ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for TIMM50

Gene summary

Gene information	Gene symbol	TIMM50
	Gene ID	92609
	Gene name	translocase of inner mitochondrial membrane 50
	Synonyms	MGCA9\|TIM50\|TIM50L
	Cytomap	19q13.2
	Type of gene	protein-coding
	Description	mitochondrial import inner membrane translocase subunit TIM50Tim50-like proteinhomolog of yeast Tim50
	Modification date	20180523
	UniProtAcc	Q3ZCQ8
	Context	PubMed: TIMM50 [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
TIMM50	GO:0001836	release of cytochrome c from mitochondria	15044455
TIMM50	GO:0006470	protein dephosphorylation	15044455

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Exon skipping events across known transcript of Ensembl for TIMM50 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 TIMM50

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 TIMM50

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_306916	19	39971567:39971601:39972522:39972673:39973524:39973556	39972522:39972673	ENSG00000105197.6	ENST00000602265.1,ENST00000595286.1,ENST00000607714.1,ENST00000602028.1,ENST00000599733.1,ENST00000597782.1,ENST00000598125.1,ENST00000544017.1,ENST00000601358.1
exon_skip_306918	19	39971567:39971601:39972522:39972673:39976183:39976242	39972522:39972673	ENSG00000105197.6	ENST00000601403.1
exon_skip_306923	19	39971567:39971601:39973524:39973556:39973774:39973796	39973524:39973556	ENSG00000105197.6	ENST00000597666.1
exon_skip_306950	19	39972522:39972673:39973524:39973556:39973774:39973796	39973524:39973556	ENSG00000105197.6	ENST00000602265.1,ENST00000314349.4,ENST00000594583.1,ENST00000595286.1,ENST00000607714.1,ENST00000597782.1,ENST00000544017.1,ENST00000601358.1
exon_skip_306952	19	39972522:39972673:39973524:39973556:39976327:39976443	39973524:39973556	ENSG00000105197.6	ENST00000602028.1
exon_skip_306956	19	39972522:39972673:39973524:39973603:39973774:39973796	39973524:39973603	ENSG00000105197.6	ENST00000599733.1
exon_skip_306961	19	39972522:39972673:39976183:39976242:39976327:39976443	39976183:39976242	ENSG00000105197.6	ENST00000601403.1
exon_skip_306963	19	39973524:39973556:39973774:39973796:39976183:39976242	39973774:39973796	ENSG00000105197.6	ENST00000314349.4,ENST00000594583.1,ENST00000607714.1
exon_skip_306964	19	39973524:39973556:39973774:39973796:39976327:39976443	39973774:39973796	ENSG00000105197.6	ENST00000602265.1,ENST00000597666.1,ENST00000544017.1,ENST00000601358.1
exon_skip_306970	19	39973524:39973603:39973774:39973796:39976183:39976242	39973774:39973796	ENSG00000105197.6	ENST00000599733.1
exon_skip_306974	19	39973774:39973796:39975791:39975903:39976183:39976242	39975791:39975903	ENSG00000105197.6	ENST00000597782.1
exon_skip_306975	19	39973774:39973796:39976183:39976242:39976327:39976443	39976183:39976242	ENSG00000105197.6	ENST00000314349.4,ENST00000594583.1,ENST00000607714.1,ENST00000599733.1
exon_skip_306979	19	39973774:39973796:39976327:39976447:39976826:39976931	39976327:39976447	ENSG00000105197.6	ENST00000602265.1,ENST00000597666.1,ENST00000544017.1,ENST00000601358.1
exon_skip_306983	19	39976183:39976242:39976327:39976447:39976826:39976931	39976327:39976447	ENSG00000105197.6	ENST00000314349.4,ENST00000594583.1,ENST00000601403.1,ENST00000607714.1,ENST00000599733.1
exon_skip_306984	19	39976327:39976447:39976826:39976931:39977036:39977135	39976826:39976931	ENSG00000105197.6	ENST00000602265.1,ENST00000314349.4,ENST00000594583.1,ENST00000601403.1,ENST00000607714.1,ENST00000602028.1,ENST00000599733.1,ENST00000597666.1,ENST00000544017.1,ENST00000601358.1
exon_skip_306990	19	39976826:39976931:39977036:39977135:39978700:39978814	39977036:39977135	ENSG00000105197.6	ENST00000602265.1,ENST00000314349.4,ENST00000601403.1,ENST00000595961.1,ENST00000607714.1,ENST00000602028.1,ENST00000597666.1,ENST00000544017.1,ENST00000601358.1
exon_skip_306991	19	39978753:39978857:39979178:39979285:39980358:39980408	39979178:39979285	ENSG00000105197.6	ENST00000314349.4,ENST00000595961.1,ENST00000601252.1,ENST00000607714.1,ENST00000599794.1,ENST00000597552.1,ENST00000544017.1,ENST00000601358.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for TIMM50

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_306916	19	39971567:39971601:39972522:39972673:39973524:39973556	39972522:39972673	ENSG00000105197.6	ENST00000601358.1,ENST00000607714.1,ENST00000598125.1,ENST00000602028.1,ENST00000595286.1,ENST00000544017.1,ENST00000597782.1,ENST00000599733.1,ENST00000602265.1
exon_skip_306918	19	39971567:39971601:39972522:39972673:39976183:39976242	39972522:39972673	ENSG00000105197.6	ENST00000601403.1
exon_skip_306923	19	39971567:39971601:39973524:39973556:39973774:39973796	39973524:39973556	ENSG00000105197.6	ENST00000597666.1
exon_skip_306950	19	39972522:39972673:39973524:39973556:39973774:39973796	39973524:39973556	ENSG00000105197.6	ENST00000314349.4,ENST00000601358.1,ENST00000607714.1,ENST00000595286.1,ENST00000544017.1,ENST00000597782.1,ENST00000602265.1,ENST00000594583.1
exon_skip_306952	19	39972522:39972673:39973524:39973556:39976327:39976443	39973524:39973556	ENSG00000105197.6	ENST00000602028.1
exon_skip_306956	19	39972522:39972673:39973524:39973603:39973774:39973796	39973524:39973603	ENSG00000105197.6	ENST00000599733.1
exon_skip_306961	19	39972522:39972673:39976183:39976242:39976327:39976443	39976183:39976242	ENSG00000105197.6	ENST00000601403.1
exon_skip_306963	19	39973524:39973556:39973774:39973796:39976183:39976242	39973774:39973796	ENSG00000105197.6	ENST00000314349.4,ENST00000607714.1,ENST00000594583.1
exon_skip_306964	19	39973524:39973556:39973774:39973796:39976327:39976443	39973774:39973796	ENSG00000105197.6	ENST00000601358.1,ENST00000597666.1,ENST00000544017.1,ENST00000602265.1
exon_skip_306970	19	39973524:39973603:39973774:39973796:39976183:39976242	39973774:39973796	ENSG00000105197.6	ENST00000599733.1
exon_skip_306974	19	39973774:39973796:39975791:39975903:39976183:39976242	39975791:39975903	ENSG00000105197.6	ENST00000597782.1
exon_skip_306975	19	39973774:39973796:39976183:39976242:39976327:39976443	39976183:39976242	ENSG00000105197.6	ENST00000314349.4,ENST00000607714.1,ENST00000599733.1,ENST00000594583.1
exon_skip_306979	19	39973774:39973796:39976327:39976447:39976826:39976931	39976327:39976447	ENSG00000105197.6	ENST00000601358.1,ENST00000597666.1,ENST00000544017.1,ENST00000602265.1
exon_skip_306983	19	39976183:39976242:39976327:39976447:39976826:39976931	39976327:39976447	ENSG00000105197.6	ENST00000314349.4,ENST00000607714.1,ENST00000601403.1,ENST00000599733.1,ENST00000594583.1
exon_skip_306984	19	39976327:39976447:39976826:39976931:39977036:39977135	39976826:39976931	ENSG00000105197.6	ENST00000314349.4,ENST00000601358.1,ENST00000607714.1,ENST00000597666.1,ENST00000601403.1,ENST00000602028.1,ENST00000544017.1,ENST00000599733.1,ENST00000602265.1,ENST00000594583.1
exon_skip_306991	19	39978753:39978857:39979178:39979285:39980358:39980408	39979178:39979285	ENSG00000105197.6	ENST00000314349.4,ENST00000601358.1,ENST00000607714.1,ENST00000599794.1,ENST00000544017.1,ENST00000595961.1,ENST00000597552.1,ENST00000601252.1

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 TIMM50

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
ENST00000607714	39972522	39972673	Frame-shift
ENST00000607714	39973524	39973556	Frame-shift
ENST00000607714	39973774	39973796	Frame-shift
ENST00000607714	39976183	39976242	Frame-shift
ENST00000607714	39979178	39979285	Frame-shift
ENST00000607714	39976327	39976447	In-frame
ENST00000607714	39976826	39976931	In-frame
ENST00000607714	39977036	39977135	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
ENST00000607714	39972522	39972673	Frame-shift
ENST00000607714	39973524	39973556	Frame-shift
ENST00000607714	39973774	39973796	Frame-shift
ENST00000607714	39976183	39976242	Frame-shift
ENST00000607714	39979178	39979285	Frame-shift
ENST00000607714	39976327	39976447	In-frame
ENST00000607714	39976826	39976931	In-frame

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Infer the effects of exon skipping event on protein functional features for TIMM50

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
ENST00000607714	1355	353	39976327	39976447	395	514	124	164
ENST00000607714	1355	353	39976826	39976931	515	619	164	199
ENST00000607714	1355	353	39977036	39977135	620	718	199	232

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
ENST00000607714	1355	353	39976327	39976447	395	514	124	164
ENST00000607714	1355	353	39976826	39976931	515	619	164	199

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
Q3ZCQ8	124	164	12	124	Alternative sequence	ID=VSP_047683;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.2;Dbxref=PMID:15489334
Q3ZCQ8	124	164	45	353	Chain	ID=PRO_0000043115;Note=Mitochondrial import inner membrane translocase subunit TIM50
Q3ZCQ8	124	164	143	286	Domain	Note=FCP1 homology;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00336
Q3ZCQ8	124	164	149	149	Natural variant	ID=VAR_078569;Note=In MGCA9%3B unknown pathological significance. T->M;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27573165;Dbxref=dbSNP:rs1244226820,PMID:27573165
Q3ZCQ8	124	164	87	353	Topological domain	Note=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q3ZCQ8	164	199	45	353	Chain	ID=PRO_0000043115;Note=Mitochondrial import inner membrane translocase subunit TIM50
Q3ZCQ8	164	199	143	286	Domain	Note=FCP1 homology;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00336
Q3ZCQ8	164	199	87	353	Topological domain	Note=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q3ZCQ8	199	232	45	353	Chain	ID=PRO_0000043115;Note=Mitochondrial import inner membrane translocase subunit TIM50
Q3ZCQ8	199	232	143	286	Domain	Note=FCP1 homology;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00336
Q3ZCQ8	199	232	87	353	Topological domain	Note=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255

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
Q3ZCQ8	124	164	12	124	Alternative sequence	ID=VSP_047683;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|Ref.2;Dbxref=PMID:15489334
Q3ZCQ8	124	164	45	353	Chain	ID=PRO_0000043115;Note=Mitochondrial import inner membrane translocase subunit TIM50
Q3ZCQ8	124	164	143	286	Domain	Note=FCP1 homology;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00336
Q3ZCQ8	124	164	149	149	Natural variant	ID=VAR_078569;Note=In MGCA9%3B unknown pathological significance. T->M;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27573165;Dbxref=dbSNP:rs1244226820,PMID:27573165
Q3ZCQ8	124	164	87	353	Topological domain	Note=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q3ZCQ8	164	199	45	353	Chain	ID=PRO_0000043115;Note=Mitochondrial import inner membrane translocase subunit TIM50
Q3ZCQ8	164	199	143	286	Domain	Note=FCP1 homology;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00336
Q3ZCQ8	164	199	87	353	Topological domain	Note=Mitochondrial intermembrane;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for TIMM50

- 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
GBM	TCGA-32-1977-01	exon_skip_306918 exon_skip_306916	39972523	39972673	39972604	39972604	Frame_Shift_Del	A	-	p.K167fs
LIHC	TCGA-DD-A1EG-01	exon_skip_306918 exon_skip_306916	39972523	39972673	39972604	39972604	Frame_Shift_Del	A	-	p.K168fs
LIHC	TCGA-DD-A3A0-01	exon_skip_306961 exon_skip_306975	39976184	39976242	39976188	39976188	Frame_Shift_Del	A	-	p.P209fs
LIHC	TCGA-DD-A1EG-01	exon_skip_306983 exon_skip_306979	39976328	39976447	39976351	39976351	Frame_Shift_Del	T	-	p.P235fs
LIHC	TCGA-DD-A1EG-01	exon_skip_306990	39977037	39977135	39977043	39977043	Frame_Shift_Del	T	-	p.F305fs
COAD	TCGA-AA-3663-01	exon_skip_306990	39977037	39977135	39977066	39977066	Frame_Shift_Del	C	-	p.D312fs
STAD	TCGA-BR-4370-01	exon_skip_306990	39977037	39977135	39977066	39977066	Frame_Shift_Del	C	-	p.D312fs
HNSC	TCGA-CR-7364-01	exon_skip_306983 exon_skip_306979	39976328	39976447	39976376	39976376	Nonsense_Mutation	G	T	p.E244*

- 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
DOV13_OVARY	39972523	39972673	39972536	39972536	Missense_Mutation	G	A	p.G41E
HS294T_SKIN	39972523	39972673	39972536	39972536	Missense_Mutation	G	A	p.G41E
NB1_AUTONOMIC_GANGLIA	39972523	39972673	39972573	39972573	Missense_Mutation	G	T	p.Q53H
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	39972523	39972673	39972626	39972626	Missense_Mutation	C	A	p.A71D
LS180_LARGE_INTESTINE	39972523	39972673	39972652	39972652	Missense_Mutation	G	T	p.V80L
MS751_CERVIX	39972523	39972673	39972665	39972665	Missense_Mutation	A	G	p.Y84C
NCIH358_LUNG	39976328	39976447	39976364	39976364	Missense_Mutation	G	C	p.D137H
EN_ENDOMETRIUM	39976328	39976447	39976418	39976418	Missense_Mutation	A	G	p.T155A
EWS834_BONE	39976827	39976931	39976908	39976908	Missense_Mutation	A	G	p.I192V
SNU1040_LARGE_INTESTINE	39976827	39976931	39976915	39976915	Missense_Mutation	C	T	p.T194M
JHUEM7_ENDOMETRIUM	39977037	39977135	39977078	39977078	Missense_Mutation	C	A	p.F213L
JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	39977037	39977135	39977089	39977089	Missense_Mutation	G	A	p.R217H
SKUT1_SOFT_TISSUE	39977037	39977135	39977098	39977098	Missense_Mutation	G	A	p.R220Q
639V_URINARY_TRACT	39977037	39977135	39977098	39977098	Missense_Mutation	G	A	p.R220Q
MFE319_ENDOMETRIUM	39976184	39976242	39976240	39976240	Nonsense_Mutation	C	T	p.Q124*
22RV1_PROSTATE	39976328	39976447	39976447	39976447	Splice_Site	G	A	p.S164S

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TIMM50

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

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TIMM50

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TIMM50

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RelatedDrugs for TIMM50

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 TIMM50

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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