ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for TTC39B

Gene summary

Gene information	Gene symbol	TTC39B
	Gene ID	158219
	Gene name	tetratricopeptide repeat domain 39B
	Synonyms	C9orf52
	Cytomap	9p22.3
	Type of gene	protein-coding
	Description	tetratricopeptide repeat protein 39BTPR repeat protein 39B
	Modification date	20180519
	UniProtAcc	Q5VTQ0
	Context	PubMed: TTC39B [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

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Exon skipping events across known transcript of Ensembl for TTC39B 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 TTC39B

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 TTC39B

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_502705	9	15177694:15177812:15182304:15182413:15185277:15185404	15182304:15182413	ENSG00000155158.16	ENST00000380850.4,ENST00000512701.2,ENST00000507993.1,ENST00000355694.2,ENST00000297615.5,ENST00000380853.1,ENST00000507285.1
exon_skip_502708	9	15190552:15190660:15191187:15191253:15192587:15192693	15191187:15191253	ENSG00000155158.16	ENST00000380850.4,ENST00000512701.2,ENST00000507993.1,ENST00000355694.2,ENST00000297615.5,ENST00000541445.1,ENST00000507285.1,ENST00000505732.1
exon_skip_502709	9	15192587:15192693:15199858:15199923:15203820:15203888	15199858:15199923	ENSG00000155158.16	ENST00000380850.4,ENST00000512701.2,ENST00000507993.1,ENST00000355694.2,ENST00000297615.5,ENST00000507285.1,ENST00000505732.1
exon_skip_502710	9	15199858:15199923:15203820:15203888:15210085:15210162	15203820:15203888	ENSG00000155158.16	ENST00000380850.4,ENST00000512701.2,ENST00000507993.1,ENST00000355694.2,ENST00000297615.5,ENST00000507285.1,ENST00000505732.1
exon_skip_502714	9	15211263:15211395:15214136:15214247:15225914:15226010	15214136:15214247	ENSG00000155158.16	ENST00000380850.4,ENST00000512701.2,ENST00000355694.2,ENST00000541445.1,ENST00000505732.1
exon_skip_502717	9	15214136:15214247:15224337:15224503:15225914:15226010	15224337:15224503	ENSG00000155158.16	ENST00000507285.1
exon_skip_502718	9	15214135:15214247:15224357:15224503:15225914:15226010	15224357:15224503	ENSG00000155158.16	ENST00000582994.1
exon_skip_502720	9	15214136:15214247:15225914:15226010:15267911:15267946	15225914:15226010	ENSG00000155158.16	ENST00000380850.4,ENST00000512701.2,ENST00000355694.2,ENST00000541445.1,ENST00000505732.1
exon_skip_502722	9	15225914:15226010:15267911:15267946:15307081:15307207	15267911:15267946	ENSG00000155158.16	ENST00000380850.4,ENST00000355694.2,ENST00000541445.1,ENST00000505732.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for TTC39B

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_502705	9	15177694:15177812:15182304:15182413:15185277:15185404	15182304:15182413	ENSG00000155158.16	ENST00000512701.2,ENST00000380850.4,ENST00000297615.5,ENST00000355694.2,ENST00000380853.1,ENST00000507285.1,ENST00000507993.1
exon_skip_502708	9	15190552:15190660:15191187:15191253:15192587:15192693	15191187:15191253	ENSG00000155158.16	ENST00000512701.2,ENST00000380850.4,ENST00000297615.5,ENST00000355694.2,ENST00000507285.1,ENST00000507993.1,ENST00000505732.1,ENST00000541445.1
exon_skip_502709	9	15192587:15192693:15199858:15199923:15203820:15203888	15199858:15199923	ENSG00000155158.16	ENST00000512701.2,ENST00000380850.4,ENST00000297615.5,ENST00000355694.2,ENST00000507285.1,ENST00000507993.1,ENST00000505732.1
exon_skip_502710	9	15199858:15199923:15203820:15203888:15210085:15210162	15203820:15203888	ENSG00000155158.16	ENST00000512701.2,ENST00000380850.4,ENST00000297615.5,ENST00000355694.2,ENST00000507285.1,ENST00000507993.1,ENST00000505732.1
exon_skip_502714	9	15211263:15211395:15214136:15214247:15225914:15226010	15214136:15214247	ENSG00000155158.16	ENST00000512701.2,ENST00000380850.4,ENST00000355694.2,ENST00000505732.1,ENST00000541445.1
exon_skip_502717	9	15214136:15214247:15224337:15224503:15225914:15226010	15224337:15224503	ENSG00000155158.16	ENST00000507285.1
exon_skip_502718	9	15214135:15214247:15224357:15224503:15225914:15226010	15224357:15224503	ENSG00000155158.16	ENST00000582994.1
exon_skip_502720	9	15214136:15214247:15225914:15226010:15267911:15267946	15225914:15226010	ENSG00000155158.16	ENST00000512701.2,ENST00000380850.4,ENST00000355694.2,ENST00000505732.1,ENST00000541445.1
exon_skip_502722	9	15225914:15226010:15267911:15267946:15307081:15307207	15267911:15267946	ENSG00000155158.16	ENST00000380850.4,ENST00000355694.2,ENST00000505732.1,ENST00000541445.1

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 TTC39B

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
ENST00000512701	15182304	15182413	Frame-shift
ENST00000512701	15199858	15199923	Frame-shift
ENST00000512701	15203820	15203888	Frame-shift
ENST00000512701	15191187	15191253	In-frame
ENST00000512701	15214136	15214247	In-frame
ENST00000512701	15225914	15226010	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
ENST00000512701	15182304	15182413	Frame-shift
ENST00000512701	15199858	15199923	Frame-shift
ENST00000512701	15203820	15203888	Frame-shift
ENST00000512701	15191187	15191253	In-frame
ENST00000512701	15214136	15214247	In-frame
ENST00000512701	15225914	15226010	In-frame

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Infer the effects of exon skipping event on protein functional features for TTC39B

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
ENST00000512701	10500	682	15225914	15226010	313	408	92	123
ENST00000512701	10500	682	15214136	15214247	409	519	124	160
ENST00000512701	10500	682	15191187	15191253	968	1033	310	332

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
ENST00000512701	10500	682	15225914	15226010	313	408	92	123
ENST00000512701	10500	682	15214136	15214247	409	519	124	160
ENST00000512701	10500	682	15191187	15191253	968	1033	310	332

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
Q5VTQ0	92	123	1	483	Alternative sequence	ID=VSP_042798;Note=In isoform 7. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q5VTQ0	92	123	1	165	Alternative sequence	ID=VSP_042799;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q5VTQ0	92	123	1	97	Alternative sequence	ID=VSP_026355;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q5VTQ0	92	123	92	161	Alternative sequence	ID=VSP_042800;Note=In isoform 6. ISSHSDMATSSLHFASCDTQQAPRQRGASTVSSSSSTKVDLKSGLEECAVALNLFLSNKFTDALELLRPW->M;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q5VTQ0	92	123	1	682	Chain	ID=PRO_0000292000;Note=Tetratricopeptide repeat protein 39B
Q5VTQ0	124	160	1	483	Alternative sequence	ID=VSP_042798;Note=In isoform 7. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q5VTQ0	124	160	1	165	Alternative sequence	ID=VSP_042799;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q5VTQ0	124	160	92	161	Alternative sequence	ID=VSP_042800;Note=In isoform 6. ISSHSDMATSSLHFASCDTQQAPRQRGASTVSSSSSTKVDLKSGLEECAVALNLFLSNKFTDALELLRPW->M;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q5VTQ0	124	160	1	682	Chain	ID=PRO_0000292000;Note=Tetratricopeptide repeat protein 39B
Q5VTQ0	124	160	128	128	Natural variant	ID=VAR_054078;Note=T->P;Dbxref=dbSNP:rs10961917
Q5VTQ0	310	332	1	483	Alternative sequence	ID=VSP_042798;Note=In isoform 7. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q5VTQ0	310	332	1	682	Chain	ID=PRO_0000292000;Note=Tetratricopeptide repeat protein 39B
Q5VTQ0	310	332	329	329	Sequence conflict	Note=S->F;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
Q5VTQ0	92	123	1	483	Alternative sequence	ID=VSP_042798;Note=In isoform 7. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q5VTQ0	92	123	1	165	Alternative sequence	ID=VSP_042799;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q5VTQ0	92	123	1	97	Alternative sequence	ID=VSP_026355;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q5VTQ0	92	123	92	161	Alternative sequence	ID=VSP_042800;Note=In isoform 6. ISSHSDMATSSLHFASCDTQQAPRQRGASTVSSSSSTKVDLKSGLEECAVALNLFLSNKFTDALELLRPW->M;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q5VTQ0	92	123	1	682	Chain	ID=PRO_0000292000;Note=Tetratricopeptide repeat protein 39B
Q5VTQ0	124	160	1	483	Alternative sequence	ID=VSP_042798;Note=In isoform 7. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q5VTQ0	124	160	1	165	Alternative sequence	ID=VSP_042799;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q5VTQ0	124	160	92	161	Alternative sequence	ID=VSP_042800;Note=In isoform 6. ISSHSDMATSSLHFASCDTQQAPRQRGASTVSSSSSTKVDLKSGLEECAVALNLFLSNKFTDALELLRPW->M;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q5VTQ0	124	160	1	682	Chain	ID=PRO_0000292000;Note=Tetratricopeptide repeat protein 39B
Q5VTQ0	124	160	128	128	Natural variant	ID=VAR_054078;Note=T->P;Dbxref=dbSNP:rs10961917
Q5VTQ0	310	332	1	483	Alternative sequence	ID=VSP_042798;Note=In isoform 7. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q5VTQ0	310	332	1	682	Chain	ID=PRO_0000292000;Note=Tetratricopeptide repeat protein 39B
Q5VTQ0	310	332	329	329	Sequence conflict	Note=S->F;Ontology_term=ECO:0000305;evidence=ECO:0000305

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SNVs in the skipped exons for TTC39B

- 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
LIHC	TCGA-DD-A39Y-01	exon_skip_502708	15191188	15191253	15191199	15191199	Frame_Shift_Del	A	-	p.S263fs
LIHC	TCGA-DD-A1EG-01	exon_skip_502709	15199859	15199923	15199884	15199884	Frame_Shift_Del	T	-	p.I201fs
BLCA	TCGA-UY-A78K-01	exon_skip_502705	15182305	15182413	15182308	15182308	Nonsense_Mutation	G	A	p.Q574*

- 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
EFO27_OVARY	15182305	15182413	15182351	15182352	Frame_Shift_Ins	-	T	p.N559fs
HEC251_ENDOMETRIUM	15182305	15182413	15182358	15182358	Missense_Mutation	G	A	p.S557F
L82_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	15191188	15191253	15191237	15191237	Missense_Mutation	G	A	p.P316L
SNU719_STOMACH	15199859	15199923	15199887	15199887	Missense_Mutation	T	G	p.K266Q
EOL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	15203821	15203888	15203826	15203826	Missense_Mutation	C	A	p.V252L
HCC2157_BREAST	15214137	15214247	15214143	15214143	Missense_Mutation	C	T	p.R159H
HCC2157_MATCHED_NORMAL_TISSUE	15214137	15214247	15214143	15214143	Missense_Mutation	C	T	p.R159H
UMUC1_URINARY_TRACT	15214137	15214247	15214152	15214152	Missense_Mutation	T	C	p.E156G
JHUEM1_ENDOMETRIUM	15225915	15226010	15225934	15225934	Missense_Mutation	C	T	p.G118R
JHUEM2_ENDOMETRIUM	15225915	15226010	15225975	15225975	Missense_Mutation	T	C	p.H104R
MFE319_ENDOMETRIUM	15225915	15226010	15225981	15225981	Missense_Mutation	C	T	p.S102N
SW1271_LUNG	15214137	15214247	15214185	15214185	Nonsense_Mutation	A	C	p.L145*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TTC39B

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 TTC39B

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TTC39B

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RelatedDrugs for TTC39B

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 TTC39B

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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Gene summary for TTC39B

Exon skipping events across known transcript of Ensembl for TTC39B from UCSC genome browser

Gene isoform structures and expression levels for TTC39B

Exon skipping events with PSIs in TCGA for TTC39B

Exon skipping events with PSIs in GTEx for TTC39B

Open reading frame (ORF) annotation in the exon skipping event for TTC39B

Infer the effects of exon skipping event on protein functional features for TTC39B

SNVs in the skipped exons for TTC39B

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TTC39B

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TTC39B

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TTC39B

RelatedDrugs for TTC39B

RelatedDiseases for TTC39B