ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SLC43A2

Gene summary

Gene information	Gene symbol	SLC43A2
	Gene ID	124935
	Gene name	solute carrier family 43 member 2
	Synonyms	LAT4
	Cytomap	17p13.3
	Type of gene	protein-coding
	Description	large neutral amino acids transporter small subunit 4L-type amino acid transporter 4solute carrier family 43 (amino acid system L transporter), member 2
	Modification date	20180523
	UniProtAcc	Q8N370
	Context	PubMed: SLC43A2 [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 SLC43A2 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 SLC43A2

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 SLC43A2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_285312	17	1478794:1479059:1479890:1480014:1481543:1481617	1479890:1480014	ENSG00000167703.10	ENST00000412517.3,ENST00000571650.1,ENST00000382147.4,ENST00000301335.5
exon_skip_285315	17	1479896:1480014:1481543:1481617:1486497:1486630	1481543:1481617	ENSG00000167703.10	ENST00000412517.3,ENST00000571650.1,ENST00000382147.4,ENST00000301335.5
exon_skip_285317	17	1481547:1481617:1486497:1486630:1489206:1489345	1486497:1486630	ENSG00000167703.10	ENST00000412517.3,ENST00000571650.1,ENST00000382147.4,ENST00000301335.5
exon_skip_285321	17	1486497:1486630:1489206:1489345:1494095:1494242	1489206:1489345	ENSG00000167703.10	ENST00000412517.3,ENST00000301335.5
exon_skip_285322	17	1486497:1486630:1489206:1489357:1494095:1494242	1489206:1489357	ENSG00000167703.10	ENST00000382147.4
exon_skip_285323	17	1489206:1489345:1490242:1490254:1494095:1494242	1490242:1490254	ENSG00000167703.10	ENST00000571650.1
exon_skip_285324	17	1494200:1494242:1494562:1494765:1494859:1494993	1494562:1494765	ENSG00000167703.10	ENST00000572135.1,ENST00000574274.1,ENST00000412517.3,ENST00000574743.1,ENST00000572801.1,ENST00000571650.1,ENST00000382147.4,ENST00000301335.5
exon_skip_285325	17	1494915:1494993:1496480:1496573:1516488:1516565	1496480:1496573	ENSG00000167703.10	ENST00000571376.1,ENST00000572135.1,ENST00000574743.1,ENST00000572801.1,ENST00000571650.1,ENST00000382147.4,ENST00000301335.5
exon_skip_285326	17	1496480:1496573:1506398:1506501:1508033:1508238	1506398:1506501	ENSG00000167703.10	ENST00000576721.1
exon_skip_285330	17	1518272:1518328:1519855:1519924:1520010:1520063	1519855:1519924	ENSG00000167703.10	ENST00000571376.1
exon_skip_285332	17	1518272:1518328:1519855:1520063:1531008:1531093	1519855:1520063	ENSG00000167703.10	ENST00000572135.1,ENST00000574743.1,ENST00000571650.1,ENST00000382147.4,ENST00000301335.5
exon_skip_285336	17	1519855:1519924:1520010:1520063:1531008:1531093	1520010:1520063	ENSG00000167703.10	ENST00000571376.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SLC43A2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_285312	17	1478794:1479059:1479890:1480014:1481543:1481617	1479890:1480014	ENSG00000167703.10	ENST00000301335.5,ENST00000571650.1,ENST00000382147.4,ENST00000412517.3
exon_skip_285315	17	1479896:1480014:1481543:1481617:1486497:1486630	1481543:1481617	ENSG00000167703.10	ENST00000301335.5,ENST00000571650.1,ENST00000382147.4,ENST00000412517.3
exon_skip_285317	17	1481547:1481617:1486497:1486630:1489206:1489345	1486497:1486630	ENSG00000167703.10	ENST00000301335.5,ENST00000571650.1,ENST00000382147.4,ENST00000412517.3
exon_skip_285321	17	1486497:1486630:1489206:1489345:1494095:1494242	1489206:1489345	ENSG00000167703.10	ENST00000301335.5,ENST00000412517.3
exon_skip_285322	17	1486497:1486630:1489206:1489357:1494095:1494242	1489206:1489357	ENSG00000167703.10	ENST00000382147.4
exon_skip_285323	17	1489206:1489345:1490242:1490254:1494095:1494242	1490242:1490254	ENSG00000167703.10	ENST00000571650.1
exon_skip_285324	17	1494200:1494242:1494562:1494765:1494859:1494993	1494562:1494765	ENSG00000167703.10	ENST00000301335.5,ENST00000571650.1,ENST00000382147.4,ENST00000412517.3,ENST00000572135.1,ENST00000574743.1,ENST00000572801.1,ENST00000574274.1
exon_skip_285325	17	1494915:1494993:1496480:1496573:1516488:1516565	1496480:1496573	ENSG00000167703.10	ENST00000301335.5,ENST00000571650.1,ENST00000382147.4,ENST00000572135.1,ENST00000574743.1,ENST00000572801.1,ENST00000571376.1
exon_skip_285326	17	1496480:1496573:1506398:1506501:1508033:1508238	1506398:1506501	ENSG00000167703.10	ENST00000576721.1
exon_skip_285330	17	1518272:1518328:1519855:1519924:1520010:1520063	1519855:1519924	ENSG00000167703.10	ENST00000571376.1
exon_skip_285332	17	1518272:1518328:1519855:1520063:1531008:1531093	1519855:1520063	ENSG00000167703.10	ENST00000301335.5,ENST00000571650.1,ENST00000382147.4,ENST00000572135.1,ENST00000574743.1
exon_skip_285336	17	1519855:1519924:1520010:1520063:1531008:1531093	1520010:1520063	ENSG00000167703.10	ENST00000571376.1

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 SLC43A2

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

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

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Infer the effects of exon skipping event on protein functional features for SLC43A2

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

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

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

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

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SNVs in the skipped exons for SLC43A2

- 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
BLCA	TCGA-4Z-AA81-01	exon_skip_285324	1494563	1494765	1494615	1494616	Frame_Shift_Ins	-	GT	p.K293fs
READ	TCGA-AG-A00Y-01	exon_skip_285332	1519856	1520063	1519953	1519954	Frame_Shift_Ins	-	AG	p.A91fs
HNSC	TCGA-CV-7568-01	exon_skip_285332	1519856	1520063	1519990	1519990	Nonsense_Mutation	C	T	p.W78*
HNSC	TCGA-CV-A6K1-01	exon_skip_285332	1519856	1520063	1519990	1519990	Nonsense_Mutation	C	T	p.W78*
HNSC	TCGA-CV-7568-01	exon_skip_285332	1519856	1520063	1519991	1519991	Nonsense_Mutation	C	T	p.W78*
LUAD	TCGA-86-8672-01	exon_skip_285332	1519856	1520063	1520013	1520013	Nonsense_Mutation	C	A	p.E71*
LUAD	TCGA-86-8672-01	exon_skip_285336	1520011	1520063	1520013	1520013	Nonsense_Mutation	C	A	p.E71*
COAD	TCGA-A6-5665-01	exon_skip_285315	1481544	1481617	1481619	1481620	Splice_Site	-	G	.

- 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
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1479891	1480014	1479965	1479965	Missense_Mutation	T	A	p.S492C
SNU175_LARGE_INTESTINE	1479891	1480014	1479985	1479985	Missense_Mutation	G	A	p.T485M
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1479891	1480014	1479992	1479992	Missense_Mutation	T	C	p.S483G
PACADD137_PANCREAS	1479891	1480014	1479994	1479994	Missense_Mutation	C	T	p.G482D
BB49HNC_UPPER_AERODIGESTIVE_TRACT	1486498	1486630	1486527	1486527	Missense_Mutation	T	G	p.T441P
KNS60_CENTRAL_NERVOUS_SYSTEM	1486498	1486630	1486626	1486626	Missense_Mutation	C	T	p.E408K
SNUC2A_LARGE_INTESTINE	1486498	1486630	1486626	1486626	Missense_Mutation	C	T	p.E408K
SNUC2B_LARGE_INTESTINE	1486498	1486630	1486626	1486626	Missense_Mutation	C	T	p.E408K
SW684_SOFT_TISSUE	1489207	1489345	1489232	1489232	Missense_Mutation	C	T	p.E398K
SW684_SOFT_TISSUE	1489207	1489357	1489232	1489232	Missense_Mutation	C	T	p.E398K
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1489207	1489345	1489258	1489258	Missense_Mutation	A	G	p.L389P
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1489207	1489357	1489258	1489258	Missense_Mutation	A	G	p.L389P
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1489207	1489345	1489288	1489288	Missense_Mutation	G	T	p.P379H
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	1489207	1489357	1489288	1489288	Missense_Mutation	G	T	p.P379H
DBTRG05MG_CENTRAL_NERVOUS_SYSTEM	1494563	1494765	1494634	1494634	Missense_Mutation	G	A	p.A287V
OVK18_OVARY	1494563	1494765	1494645	1494645	Missense_Mutation	C	A	p.K283N
HEC151_ENDOMETRIUM	1494563	1494765	1494734	1494734	Missense_Mutation	C	T	p.D254N
GP2D_LARGE_INTESTINE	1519856	1520063	1519865	1519865	Missense_Mutation	A	T	p.L120Q
GP2D_LARGE_INTESTINE	1519856	1519924	1519865	1519865	Missense_Mutation	A	T	p.L120Q
LU134A_LUNG	1520011	1520063	1520018	1520018	Missense_Mutation	T	C	p.H69R
LU134A_LUNG	1519856	1520063	1520018	1520018	Missense_Mutation	T	C	p.H69R
NCCIT_TESTIS	1520011	1520063	1520018	1520018	Missense_Mutation	T	C	p.H69R
NCCIT_TESTIS	1519856	1520063	1520018	1520018	Missense_Mutation	T	C	p.H69R
YH13_CENTRAL_NERVOUS_SYSTEM	1520011	1520063	1520018	1520018	Missense_Mutation	T	C	p.H69R
YH13_CENTRAL_NERVOUS_SYSTEM	1519856	1520063	1520018	1520018	Missense_Mutation	T	C	p.H69R
SNU1040_LARGE_INTESTINE	1494563	1494765	1494629	1494629	Nonsense_Mutation	G	A	p.Q289*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC43A2

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 SLC43A2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLC43A2

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RelatedDrugs for SLC43A2

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 SLC43A2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SLC43A2	C0023893	Liver Cirrhosis, Experimental	1	CTD_human

	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 SLC43A2

Exon skipping events across known transcript of Ensembl for SLC43A2 from UCSC genome browser

Gene isoform structures and expression levels for SLC43A2

Exon skipping events with PSIs in TCGA for SLC43A2

Exon skipping events with PSIs in GTEx for SLC43A2

Open reading frame (ORF) annotation in the exon skipping event for SLC43A2

Infer the effects of exon skipping event on protein functional features for SLC43A2

SNVs in the skipped exons for SLC43A2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC43A2

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLC43A2

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLC43A2

RelatedDrugs for SLC43A2

RelatedDiseases for SLC43A2