ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SLC6A9

Gene summary

Gene information	Gene symbol	SLC6A9
	Gene ID	6536
	Gene name	solute carrier family 6 member 9
	Synonyms	GCENSG\|GLYT1
	Cytomap	1p34.1
	Type of gene	protein-coding
	Description	sodium- and chloride-dependent glycine transporter 1glyT-1solute carrier family 6 (neurotransmitter transporter, glycine), member 9
	Modification date	20180523
	UniProtAcc	P48067
	Context	PubMed: SLC6A9 [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 SLC6A9 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 SLC6A9

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 SLC6A9

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_25842	1	44463199:44463411:44463526:44463697:44466438:44466474	44463526:44463697	ENSG00000196517.7	ENST00000372310.3,ENST00000360584.2,ENST00000475075.2,ENST00000357730.2
exon_skip_25844	1	44466835:44466970:44467061:44467299:44467984:44468088	44467061:44467299	ENSG00000196517.7	ENST00000372310.3,ENST00000372306.3,ENST00000372307.3,ENST00000360584.2,ENST00000537678.1,ENST00000475075.2,ENST00000357730.2
exon_skip_25848	1	44468524:44468657:44474024:44474295:44475636:44475768	44474024:44474295	ENSG00000196517.7	ENST00000372310.3,ENST00000372306.3,ENST00000372307.3,ENST00000360584.2,ENST00000537678.1,ENST00000357730.2
exon_skip_25849	1	44468524:44468657:44474024:44474295:44489919:44490034	44474024:44474295	ENSG00000196517.7	ENST00000475075.2
exon_skip_25854	1	44474268:44474295:44475636:44475768:44489919:44490034	44475636:44475768	ENSG00000196517.7	ENST00000537678.1
exon_skip_25859	1	44475636:44475768:44476397:44476554:44482718:44482811	44476397:44476554	ENSG00000196517.7	ENST00000528803.1,ENST00000357730.2
exon_skip_25860	1	44475636:44475768:44476397:44476554:44489919:44490034	44476397:44476554	ENSG00000196517.7	ENST00000372310.3,ENST00000372306.3
exon_skip_25867	1	44475636:44475768:44476480:44476554:44489919:44490034	44476480:44476554	ENSG00000196517.7	ENST00000492434.2
exon_skip_25871	1	44476480:44476554:44477232:44477394:44482718:44482811	44477232:44477394	ENSG00000196517.7	ENST00000360584.2
exon_skip_25872	1	44476480:44476554:44477232:44477394:44489919:44490034	44477232:44477394	ENSG00000196517.7	ENST00000466926.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SLC6A9

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_25842	1	44463199:44463411:44463526:44463697:44466438:44466474	44463526:44463697	ENSG00000196517.7	ENST00000372310.3,ENST00000475075.2,ENST00000360584.2,ENST00000357730.2
exon_skip_25844	1	44466835:44466970:44467061:44467299:44467984:44468088	44467061:44467299	ENSG00000196517.7	ENST00000372307.3,ENST00000372306.3,ENST00000372310.3,ENST00000475075.2,ENST00000360584.2,ENST00000357730.2,ENST00000537678.1
exon_skip_25848	1	44468524:44468657:44474024:44474295:44475636:44475768	44474024:44474295	ENSG00000196517.7	ENST00000372307.3,ENST00000372306.3,ENST00000372310.3,ENST00000360584.2,ENST00000357730.2,ENST00000537678.1
exon_skip_25849	1	44468524:44468657:44474024:44474295:44489919:44490034	44474024:44474295	ENSG00000196517.7	ENST00000475075.2
exon_skip_25854	1	44474268:44474295:44475636:44475768:44489919:44490034	44475636:44475768	ENSG00000196517.7	ENST00000537678.1
exon_skip_25859	1	44475636:44475768:44476397:44476554:44482718:44482811	44476397:44476554	ENSG00000196517.7	ENST00000357730.2,ENST00000528803.1
exon_skip_25860	1	44475636:44475768:44476397:44476554:44489919:44490034	44476397:44476554	ENSG00000196517.7	ENST00000372306.3,ENST00000372310.3
exon_skip_25867	1	44475636:44475768:44476480:44476554:44489919:44490034	44476480:44476554	ENSG00000196517.7	ENST00000492434.2
exon_skip_25871	1	44476480:44476554:44477232:44477394:44482718:44482811	44477232:44477394	ENSG00000196517.7	ENST00000360584.2
exon_skip_25872	1	44476480:44476554:44477232:44477394:44489919:44490034	44477232:44477394	ENSG00000196517.7	ENST00000466926.1

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 SLC6A9

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
ENST00000360584	44467061	44467299	Frame-shift
ENST00000360584	44474024	44474295	Frame-shift
ENST00000360584	44463526	44463697	In-frame
ENST00000360584	44477232	44477394	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
ENST00000360584	44467061	44467299	Frame-shift
ENST00000360584	44474024	44474295	Frame-shift
ENST00000360584	44463526	44463697	In-frame
ENST00000360584	44477232	44477394	In-frame

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Infer the effects of exon skipping event on protein functional features for SLC6A9

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
ENST00000360584	2347	706	44477232	44477394	280	441	29	83
ENST00000360584	2347	706	44463526	44463697	1948	2118	585	642

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
ENST00000360584	2347	706	44477232	44477394	280	441	29	83
ENST00000360584	2347	706	44463526	44463697	1948	2118	585	642

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
P48067	29	83	1	83	Alternative sequence	ID=VSP_006270;Note=In isoform GlyT-1A. MSGGDTRAAIARPRMAAAHGPVAPSSPEQVTLLPVQRSFFLPPFSGATPSTSLAESVLKVWHGAYNSGLLPQLMAQHSLAMAQ->MVGKGAKGML;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:8183239;Dbxref=PMID:8183239
P48067	29	83	29	82	Alternative sequence	ID=VSP_006271;Note=In isoform GlyT-1B. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:8183239;Dbxref=PMID:8183239
P48067	29	83	1	706	Chain	ID=PRO_0000214780;Note=Sodium- and chloride-dependent glycine transporter 1
P48067	29	83	1	108	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
P48067	585	642	1	706	Chain	ID=PRO_0000214780;Note=Sodium- and chloride-dependent glycine transporter 1
P48067	585	642	631	706	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
P48067	585	642	570	590	Transmembrane	Note=Helical%3B Name%3D11;Ontology_term=ECO:0000255;evidence=ECO:0000255
P48067	585	642	610	630	Transmembrane	Note=Helical%3B Name%3D12;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
P48067	29	83	1	83	Alternative sequence	ID=VSP_006270;Note=In isoform GlyT-1A. MSGGDTRAAIARPRMAAAHGPVAPSSPEQVTLLPVQRSFFLPPFSGATPSTSLAESVLKVWHGAYNSGLLPQLMAQHSLAMAQ->MVGKGAKGML;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:8183239;Dbxref=PMID:8183239
P48067	29	83	29	82	Alternative sequence	ID=VSP_006271;Note=In isoform GlyT-1B. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:8183239;Dbxref=PMID:8183239
P48067	29	83	1	706	Chain	ID=PRO_0000214780;Note=Sodium- and chloride-dependent glycine transporter 1
P48067	29	83	1	108	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
P48067	585	642	1	706	Chain	ID=PRO_0000214780;Note=Sodium- and chloride-dependent glycine transporter 1
P48067	585	642	631	706	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
P48067	585	642	570	590	Transmembrane	Note=Helical%3B Name%3D11;Ontology_term=ECO:0000255;evidence=ECO:0000255
P48067	585	642	610	630	Transmembrane	Note=Helical%3B Name%3D12;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for SLC6A9

- 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.

SLC6A9_BRCA_exon_skip_25867_psi_boxplot.png
boxplot

- 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-G3-A3CJ-01	exon_skip_25842	44463527	44463697	44463577	44463577	Frame_Shift_Del	G	-	p.L553fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_25854	44475637	44475768	44475647	44475647	Frame_Shift_Del	G	-	p.P103fs
LIHC	TCGA-DD-A3A0-01	exon_skip_25854	44475637	44475768	44475664	44475664	Frame_Shift_Del	C	-	p.V98fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_25871 exon_skip_25872	44477233	44477394	44477349	44477349	Frame_Shift_Del	A	-	p.S45fs
UCEC	TCGA-BS-A0UM-01	exon_skip_25867	44476481	44476554	44476479	44476479	Splice_Site	A	G	NULL
BRCA	TCGA-BH-A209-01	exon_skip_25859 exon_skip_25860	44476398	44476554	44476555	44476555	Splice_Site	C	T	e3-1
BRCA	TCGA-BH-A209-01	exon_skip_25867	44476481	44476554	44476555	44476555	Splice_Site	C	T	e3-1

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-BH-A209-01
	Cancer type: BRCA
	ESID: exon_skip_25860
	Skipped exon start: 44476398
	Skipped exon end: 44476554
	Mutation start: 44476555
	Mutation end: 44476555
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: T
	AAchange: e3-1
	Sample: TCGA-BH-A209-01
	Cancer type: BRCA
	ESID: exon_skip_25867
	Skipped exon start: 44476481
	Skipped exon end: 44476554
	Mutation start: 44476555
	Mutation end: 44476555
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: T
	AAchange: e3-1
exon_skip_25860_BRCA_TCGA-BH-A209-01.png
exon_skip_25867_BRCA_TCGA-BH-A209-01.png
exon_skip_464459_BRCA_TCGA-BH-A209-01.png
	Sample: TCGA-BH-A209-01
	Cancer type: BRCA
	ESID: exon_skip_25860
	Skipped exon start: 44476398
	Skipped exon end: 44476554
	Mutation start: 44476555
	Mutation end: 44476555
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: T
	AAchange: e3-1
	Sample: TCGA-BH-A209-01
	Cancer type: BRCA
	ESID: exon_skip_25867
	Skipped exon start: 44476481
	Skipped exon end: 44476554
	Mutation start: 44476555
	Mutation end: 44476555
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: T
	AAchange: e3-1
exon_skip_25860_BRCA_TCGA-BH-A209-01.png
exon_skip_25867_BRCA_TCGA-BH-A209-01.png
exon_skip_464459_BRCA_TCGA-BH-A209-01.png

- 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
OVMANA_OVARY	44474025	44474295	44474138	44474153	Frame_Shift_Del	TACACCGGCGCAGTCA	-	p.HDCAGV227fs
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44463527	44463697	44463571	44463571	Missense_Mutation	C	T	p.A628T
BT474_BREAST	44463527	44463697	44463597	44463597	Missense_Mutation	G	A	p.S619F
H290_PLEURA	44463527	44463697	44463618	44463618	Missense_Mutation	A	G	p.I612T
ONS76_CENTRAL_NERVOUS_SYSTEM	44463527	44463697	44463663	44463663	Missense_Mutation	G	A	p.P597L
OAW42_OVARY	44467062	44467299	44467114	44467114	Missense_Mutation	A	T	p.L456Q
HEC251_ENDOMETRIUM	44467062	44467299	44467258	44467258	Missense_Mutation	A	C	p.V408G
SUDHL6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44467062	44467299	44467274	44467274	Missense_Mutation	T	G	p.N403H
MAC2A_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44474025	44474295	44474131	44474131	Missense_Mutation	C	T	p.A235T
FTC238_THYROID	44474025	44474295	44474131	44474131	Missense_Mutation	C	A	p.A235S
FTC133_THYROID	44474025	44474295	44474131	44474131	Missense_Mutation	C	A	p.A235S
HEC59_ENDOMETRIUM	44474025	44474295	44474148	44474148	Missense_Mutation	C	T	p.C229Y
SNU324_PANCREAS	44474025	44474295	44474227	44474227	Missense_Mutation	C	T	p.A203T
SNU1040_LARGE_INTESTINE	44474025	44474295	44474227	44474227	Missense_Mutation	C	T	p.A203T
HEC59_ENDOMETRIUM	44476398	44476554	44476409	44476409	Missense_Mutation	C	T	p.R132H
HCC2998_LARGE_INTESTINE	44476398	44476554	44476409	44476409	Missense_Mutation	C	T	p.R132H
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44476398	44476554	44476464	44476464	Missense_Mutation	C	T	p.V114M
BICR18_UPPER_AERODIGESTIVE_TRACT	44476398	44476554	44476508	44476508	Missense_Mutation	T	G	p.K99T
BICR18_UPPER_AERODIGESTIVE_TRACT	44476481	44476554	44476508	44476508	Missense_Mutation	T	G	p.K99T
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44476398	44476554	44476508	44476508	Missense_Mutation	T	G	p.K99T
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44476481	44476554	44476508	44476508	Missense_Mutation	T	G	p.K99T
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44476398	44476554	44476508	44476508	Missense_Mutation	T	G	p.K99T
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44476481	44476554	44476508	44476508	Missense_Mutation	T	G	p.K99T
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44476398	44476554	44476508	44476508	Missense_Mutation	T	G	p.K99T
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44476481	44476554	44476508	44476508	Missense_Mutation	T	G	p.K99T
BICR18_UPPER_AERODIGESTIVE_TRACT	44476398	44476554	44476523	44476523	Missense_Mutation	C	T	p.R94K
BICR18_UPPER_AERODIGESTIVE_TRACT	44476481	44476554	44476523	44476523	Missense_Mutation	C	T	p.R94K
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44476398	44476554	44476523	44476523	Missense_Mutation	C	T	p.R94K
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44476481	44476554	44476523	44476523	Missense_Mutation	C	T	p.R94K
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44476398	44476554	44476523	44476523	Missense_Mutation	C	T	p.R94K
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	44476481	44476554	44476523	44476523	Missense_Mutation	C	T	p.R94K
SNU175_LARGE_INTESTINE	44477233	44477394	44477239	44477239	Missense_Mutation	C	T	p.M81I
GMS10_CENTRAL_NERVOUS_SYSTEM	44474025	44474295	44474028	44474028	Nonsense_Mutation	C	T	p.W269*
BICR18_UPPER_AERODIGESTIVE_TRACT	44475637	44475768	44475767	44475767	Splice_Site	G	T	p.G136G

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC6A9

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 SLC6A9

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLC6A9

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RelatedDrugs for SLC6A9

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
	P48067	DB00145	Glycine	Sodium- and chloride-dependent glycine transporter 1	small molecule	approved\|nutraceutical\|vet_approved

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RelatedDiseases for SLC6A9

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SLC6A9	C0036341	Schizophrenia	4	PSYGENET
SLC6A9	C0001973	Alcoholic Intoxication, Chronic	1	PSYGENET
SLC6A9	C0033975	Psychotic Disorders	1	PSYGENET
SLC6A9	C0236733	Amphetamine-Related Disorders	1	CTD_human
SLC6A9	C0349204	Nonorganic psychosis	1	PSYGENET

	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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