ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SLC38A9

Gene summary

Gene information	Gene symbol	SLC38A9
	Gene ID	153129
	Gene name	solute carrier family 38 member 9
	Synonyms	URLC11
	Cytomap	5q11.2
	Type of gene	protein-coding
	Description	sodium-coupled neutral amino acid transporter 9putative sodium-coupled neutral amino acid transporter 9up-regulated in lung cancer 11
	Modification date	20200313
	UniProtAcc	B3KVK8, D6R9Q7, D6R9X0, D6RBB9, D6RDH2, D6RE72, D6RER8, D6RG31, D6RHF5, D6RHW0, D6RIW7, E7ESU6, Q8NBW4,
	Context

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

Gene	GO ID	GO term	PubMed ID
SLC38A9	GO:0003333	amino acid transmembrane transport	25567906\|29053970
SLC38A9	GO:0032008	positive regulation of TOR signaling	25561175\|25567906
SLC38A9	GO:0071230	cellular response to amino acid stimulus	25561175\|25567906\|29053970

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Gene structures and expression levels for SLC38A9

Skipped exons in the ROSMAP, MSBB, and Mayo 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.

ENSG00000177058

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
PG	UP	ENST00000512208.5	SLC38A9-217:protein_coding:SLC38A9	4.277851e+00	1.643717e+00	1.526752e-03	1.972229e-02
CB	UP	ENST00000503891.5	SLC38A9-207:protein_coding:SLC38A9	2.334336e+00	1.137462e+00	7.270459e-05	5.653459e-04
CB	DOWN	ENST00000416547.6	SLC38A9-203:protein_coding:SLC38A9	9.673072e+01	-1.768012e+00	1.716361e-04	1.169489e-03
CB	UP	ENST00000505563.5	SLC38A9-209:nonsense_mediated_decay:SLC38A9	2.407085e+00	8.441141e-01	2.169794e-04	1.426814e-03
TC	DOWN	ENST00000505708.5	SLC38A9-210:nonsense_mediated_decay:SLC38A9	2.828149e+00	-2.569153e+00	2.510082e-03	1.994667e-02
TC	DOWN	ENST00000416547.6	SLC38A9-203:protein_coding:SLC38A9	5.131703e+01	-1.496494e+00	6.205567e-03	3.933882e-02

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SLC38A9

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_103336	chr5	55672563:55672695:55697846:55697992:55711452:55711499	55697846:55697992
exon_skip_105510	chr5	55645789:55645895:55649207:55649314:55652529:55652723	55649207:55649314
exon_skip_11488	chr5	55649210:55649314:55652529:55652723:55656715:55656774	55652529:55652723
exon_skip_117821	chr5	55645789:55645895:55652529:55652723:55656715:55656774	55652529:55652723
exon_skip_160328	chr5	55697959:55697992:55704322:55704434:55711452:55711499	55704322:55704434
exon_skip_161564	chr5	55697959:55697992:55711352:55711499:55712217:55712261	55711352:55711499
exon_skip_178816	chr5	55697959:55697992:55702739:55702894:55711452:55711499	55702739:55702894
exon_skip_182131	chr5	55627891:55627980:55633695:55635657:55645789:55645868	55633695:55635657
exon_skip_182186	chr5	55697959:55697992:55702739:55702894:55704322:55704434	55702739:55702894
exon_skip_184545	chr5	55697846:55697992:55704322:55704434:55711452:55711499	55704322:55704434
exon_skip_225821	chr5	55664693:55664863:55669228:55669321:55669557:55669620	55669228:55669321
exon_skip_227450	chr5	55669836:55669879:55672563:55672695:55697846:55697992	55672563:55672695
exon_skip_235511	chr5	55702739:55702894:55704322:55704434:55711452:55711499	55704322:55704434
exon_skip_252587	chr5	55702739:55702894:55704043:55704140:55704322:55704434	55704043:55704140
exon_skip_258651	chr5	55669758:55669879:55672563:55672695:55697846:55697992	55672563:55672695
exon_skip_268801	chr5	55635544:55635657:55645789:55645895:55649207:55649314	55645789:55645895
exon_skip_283428	chr5	55697959:55697992:55711452:55711499:55712217:55712261	55711452:55711499
exon_skip_285381	chr5	55626560:55626659:55627891:55627980:55633754:55633902	55627891:55627980
exon_skip_31137	chr5	55652529:55652723:55656715:55656774:55664693:55664863	55656715:55656774
exon_skip_31843	chr5	55633754:55633902:55635544:55635657:55645789:55645868	55635544:55635657
exon_skip_49995	chr5	55704322:55704434:55711452:55711499:55712217:55712261	55711452:55711499
exon_skip_50098	chr5	55697846:55697992:55711452:55711499:55712217:55712330	55711452:55711499
exon_skip_53288	chr5	55656745:55656774:55664693:55664863:55669228:55669321	55664693:55664863

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information

Tissue type

Avg(PSIs) in AD

Avg(PSIs) in control

Difference (PSI)

Adj. p-value

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Open reading frame (ORF) annotation in the exon skipping event for SLC38A9

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000396865	55697846	55697992	3UTR-3CDS
ENST00000396865	55711452	55711499	3UTR-3UTR
ENST00000318672	55672563	55672695	Frame-shift
ENST00000396865	55672563	55672695	Frame-shift
ENST00000318672	55627891	55627980	In-frame
ENST00000396865	55627891	55627980	In-frame
ENST00000318672	55649207	55649314	In-frame
ENST00000396865	55649207	55649314	In-frame
ENST00000318672	55652529	55652723	In-frame
ENST00000396865	55652529	55652723	In-frame
ENST00000318672	55656715	55656774	In-frame
ENST00000396865	55656715	55656774	In-frame
ENST00000318672	55664693	55664863	In-frame
ENST00000396865	55664693	55664863	In-frame

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000396865	55697846	55697992	3UTR-3CDS
ENST00000396865	55711452	55711499	3UTR-3UTR
ENST00000318672	55672563	55672695	Frame-shift
ENST00000396865	55672563	55672695	Frame-shift
ENST00000318672	55627891	55627980	In-frame
ENST00000396865	55627891	55627980	In-frame
ENST00000318672	55649207	55649314	In-frame
ENST00000396865	55649207	55649314	In-frame
ENST00000318672	55652529	55652723	In-frame
ENST00000396865	55652529	55652723	In-frame
ENST00000318672	55664693	55664863	In-frame
ENST00000396865	55664693	55664863	In-frame

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000396865	55711452	55711499	3UTR-3UTR
ENST00000318672	55645789	55645895	Frame-shift
ENST00000396865	55645789	55645895	Frame-shift
ENST00000318672	55669228	55669321	Frame-shift
ENST00000396865	55669228	55669321	Frame-shift
ENST00000318672	55672563	55672695	Frame-shift
ENST00000396865	55672563	55672695	Frame-shift
ENST00000318672	55627891	55627980	In-frame
ENST00000396865	55627891	55627980	In-frame
ENST00000318672	55635544	55635657	In-frame
ENST00000396865	55635544	55635657	In-frame
ENST00000318672	55649207	55649314	In-frame
ENST00000396865	55649207	55649314	In-frame
ENST00000318672	55652529	55652723	In-frame
ENST00000396865	55652529	55652723	In-frame
ENST00000318672	55664693	55664863	In-frame
ENST00000396865	55664693	55664863	In-frame

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Infer the effects of exon skipping event on protein functional features for SLC38A9

p-ENSG00000177058_img4.png
boxplot

Loci of skipped exons in ROSMAP 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
ENST00000318672	2386	561	55664693	55664863	563	732	175	232
ENST00000396865	2944	561	55664693	55664863	1119	1288	175	232
ENST00000318672	2386	561	55656715	55656774	734	792	232	252
ENST00000396865	2944	561	55656715	55656774	1290	1348	232	252
ENST00000318672	2386	561	55652529	55652723	794	987	252	317
ENST00000396865	2944	561	55652529	55652723	1350	1543	252	317
ENST00000318672	2386	561	55649207	55649314	989	1095	317	353
ENST00000396865	2944	561	55649207	55649314	1545	1651	317	353
ENST00000318672	2386	561	55627891	55627980	1467	1555	477	506
ENST00000396865	2944	561	55627891	55627980	2023	2111	477	506

Loci of skipped exons in MSBB 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
ENST00000318672	2386	561	55664693	55664863	563	732	175	232
ENST00000396865	2944	561	55664693	55664863	1119	1288	175	232
ENST00000318672	2386	561	55652529	55652723	794	987	252	317
ENST00000396865	2944	561	55652529	55652723	1350	1543	252	317
ENST00000318672	2386	561	55649207	55649314	989	1095	317	353
ENST00000396865	2944	561	55649207	55649314	1545	1651	317	353
ENST00000318672	2386	561	55627891	55627980	1467	1555	477	506
ENST00000396865	2944	561	55627891	55627980	2023	2111	477	506

Loci of skipped exons in Mayo 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
ENST00000318672	2386	561	55664693	55664863	563	732	175	232
ENST00000396865	2944	561	55664693	55664863	1119	1288	175	232
ENST00000318672	2386	561	55652529	55652723	794	987	252	317
ENST00000396865	2944	561	55652529	55652723	1350	1543	252	317
ENST00000318672	2386	561	55649207	55649314	989	1095	317	353
ENST00000396865	2944	561	55649207	55649314	1545	1651	317	353
ENST00000318672	2386	561	55635544	55635657	1204	1316	389	426
ENST00000396865	2944	561	55635544	55635657	1760	1872	389	426
ENST00000318672	2386	561	55627891	55627980	1467	1555	477	506
ENST00000396865	2944	561	55627891	55627980	2023	2111	477	506

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

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
Q8NBW4	175	232	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	175	232	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	175	232	182	182	Natural variant	ID=VAR_042546;Note=S->T;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:14702039,ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:17974005;Dbxref=dbSNP:rs4865615,PMID:14702039,PMID:15489334,PMID:17974005
Q8NBW4	175	232	182	182	Natural variant	ID=VAR_042546;Note=S->T;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:14702039,ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:17974005;Dbxref=dbSNP:rs4865615,PMID:14702039,PMID:15489334,PMID:17974005
Q8NBW4	175	232	166	198	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	166	198	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	199	219	Transmembrane	Note=Helical%3B Name%3D3;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	175	232	199	219	Transmembrane	Note=Helical%3B Name%3D3;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	232	252	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	232	252	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	232	252	239	239	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	232	252	239	239	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	232	252	248	248	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	232	252	248	248	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	232	252	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	232	252	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	252	317	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	252	317	266	266	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	266	266	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	274	274	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	274	274	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	312	313	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	312	313	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	291	311	Transmembrane	Note=Helical%3B Name%3D4;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	252	317	291	311	Transmembrane	Note=Helical%3B Name%3D4;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	252	317	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	252	317	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	317	353	318	353	Alternative sequence	ID=VSP_045112;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8NBW4	317	353	318	353	Alternative sequence	ID=VSP_045112;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8NBW4	317	353	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	317	353	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	317	353	335	358	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	317	353	335	358	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	317	353	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	317	353	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	477	506	428	561	Alternative sequence	ID=VSP_032815;Note=In isoform 2. NFLDNFPSSDTLSFIARIFLLFQMMTVYPLLGYLARVQLLGHIFGDIYPSIFHVLILNLIIVGAGVIMACFYPNIGGIIRYSGAACGLAFVFIYPSLIYIISLHQEERLTWPKLIFHVFIIILGVANLIVQFFM->VRHRVPSLCDCVHFHVFIVGRVIQWQDITSDRPGF;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Pub
Q8NBW4	477	506	428	561	Alternative sequence	ID=VSP_032815;Note=In isoform 2. NFLDNFPSSDTLSFIARIFLLFQMMTVYPLLGYLARVQLLGHIFGDIYPSIFHVLILNLIIVGAGVIMACFYPNIGGIIRYSGAACGLAFVFIYPSLIYIISLHQEERLTWPKLIFHVFIIILGVANLIVQFFM->VRHRVPSLCDCVHFHVFIVGRVIQWQDITSDRPGF;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Pub
Q8NBW4	477	506	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	477	506	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	477	506	462	477	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	462	477	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	499	509	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	499	509	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	478	498	Transmembrane	Note=Helical%3B Name%3D9;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	477	506	478	498	Transmembrane	Note=Helical%3B Name%3D9;Ontology_term=ECO:0000255;evidence=ECO:0000255

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

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
Q8NBW4	175	232	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	175	232	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	175	232	182	182	Natural variant	ID=VAR_042546;Note=S->T;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:14702039,ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:17974005;Dbxref=dbSNP:rs4865615,PMID:14702039,PMID:15489334,PMID:17974005
Q8NBW4	175	232	182	182	Natural variant	ID=VAR_042546;Note=S->T;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:14702039,ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:17974005;Dbxref=dbSNP:rs4865615,PMID:14702039,PMID:15489334,PMID:17974005
Q8NBW4	175	232	166	198	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	166	198	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	199	219	Transmembrane	Note=Helical%3B Name%3D3;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	175	232	199	219	Transmembrane	Note=Helical%3B Name%3D3;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	252	317	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	252	317	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	252	317	266	266	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	266	266	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	274	274	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	274	274	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	312	313	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	312	313	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	291	311	Transmembrane	Note=Helical%3B Name%3D4;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	252	317	291	311	Transmembrane	Note=Helical%3B Name%3D4;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	252	317	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	252	317	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	317	353	318	353	Alternative sequence	ID=VSP_045112;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8NBW4	317	353	318	353	Alternative sequence	ID=VSP_045112;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8NBW4	317	353	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	317	353	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	317	353	335	358	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	317	353	335	358	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	317	353	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	317	353	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	477	506	428	561	Alternative sequence	ID=VSP_032815;Note=In isoform 2. NFLDNFPSSDTLSFIARIFLLFQMMTVYPLLGYLARVQLLGHIFGDIYPSIFHVLILNLIIVGAGVIMACFYPNIGGIIRYSGAACGLAFVFIYPSLIYIISLHQEERLTWPKLIFHVFIIILGVANLIVQFFM->VRHRVPSLCDCVHFHVFIVGRVIQWQDITSDRPGF;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Pub
Q8NBW4	477	506	428	561	Alternative sequence	ID=VSP_032815;Note=In isoform 2. NFLDNFPSSDTLSFIARIFLLFQMMTVYPLLGYLARVQLLGHIFGDIYPSIFHVLILNLIIVGAGVIMACFYPNIGGIIRYSGAACGLAFVFIYPSLIYIISLHQEERLTWPKLIFHVFIIILGVANLIVQFFM->VRHRVPSLCDCVHFHVFIVGRVIQWQDITSDRPGF;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Pub
Q8NBW4	477	506	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	477	506	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	477	506	462	477	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	462	477	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	499	509	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	499	509	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	478	498	Transmembrane	Note=Helical%3B Name%3D9;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	477	506	478	498	Transmembrane	Note=Helical%3B Name%3D9;Ontology_term=ECO:0000255;evidence=ECO:0000255

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

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
Q8NBW4	175	232	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	175	232	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	175	232	182	182	Natural variant	ID=VAR_042546;Note=S->T;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:14702039,ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:17974005;Dbxref=dbSNP:rs4865615,PMID:14702039,PMID:15489334,PMID:17974005
Q8NBW4	175	232	182	182	Natural variant	ID=VAR_042546;Note=S->T;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:14702039,ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:17974005;Dbxref=dbSNP:rs4865615,PMID:14702039,PMID:15489334,PMID:17974005
Q8NBW4	175	232	166	198	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	166	198	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	175	232	199	219	Transmembrane	Note=Helical%3B Name%3D3;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	175	232	199	219	Transmembrane	Note=Helical%3B Name%3D3;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	252	317	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	252	317	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	252	317	266	266	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	266	266	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	274	274	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	274	274	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00498
Q8NBW4	252	317	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	220	290	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	312	313	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	312	313	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	252	317	291	311	Transmembrane	Note=Helical%3B Name%3D4;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	252	317	291	311	Transmembrane	Note=Helical%3B Name%3D4;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	252	317	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	252	317	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	317	353	318	353	Alternative sequence	ID=VSP_045112;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8NBW4	317	353	318	353	Alternative sequence	ID=VSP_045112;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8NBW4	317	353	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	317	353	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	317	353	335	358	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	317	353	335	358	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	317	353	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	317	353	314	334	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	389	426	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	389	426	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	389	426	380	392	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	389	426	380	392	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	389	426	414	440	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	389	426	414	440	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	389	426	393	413	Transmembrane	Note=Helical%3B Name%3D7;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	389	426	393	413	Transmembrane	Note=Helical%3B Name%3D7;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	477	506	428	561	Alternative sequence	ID=VSP_032815;Note=In isoform 2. NFLDNFPSSDTLSFIARIFLLFQMMTVYPLLGYLARVQLLGHIFGDIYPSIFHVLILNLIIVGAGVIMACFYPNIGGIIRYSGAACGLAFVFIYPSLIYIISLHQEERLTWPKLIFHVFIIILGVANLIVQFFM->VRHRVPSLCDCVHFHVFIVGRVIQWQDITSDRPGF;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Pub
Q8NBW4	477	506	428	561	Alternative sequence	ID=VSP_032815;Note=In isoform 2. NFLDNFPSSDTLSFIARIFLLFQMMTVYPLLGYLARVQLLGHIFGDIYPSIFHVLILNLIIVGAGVIMACFYPNIGGIIRYSGAACGLAFVFIYPSLIYIISLHQEERLTWPKLIFHVFIIILGVANLIVQFFM->VRHRVPSLCDCVHFHVFIVGRVIQWQDITSDRPGF;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Pub
Q8NBW4	477	506	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	477	506	1	561	Chain	ID=PRO_0000328840;Note=Sodium-coupled neutral amino acid transporter 9
Q8NBW4	477	506	462	477	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	462	477	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	499	509	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	499	509	Topological domain	Note=Lumenal;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NBW4	477	506	478	498	Transmembrane	Note=Helical%3B Name%3D9;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NBW4	477	506	478	498	Transmembrane	Note=Helical%3B Name%3D9;Ontology_term=ECO:0000255;evidence=ECO:0000255

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3'-UTR located exon skipping events that lost miRNA binding sites in SLC38A9

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type	ENST	Exon skip start	Exon skip end	microRNA	Binding site by TargetScan	Binding type by TargetScan	Bdinding site by miRanda	Score of miRanda	Energy by miRanda
Mayo	ENST00000396865	55711452	55711499	hsa-miR-4531	chr5:55711468-55711475	8mer-1a	chr5:55711457-55711476	165.00	-19.98
MSBB	ENST00000396865	55711452	55711499	hsa-miR-4531	chr5:55711468-55711475	8mer-1a	chr5:55711457-55711476	165.00	-19.98
ROSMAP	ENST00000396865	55711452	55711499	hsa-miR-4531	chr5:55711468-55711475	8mer-1a	chr5:55711457-55711476	165.00	-19.98

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SNVs in the skipped exons for SLC38A9

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- 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

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AD stage-associated exon skippint events for SLC38A9

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC38A9

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
HCC	exon_skip_11488	rs9687838	chr5:55652905	1.010725e-05	1.264133e-03
HCC	exon_skip_11488	rs2408030	chr5:55653361	1.816434e-05	2.121297e-03
HCC	exon_skip_11488	rs4865614	chr5:55664781	1.816434e-05	2.121297e-03
HCC	exon_skip_11488	rs3846502	chr5:55668755	1.816434e-05	2.121297e-03
HCC	exon_skip_11488	rs3846503	chr5:55668902	1.816434e-05	2.121297e-03
HCC	exon_skip_11488	rs16884434	chr5:55683170	1.816434e-05	2.121297e-03
HCC	exon_skip_11488	rs13165328	chr5:55676468	2.015630e-05	2.325442e-03
HCC	exon_skip_11488	rs16884436	chr5:55685067	3.894961e-05	4.067112e-03
HCC	exon_skip_11488	rs3761769	chr5:55698236	3.894961e-05	4.067112e-03
HCC	exon_skip_11488	rs11738757	chr5:55719439	3.894961e-05	4.067112e-03
HCC	exon_skip_11488	rs13177722	chr5:55666048	1.627044e-04	1.371601e-02
HCC	exon_skip_11488	rs11745519	chr5:55608977	1.802742e-04	1.490947e-02
HCC	exon_skip_11488	rs6897117	chr5:55690947	5.209557e-04	3.502923e-02
HCC	exon_skip_11488	rs11748878	chr5:55609011	7.034241e-04	4.436237e-02

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Correlation with RNA binding proteins (RBPs) for SLC38A9

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	TARDBP	exon_skip_227450	-4.642354e-01	1.733545e-07
CB	U2AF2	exon_skip_160328	-5.036910e-01	1.357166e-09
CB	TRA2A	exon_skip_160328	-4.277195e-01	4.759563e-07
CB	FUBP1	exon_skip_160328	-4.052752e-01	2.080596e-06
CB	PTBP1	exon_skip_160328	-4.115715e-01	1.390369e-06

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RelatedDrugs for SLC38A9

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

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for SLC38A9

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 RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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