ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for MTMR3

Gene summary

Gene information	Gene symbol	MTMR3
	Gene ID	8897
	Gene name	myotubularin related protein 3
	Synonyms	FYVE-DSP1\|ZFYVE10
	Cytomap	22q12.2
	Type of gene	protein-coding
	Description	myotubularin-related protein 3FYVE (Fab1 YGLO23 Vsp27 EEA1 domain) dual-specificity protein phosphataseFYVE domain-containing dual specificity protein phosphatase 1phosphatidylinositol-3,5-bisphosphate 3-phosphatasephosphatidylinositol-3-phosphate pho
	Modification date	20180519
	UniProtAcc	Q13615
	Context	PubMed: MTMR3 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

Gene	GO ID	GO term	PubMed ID
MTMR3	GO:0006470	protein dephosphorylation	10733931
MTMR3	GO:0046856	phosphatidylinositol dephosphorylation	10900271\|11676921
MTMR3	GO:0060304	regulation of phosphatidylinositol dephosphorylation	16787938
MTMR3	GO:1904562	phosphatidylinositol 5-phosphate metabolic process	11676921

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Exon skipping events across known transcript of Ensembl for MTMR3 from UCSC genome browser

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Gene isoform structures and expression levels for MTMR3

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for MTMR3

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_364343	22	30279257:30279348:30353024:30353077:30366964:30367051	30353024:30353077	ENSG00000100330.11	ENST00000495098.1,ENST00000333027.3,ENST00000415511.1,ENST00000351488.3
exon_skip_364344	22	30279257:30279348:30353024:30353077:30374430:30374520	30353024:30353077	ENSG00000100330.11	ENST00000323630.5
exon_skip_364345	22	30279257:30279348:30366964:30367051:30374430:30374520	30366964:30367051	ENSG00000100330.11	ENST00000445401.1
exon_skip_364346	22	30353024:30353077:30366964:30367051:30374430:30374520	30366964:30367051	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000415511.1,ENST00000351488.3
exon_skip_364350	22	30374924:30375041:30384468:30384551:30387492:30387617	30384468:30384551	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000445401.1,ENST00000406629.1,ENST00000351488.3,ENST00000323630.5
exon_skip_364353	22	30384468:30384551:30387492:30387659:30394749:30394846	30387492:30387659	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000406629.1,ENST00000351488.3,ENST00000323630.5
exon_skip_364355	22	30394749:30394846:30398868:30398982:30403102:30403308	30398868:30398982	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000406629.1,ENST00000351488.3,ENST00000323630.5
exon_skip_364358	22	30398868:30398982:30403102:30403308:30403889:30403964	30403102:30403308	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000406629.1,ENST00000351488.3,ENST00000323630.5
exon_skip_364362	22	30412516:30412687:30413915:30414061:30415468:30415640	30413915:30414061	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000406629.1,ENST00000351488.3,ENST00000323630.5
exon_skip_364364	22	30415468:30416873:30418017:30418128:30418597:30418686	30418017:30418128	ENSG00000100330.11	ENST00000401950.2,ENST00000323630.5
exon_skip_364366	22	30418597:30418686:30419445:30419472:30421618:30421952	30419445:30419472	ENSG00000100330.11	ENST00000333027.3,ENST00000406629.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for MTMR3

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_364343	22	30279257:30279348:30353024:30353077:30366964:30367051	30353024:30353077	ENSG00000100330.11	ENST00000333027.3,ENST00000495098.1,ENST00000351488.3,ENST00000415511.1
exon_skip_364344	22	30279257:30279348:30353024:30353077:30374430:30374520	30353024:30353077	ENSG00000100330.11	ENST00000323630.5
exon_skip_364345	22	30279257:30279348:30366964:30367051:30374430:30374520	30366964:30367051	ENSG00000100330.11	ENST00000445401.1
exon_skip_364346	22	30353024:30353077:30366964:30367051:30374430:30374520	30366964:30367051	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000351488.3,ENST00000415511.1
exon_skip_364350	22	30374924:30375041:30384468:30384551:30387492:30387617	30384468:30384551	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000445401.1,ENST00000323630.5,ENST00000351488.3,ENST00000406629.1
exon_skip_364353	22	30384468:30384551:30387492:30387659:30394749:30394846	30387492:30387659	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000323630.5,ENST00000351488.3,ENST00000406629.1
exon_skip_364355	22	30394749:30394846:30398868:30398982:30403102:30403308	30398868:30398982	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000323630.5,ENST00000351488.3,ENST00000406629.1
exon_skip_364358	22	30398868:30398982:30403102:30403308:30403889:30403964	30403102:30403308	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000323630.5,ENST00000351488.3,ENST00000406629.1
exon_skip_364362	22	30412516:30412687:30413915:30414061:30415468:30415640	30413915:30414061	ENSG00000100330.11	ENST00000401950.2,ENST00000333027.3,ENST00000323630.5,ENST00000351488.3,ENST00000406629.1
exon_skip_364364	22	30415468:30416873:30418017:30418128:30418597:30418686	30418017:30418128	ENSG00000100330.11	ENST00000401950.2,ENST00000323630.5
exon_skip_364366	22	30418597:30418686:30419445:30419472:30421618:30421952	30419445:30419472	ENSG00000100330.11	ENST00000333027.3,ENST00000406629.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for MTMR3

Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000401950	30366964	30367051	5CDS-5UTR
ENST00000401950	30384468	30384551	Frame-shift
ENST00000401950	30387492	30387659	Frame-shift
ENST00000401950	30403102	30403308	Frame-shift
ENST00000401950	30413915	30414061	Frame-shift
ENST00000401950	30398868	30398982	In-frame
ENST00000401950	30418017	30418128	In-frame

Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000401950	30366964	30367051	5CDS-5UTR
ENST00000401950	30384468	30384551	Frame-shift
ENST00000401950	30387492	30387659	Frame-shift
ENST00000401950	30403102	30403308	Frame-shift
ENST00000401950	30413915	30414061	Frame-shift
ENST00000401950	30398868	30398982	In-frame
ENST00000401950	30418017	30418128	In-frame

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Infer the effects of exon skipping event on protein functional features for MTMR3

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000401950	6035	1198	30398868	30398982	900	1013	186	223
ENST00000401950	6035	1198	30418017	30418128	3568	3678	1075	1112

Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000401950	6035	1198	30398868	30398982	900	1013	186	223
ENST00000401950	6035	1198	30418017	30418128	3568	3678	1075	1112

Lost protein functional features of individual exon skipping events in TCGA.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
Q13615	186	223	1	1198	Chain	ID=PRO_0000094936;Note=Myotubularin-related protein 3
Q13615	186	223	155	576	Domain	Note=Myotubularin phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00669
Q13615	186	223	221	221	Natural variant	ID=VAR_035656;Note=In a breast cancer sample%3B somatic mutation. V->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16959974;Dbxref=PMID:16959974
Q13615	1075	1112	1076	1112	Alternative sequence	ID=VSP_007781;Note=In isoform A and isoform C. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q13615	1075	1112	1	1198	Chain	ID=PRO_0000094936;Note=Myotubularin-related protein 3

Lost protein functional features of individual exon skipping events in GTEx.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
Q13615	186	223	1	1198	Chain	ID=PRO_0000094936;Note=Myotubularin-related protein 3
Q13615	186	223	155	576	Domain	Note=Myotubularin phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00669
Q13615	186	223	221	221	Natural variant	ID=VAR_035656;Note=In a breast cancer sample%3B somatic mutation. V->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16959974;Dbxref=PMID:16959974
Q13615	1075	1112	1076	1112	Alternative sequence	ID=VSP_007781;Note=In isoform A and isoform C. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q13615	1075	1112	1	1198	Chain	ID=PRO_0000094936;Note=Myotubularin-related protein 3

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SNVs in the skipped exons for MTMR3

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
STAD	TCGA-D7-A4YY-01	exon_skip_364362	30413916	30414061	30414048	30414048	Frame_Shift_Del	C	-	p.D602fs
BLCA	TCGA-XF-A9SM-01	exon_skip_364353	30387493	30387659	30387504	30387504	Nonsense_Mutation	C	G	p.S102*
SARC	TCGA-FX-A3RE-01	exon_skip_364353	30387493	30387659	30387566	30387566	Nonsense_Mutation	A	T	p.K123*
ESCA	TCGA-XP-A8T8-01	exon_skip_364353	30387493	30387659	30387632	30387632	Nonsense_Mutation	G	T	p.E145*
ESCA	TCGA-XP-A8T8-01	exon_skip_364353	30387493	30387659	30387632	30387632	Nonsense_Mutation	G	T	p.E145X
UCEC	TCGA-D1-A17Q-01	exon_skip_364358	30403103	30403308	30403266	30403266	Nonsense_Mutation	C	T	p.R279*

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
HEC151_ENDOMETRIUM	30413916	30414061	30414048	30414048	Frame_Shift_Del	C	-	p.P604fs
HEC6_ENDOMETRIUM	30413916	30414061	30414048	30414048	Frame_Shift_Del	C	-	p.P604fs
HSC2_UPPER_AERODIGESTIVE_TRACT	30384469	30384551	30384542	30384542	Missense_Mutation	A	G	p.K95R
U698M_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	30384469	30384551	30384542	30384542	Missense_Mutation	A	G	p.K95R
BICR18_UPPER_AERODIGESTIVE_TRACT	30387493	30387659	30387503	30387503	Missense_Mutation	T	C	p.S102P
MDAMB175VII_BREAST	30387493	30387659	30387555	30387555	Missense_Mutation	G	A	p.R119Q
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	30387493	30387659	30387564	30387564	Missense_Mutation	C	G	p.A122G
BICR18_UPPER_AERODIGESTIVE_TRACT	30387493	30387659	30387564	30387564	Missense_Mutation	C	G	p.A122G
JHUEM7_ENDOMETRIUM	30387493	30387659	30387581	30387581	Missense_Mutation	T	G	p.F128V
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	30387493	30387659	30387590	30387590	Missense_Mutation	G	A	p.A131T
CW2_LARGE_INTESTINE	30387493	30387659	30387613	30387613	Missense_Mutation	G	T	p.E138D
LN18_CENTRAL_NERVOUS_SYSTEM	30387493	30387659	30387657	30387657	Missense_Mutation	C	A	p.P153Q
HCC1937_BREAST	30398869	30398982	30398972	30398972	Missense_Mutation	G	C	p.V221L
DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	30403103	30403308	30403123	30403123	Missense_Mutation	T	C	p.V231A
HT115_LARGE_INTESTINE	30403103	30403308	30403168	30403168	Missense_Mutation	G	A	p.R246Q
HEC59_ENDOMETRIUM	30403103	30403308	30403183	30403183	Missense_Mutation	A	G	p.E251G
SQ1_LUNG	30403103	30403308	30403185	30403185	Missense_Mutation	C	T	p.H252Y
OC316_OVARY	30413916	30414061	30413941	30413941	Missense_Mutation	G	A	p.R567H
OC314_OVARY	30413916	30414061	30413941	30413941	Missense_Mutation	G	A	p.R567H
NCIH2170_LUNG	30413916	30414061	30414019	30414019	Missense_Mutation	A	C	p.Y593S
SKMEL31_SKIN	30418018	30418128	30418024	30418024	Missense_Mutation	A	G	p.I1078V
BB49EBV_MATCHED_NORMAL_TISSUE	30418018	30418128	30418034	30418034	Missense_Mutation	C	T	p.S1081L
YH13_CENTRAL_NERVOUS_SYSTEM	30418018	30418128	30418048	30418048	Missense_Mutation	G	T	p.D1086Y
BICR18_UPPER_AERODIGESTIVE_TRACT	30418018	30418128	30418060	30418060	Missense_Mutation	T	G	p.L1090V
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	30418018	30418128	30418060	30418060	Missense_Mutation	T	G	p.L1090V
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	30418018	30418128	30418060	30418060	Missense_Mutation	T	G	p.L1090V
RCCFG2_KIDNEY	30418018	30418128	30418088	30418088	Missense_Mutation	C	G	p.S1099C
HCC1806_BREAST	30418018	30418128	30418090	30418090	Missense_Mutation	G	C	p.E1100Q
OC316_OVARY	30418018	30418128	30418098	30418098	Missense_Mutation	C	A	p.S1102R
OC314_OVARY	30418018	30418128	30418098	30418098	Missense_Mutation	C	A	p.S1102R
JHH4_LIVER	30384469	30384551	30384487	30384487	Nonsense_Mutation	G	T	p.E77*
TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	30384469	30384551	30384502	30384502	Nonsense_Mutation	C	T	p.R82*
RCCJF_KIDNEY	30403103	30403308	30403166	30403166	Nonsense_Mutation	G	A	p.W245*
SMSCTR_SOFT_TISSUE	30418018	30418128	30418105	30418105	Nonsense_Mutation	C	T	p.Q1105*
LS411N_LARGE_INTESTINE	30398869	30398982	30398982	30398982	Splice_Site	G	T	p.R224M
SNU878_LIVER	30418018	30418128	30418128	30418128	Splice_Site	G	C	p.E1112D

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MTMR3

sQTL information located at the skipped exons.

Exon skip ID	Chromosome	Three exons	Skippped exon	ENST	Cancer type	SNP id	Location	DNA change (ref/var)	P-value
exon_skip_364345	22	30279257:30279348:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000445401.1	BRCA	rs16988135	chr22:30367014	A/T	2.63e-03
exon_skip_364345	22	30279257:30279348:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000445401.1	KIRP	rs16988135	chr22:30367014	A/T	1.01e-04
exon_skip_364345	22	30279257:30279348:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000445401.1	LGG	rs16988135	chr22:30367014	A/T	9.12e-08
exon_skip_364345	22	30279257:30279348:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000445401.1	KIRC	rs16988135	chr22:30367014	A/T	9.16e-05
exon_skip_364345	22	30279257:30279348:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000445401.1	LUAD	rs16988135	chr22:30367014	A/T	1.28e-04
exon_skip_364345	22	30279257:30279348:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000445401.1	THYM	rs16988135	chr22:30367014	A/T	2.64e-04
exon_skip_364345	22	30279257:30279348:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000445401.1	STAD	rs16988135	chr22:30367014	A/T	5.18e-04
exon_skip_364346	22	30353024:30353077:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000401950.2,ENST00000333027.3,ENST00000415511.1,ENST00000351488.3	BRCA	rs16988135	chr22:30367014	A/T	2.63e-03
exon_skip_364346	22	30353024:30353077:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000401950.2,ENST00000333027.3,ENST00000415511.1,ENST00000351488.3	KIRP	rs16988135	chr22:30367014	A/T	1.01e-04
exon_skip_364346	22	30353024:30353077:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000401950.2,ENST00000333027.3,ENST00000415511.1,ENST00000351488.3	LGG	rs16988135	chr22:30367014	A/T	9.12e-08
exon_skip_364346	22	30353024:30353077:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000401950.2,ENST00000333027.3,ENST00000415511.1,ENST00000351488.3	KIRC	rs16988135	chr22:30367014	A/T	9.16e-05
exon_skip_364346	22	30353024:30353077:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000401950.2,ENST00000333027.3,ENST00000415511.1,ENST00000351488.3	LUAD	rs16988135	chr22:30367014	A/T	1.28e-04
exon_skip_364346	22	30353024:30353077:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000401950.2,ENST00000333027.3,ENST00000415511.1,ENST00000351488.3	THYM	rs16988135	chr22:30367014	A/T	2.64e-04
exon_skip_364346	22	30353024:30353077:30366964:30367051:30374430:30374520	30366964:30367051	ENST00000401950.2,ENST00000333027.3,ENST00000415511.1,ENST00000351488.3	STAD	rs16988135	chr22:30367014	A/T	5.18e-04

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MTMR3

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MTMR3

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RelatedDrugs for MTMR3

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for MTMR3

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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