNA editing positional annotations for FRMD3 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_692013	chr9_83245786_-	UTR3
CAediting_692014	chr9_83246394_-	UTR3
CAediting_692015	chr9_83246429_-	UTR3
CAediting_692016	chr9_83246450_-	UTR3
CAediting_692017	chr9_83340038_-	intronic
CAediting_692018	chr9_83340043_-	intronic
CAediting_692019	chr9_83370796_-	intronic
CAediting_692020	chr9_83423693_-	intronic
CAediting_692021	chr9_83423708_-	intronic
CAediting_692022	chr9_83423712_-	intronic
CAediting_692023	chr9_83423721_-	intronic
CAediting_692024	chr9_83423742_-	intronic
CAediting_692025	chr9_83423809_-	intronic
CAediting_692026	chr9_83423823_-	intronic
CAediting_692027	chr9_83442418_-	intronic
CAediting_692028	chr9_83442437_-	intronic
CAediting_692029	chr9_83442451_-	intronic
CAediting_692030	chr9_83442452_-	intronic
CAediting_692031	chr9_83442471_-	intronic
CAediting_692032	chr9_83445179_-	intronic
CAediting_692033	chr9_83445210_-	intronic
CAediting_692034	chr9_83452965_-	intronic
CAediting_692035	chr9_83453974_-	intronic
CAediting_692036	chr9_83461756_-	intronic
CAediting_692037	chr9_83461764_-	intronic
CAediting_692038	chr9_83461799_-	intronic
CAediting_692039	chr9_83461803_-	intronic
CAediting_692040	chr9_83461852_-	intronic
CAediting_692041	chr9_83461867_-	intronic
CAediting_692042	chr9_83461870_-	intronic
CAediting_692043	chr9_83461918_-	intronic
CAediting_692044	chr9_83461919_-	intronic
CAediting_692045	chr9_83461924_-	intronic
CAediting_692046	chr9_83461968_-	intronic
CAediting_692047	chr9_83467079_-	intronic
CAediting_692048	chr9_83467098_-	intronic
CAediting_692049	chr9_83483656_-	intronic
CAediting_692050	chr9_83483738_-	intronic
CAediting_692051	chr9_83484555_-	intronic
CAediting_692052	chr9_83484655_-	intronic
CAediting_692053	chr9_83520942_-	intronic

Repat-regional RNA editing(s).

CAeditome ID	Position	Repeat family	Repeat sub family	Repeat name
CAediting_692019	chr9_83370796_-	SINE	Alu	AluSx
CAediting_692020	chr9_83423693_-	SINE	Alu	AluSx
CAediting_692021	chr9_83423708_-	SINE	Alu	AluSx
CAediting_692022	chr9_83423712_-	SINE	Alu	AluSx
CAediting_692023	chr9_83423721_-	SINE	Alu	AluSx
CAediting_692024	chr9_83423742_-	SINE	Alu	AluSx
CAediting_692025	chr9_83423809_-	SINE	Alu	AluSx
CAediting_692026	chr9_83423823_-	SINE	Alu	AluSx
CAediting_692027	chr9_83442418_-	SINE	Alu	AluSz
CAediting_692028	chr9_83442437_-	SINE	Alu	AluSz
CAediting_692029	chr9_83442451_-	SINE	Alu	AluSz
CAediting_692030	chr9_83442452_-	SINE	Alu	AluSz
CAediting_692031	chr9_83442471_-	SINE	Alu	AluSz
CAediting_692032	chr9_83445179_-	SINE	Alu	AluSx1
CAediting_692033	chr9_83445210_-	SINE	Alu	AluSx1
CAediting_692034	chr9_83452965_-	SINE	Alu	AluSz6
CAediting_692035	chr9_83453974_-	SINE	Alu	AluY
CAediting_692036	chr9_83461756_-	SINE	Alu	AluSx1
CAediting_692037	chr9_83461764_-	SINE	Alu	AluSx1
CAediting_692038	chr9_83461799_-	SINE	Alu	AluSx1
CAediting_692039	chr9_83461803_-	SINE	Alu	AluSx1
CAediting_692040	chr9_83461852_-	SINE	Alu	AluSx1
CAediting_692041	chr9_83461867_-	SINE	Alu	AluSx1
CAediting_692042	chr9_83461870_-	SINE	Alu	AluSx1
CAediting_692043	chr9_83461918_-	SINE	Alu	AluSx1
CAediting_692044	chr9_83461919_-	SINE	Alu	AluSx1
CAediting_692045	chr9_83461924_-	SINE	Alu	AluSx1
CAediting_692046	chr9_83461968_-	SINE	Alu	AluSx1
CAediting_692049	chr9_83483656_-	SINE	Alu	AluJr
CAediting_692050	chr9_83483738_-	SINE	Alu	AluJr
CAediting_692051	chr9_83484555_-	SINE	Alu	AluSz6
CAediting_692052	chr9_83484655_-	SINE	Alu	AluSz6
CAediting_692053	chr9_83520942_-	SINE	Alu	AluSx1

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RNA A-to-I editing events in the alternative splicing sites for FRMD3

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 ENSG00000172159.14.FRMD3.

Correlation between RNA A-to-I editing and PSI for ENSG00000172159.14.FRMD3.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for FRMD3

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.

THCA.CAediting_692013.ENSG00000172159.FRMD3.png
Soverview

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Protein coding region RNA A-to-I editings for FRMD3

- 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 FRMD3

**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
CAediting_692013	chr9_83245786_-	ENSG00000172159.14	ENST00000304195	hsa-miR-3157-3p	83245781	83245788	8mer-1a	83245781	83245800	150.00	-16.95
CAediting_692013	chr9_83245786_-	ENSG00000172159.14	ENST00000621208	hsa-miR-3157-3p	83245781	83245788	8mer-1a	83245781	83245800	150.00	-16.95
CAediting_692016	chr9_83246450_-	ENSG00000172159.14	ENST00000304195	hsa-miR-6501-3p	83246450	83246456	7mer-m8	83246449	83246469	142.00	-18.84
CAediting_692016	chr9_83246450_-	ENSG00000172159.14	ENST00000621208	hsa-miR-6501-3p	83246450	83246456	7mer-m8	83246449	83246469	142.00	-18.84

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_688080	chr9_63819626_+	ENSG00000172159.14	ENST00000304195	hsa-miR-4477b	83245888	83245894	7mer-m8	83245887	83245908	144	-9.02
CAediting_688081	chr9_63819627_+	ENSG00000172159.14	ENST00000304195	hsa-miR-4477b	83244643	83244649	7mer-m8	83244642	83244663	152	-16.71
CAediting_688080	chr9_63819626_+	ENSG00000172159.14	ENST00000621208	hsa-miR-4477b	83245888	83245894	7mer-m8	83245887	83245908	144	-9.02
CAediting_688081	chr9_63819627_+	ENSG00000172159.14	ENST00000621208	hsa-miR-4477b	83244643	83244649	7mer-m8	83244642	83244663	152	-16.71
CAediting_442554	chr5_154685830_+	ENSG00000172159.14	ENST00000328788	hsa-miR-1303	83243020	83243026	7mer-m8	83243019	83243040	143	-16.72
CAediting_442554	chr5_154685830_+	ENSG00000172159.14	ENST00000376434	hsa-miR-1303	83243020	83243026	7mer-m8	83243019	83243040	143	-16.72
CAediting_442554	chr5_154685830_+	ENSG00000172159.14	ENST00000376438	hsa-miR-1303	83243020	83243026	7mer-m8	83243019	83243040	143	-16.72
CAediting_1229414	chr17_67471546_+	ENSG00000172159.14	ENST00000304195	hsa-miR-548aa	83247702	83247708	7mer-m8	83247701	83247726	143	-15.6
CAediting_1229415	chr17_67471547_+	ENSG00000172159.14	ENST00000304195	hsa-miR-548aa	83246629	83246635	7mer-m8	83246628	83246654	155	-12.76
CAediting_117844	chr1_162342605_+	ENSG00000172159.14	ENST00000304195	hsa-miR-556-3p	83246135	83246141	7mer-m8	83246134	83246161	149	-13.35
CAediting_1229414	chr17_67471546_+	ENSG00000172159.14	ENST00000621208	hsa-miR-548aa	83247702	83247708	7mer-m8	83247701	83247726	143	-15.6
CAediting_1229415	chr17_67471547_+	ENSG00000172159.14	ENST00000621208	hsa-miR-548aa	83246629	83246635	7mer-m8	83246628	83246654	155	-12.76
CAediting_117844	chr1_162342605_+	ENSG00000172159.14	ENST00000621208	hsa-miR-556-3p	83246135	83246141	7mer-m8	83246134	83246161	149	-13.35
CAediting_468389	chr6_31355314_-	ENSG00000172159.14	ENST00000431299	hsa-miR-6891-5p	83297608	83297614	7mer-m8	83297607	83297627	156	-24.96

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
CAediting_1160181	chr17_7017644_-	ENSG00000172159.14	ENST00000304195	hsa-miR-195-3p	83244858	83244864	7mer-m8	83244857	83244878	140	-6.29
CAediting_748296	chr10_51299626_+	ENSG00000172159.14	ENST00000304195	hsa-miR-605-3p	83246338	83246344	7mer-m8	83246337	83246358	146	-12.77
CAediting_1160181	chr17_7017644_-	ENSG00000172159.14	ENST00000621208	hsa-miR-195-3p	83244858	83244864	7mer-m8	83244857	83244878	140	-6.29
CAediting_748296	chr10_51299626_+	ENSG00000172159.14	ENST00000621208	hsa-miR-605-3p	83246338	83246344	7mer-m8	83246337	83246358	146	-12.77

Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for FRMD3

- 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 FRMD3

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.)
LGG	CAediting_692013	chr9_83245786_-	0.00223670842566311	0.223411213988937	.	.	.	.
GBM	CAediting_692013	chr9_83245786_-	0.0281336407630371	0.29091419142546	.	.	.	.
SKCM	CAediting_692013	chr9_83245786_-	0.00769695856030947	0.340860908726017	.	.	.	.
LGG	CAediting_692014	chr9_83246394_-	0.000279365854893034	0.33138605582951	.	.	0.00442127792248376	0.262476431603552
BRCA	CAediting_692014	chr9_83246394_-	1.24008861322613e-09	0.526835478940747	.	.	.	.
GBM	CAediting_692014	chr9_83246394_-	0.000885304387197826	0.399673007290704	.	.	.	.
STAD	CAediting_692014	chr9_83246394_-	0.0010386910725597	0.400561710867293	.	.	.	.
THCA	CAediting_692014	chr9_83246394_-	3.96274895681841e-10	0.323709736875379	.	.	.	.
KIRC	CAediting_692014	chr9_83246394_-	1.32688349630458e-05	0.237237767461088	.	.	.	.
OV	CAediting_692014	chr9_83246394_-	1.79482495951355e-05	0.479195473711655	.	.	.	.
BRCA	CAediting_692016	chr9_83246450_-	0.0260849000354479	0.289621039897055	.	.	.	.

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Relation with cancer stages for FRMD3

Correlation between Cancer stages and RNA editing frequency

Cancer	Stage_type	CAeditomID	position	P-val	Coeff.
KIRC	pathologic_stage	CAediting_692014	chr9_83246394_-	8.9989753793858e-06	0.242052718060055
SKCM	pathologic_stage	CAediting_692013	chr9_83245786_-	0.0445127045901615	0.274566615975989
THCA	pathologic_stage	CAediting_692013	chr9_83245786_-	0.0338348291597754	0.146868129661853
THCA	pathologic_stage	CAediting_692014	chr9_83246394_-	0.0161570816908033	0.128132343816435

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Relation with survival for FRMD3

Correlation between RNA editing and survival

Cancer	CAeditomID	position	KMpvalue	Coxpvalue	CoxHR
STAD	CAediting_692014	chr9_83246394_-	0.0454968791049882	0.0443419	10.9383

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RelatedDrugs for FRMD3

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 FRMD3

Diseases associated with this gene.
(DisGeNet 7.0)

Gene	Disease ID	Disease name	# pubmeds	Source
FRMD3	C0263454	Chloracne	1	CTD_human

	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