ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SLC1A3

Gene summary

Gene information	Gene symbol	SLC1A3
	Gene ID	6507
	Gene name	solute carrier family 1 member 3
	Synonyms	EA6\|EAAT1\|GLAST\|GLAST1
	Cytomap	5p13.2
	Type of gene	protein-coding
	Description	excitatory amino acid transporter 1GLAST-1sodium-dependent glutamate/aspartate transporter 1solute carrier family 1 (glial high affinity glutamate transporter), member 3
	Modification date	20200320
	UniProtAcc	A0A024R050, A0A087WT87, A0A087X0U3, E7EUS7, E7EUV6, P43003, Q8N169,
	Context	- 23506861(The SLC1 High-Affinity Glutamate and Neutral Amino Acid Transporter Family)

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

Gene	GO ID	GO term	PubMed ID
SLC1A3	GO:0015813	L-glutamate transmembrane transport	26690923
SLC1A3	GO:0051938	L-glutamate import	7521911
SLC1A3	GO:0070779	D-aspartate import across plasma membrane	7521911
SLC1A3	GO:0071805	potassium ion transmembrane transport	20477940
SLC1A3	GO:0098712	L-glutamate import across plasma membrane	26690923
SLC1A3	GO:0140009	L-aspartate import across plasma membrane	20477940
SLC1A3	GO:1902476	chloride transmembrane transport	20477940

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Gene structures and expression levels for SLC1A3

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.

ENSG00000079215

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
PCC	UP	ENST00000381918.3	SLC1A3-202:protein_coding:SLC1A3	1.304767e+03	1.102369e+00	4.572457e-06	7.461081e-04
PG	UP	ENST00000381918.3	SLC1A3-202:protein_coding:SLC1A3	8.772302e+02	1.065296e+00	1.724138e-05	7.503325e-04
PG	UP	ENST00000505202.5	SLC1A3-206:protein_coding:SLC1A3	2.972692e+01	8.570070e-01	2.517323e-03	2.812347e-02
CB	DOWN	ENST00000381918.3	SLC1A3-202:protein_coding:SLC1A3	6.270998e+03	-1.358741e+00	2.490587e-12	3.183443e-10
CB	DOWN	ENST00000612708.4	SLC1A3-215:protein_coding:SLC1A3	8.307541e+02	-1.335104e+00	1.099463e-07	2.302133e-06
TC	DOWN	ENST00000612708.4	SLC1A3-215:protein_coding:SLC1A3	5.042305e+02	-1.131036e+00	1.324943e-06	5.037419e-05

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 SLC1A3

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_116035	chr5	36671029:36671233:36674049:36674091:36676892:36677127	36674049:36674091
exon_skip_118651	chr5	36608329:36608604:36629450:36629587:36671029:36671082	36629450:36629587
exon_skip_139333	chr5	36606617:36606735:36608329:36608604:36629450:36629572	36608329:36608604
exon_skip_148070	chr5	36679627:36679860:36680395:36680589:36683864:36683998	36680395:36680589
exon_skip_150011	chr5	36606617:36606735:36607224:36607311:36608329:36608346	36607224:36607311
exon_skip_153031	chr5	36608545:36608604:36629450:36629587:36671029:36671233	36629450:36629587
exon_skip_158525	chr5	36677120:36677184:36679627:36679860:36680395:36680589	36679627:36679860
exon_skip_158556	chr5	36671029:36671233:36679627:36679860:36680395:36680589	36679627:36679860
exon_skip_171453	chr5	36608329:36608604:36629450:36629587:36671029:36671233	36629450:36629587
exon_skip_198361	chr5	36606617:36606735:36607224:36607311:36608329:36608604	36607224:36607311
exon_skip_218358	chr5	36679627:36679860:36680395:36680589:36686065:36686233	36680395:36680589
exon_skip_261203	chr5	36680395:36680589:36683864:36683998:36686065:36686216	36683864:36683998
exon_skip_262226	chr5	36608330:36608604:36629450:36629587:36671029:36671233	36629450:36629587
exon_skip_269695	chr5	36608442:36608604:36629450:36629587:36671029:36671233	36629450:36629587
exon_skip_281845	chr5	36680395:36680589:36683864:36683998:36686065:36686132	36683864:36683998
exon_skip_283512	chr5	36680395:36680589:36683864:36683998:36686065:36686144	36683864:36683998
exon_skip_41918	chr5	36676892:36677184:36679627:36679860:36680395:36680589	36679627:36679860
exon_skip_59109	chr5	36674049:36674091:36676892:36677184:36679627:36679860	36676892:36677184
exon_skip_62528	chr5	36671029:36671233:36674049:36674091:36676892:36677050	36674049:36674091
exon_skip_91045	chr5	36606617:36606735:36607224:36607311:36608329:36608503	36607224:36607311
exon_skip_96211	chr5	36680395:36680589:36683864:36683998:36686065:36686233	36683864:36683998
exon_skip_98529	chr5	36680571:36680589:36683864:36683998:36686065:36686233	36683864:36683998

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 SLC1A3

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
ENST00000265113	36608329	36608604	5CDS-5UTR
ENST00000265113	36674049	36674091	Frame-shift
ENST00000265113	36676892	36677184	Frame-shift
ENST00000265113	36629450	36629587	In-frame
ENST00000265113	36679627	36679860	In-frame
ENST00000265113	36680395	36680589	In-frame
ENST00000265113	36683864	36683998	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
ENST00000265113	36674049	36674091	Frame-shift
ENST00000265113	36629450	36629587	In-frame
ENST00000265113	36683864	36683998	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
ENST00000265113	36608329	36608604	5CDS-5UTR
ENST00000265113	36674049	36674091	Frame-shift
ENST00000265113	36676892	36677184	Frame-shift
ENST00000265113	36629450	36629587	In-frame
ENST00000265113	36679627	36679860	In-frame
ENST00000265113	36680395	36680589	In-frame
ENST00000265113	36683864	36683998	In-frame

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Infer the effects of exon skipping event on protein functional features for SLC1A3

p-ENSG00000079215_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
ENST00000265113	4187	542	36629450	36629587	659	795	61	106
ENST00000265113	4187	542	36679627	36679860	1338	1570	287	364
ENST00000265113	4187	542	36680395	36680589	1572	1765	365	429
ENST00000265113	4187	542	36683864	36683998	1767	1900	430	474

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
ENST00000265113	4187	542	36629450	36629587	659	795	61	106
ENST00000265113	4187	542	36683864	36683998	1767	1900	430	474

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
ENST00000265113	4187	542	36629450	36629587	659	795	61	106
ENST00000265113	4187	542	36679627	36679860	1338	1570	287	364
ENST00000265113	4187	542	36680395	36680589	1572	1765	365	429
ENST00000265113	4187	542	36683864	36683998	1767	1900	430	474

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
P43003	61	106	1	542	Chain	ID=PRO_0000202057;Note=Excitatory amino acid transporter 1
P43003	61	106	76	81	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	83	95	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	102	104	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	106	109	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	69	86	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	61	106	48	68	Transmembrane	Note=Helical%3B Name%3D1;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	61	106	87	108	Transmembrane	Note=Helical%3B Name%3D2;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	1	542	Chain	ID=PRO_0000202057;Note=Excitatory amino acid transporter 1
P43003	287	364	283	300	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	287	364	316	328	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	287	364	332	335	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	287	364	347	351	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	287	364	353	362	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	287	364	346	376	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	363	363	Mutagenesis	Note=Loss of electrogenic glutamate transport. Strongly decreased L-aspartate and L-glutamate uptake combined with strongly increased permeability ot other ions%3B when associated with M-477. S->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:2047
P43003	287	364	290	290	Natural variant	ID=VAR_031733;Note=In EA6. P->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16116111;Dbxref=dbSNP:rs137852619,PMID:16116111
P43003	287	364	363	365	Region	Note=Aspartate binding;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5LM4,ECO:0000269\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	298	318	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	341	345	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	270	297	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	319	340	Transmembrane	Note=Helical%3B Name%3D6;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	402	402	Binding site	Note=Aspartate;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5LM4,ECO:0000269\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	1	542	Chain	ID=PRO_0000202057;Note=Excitatory amino acid transporter 1
P43003	365	429	369	377	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	387	396	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	400	407	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	411	414	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	424	439	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	346	376	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	426	459	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	394	394	Metal binding	Note=Sodium 1%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:O59010
P43003	365	429	396	396	Metal binding	Note=Sodium 2%3B via carbonyl oxygen;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5LM4,ECO:0000269\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	398	398	Metal binding	Note=Sodium 1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:O59010
P43003	365	429	363	365	Region	Note=Aspartate binding;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5LM4,ECO:0000269\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	366	366	Sequence conflict	Note=S->CT;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43003	365	429	377	385	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	413	425	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	386	412	Transmembrane	Note=Helical%3B Name%3D7;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	365	367	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	378	380	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	430	475	Alternative sequence	ID=VSP_043913;Note=In isoform 2. SITATAASIGAAGIPQAGLVTMVIVLTSVGLPTDDITLIIAVDWFL->R;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:16042756;Dbxref=PMID:16042756
P43003	430	474	1	542	Chain	ID=PRO_0000202057;Note=Excitatory amino acid transporter 1
P43003	430	474	424	439	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	446	449	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	451	456	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	462	464	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	465	473	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	426	459	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	430	474	443	447	Region	Note=Aspartate binding;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5LM4,ECO:0000269\|PubMed:28424515;Dbxref=PMID:28424515
P43003	430	474	460	472	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	430	474	473	494	Transmembrane	Note=Helical%3B Name%3D8;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515

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
P43003	61	106	1	542	Chain	ID=PRO_0000202057;Note=Excitatory amino acid transporter 1
P43003	61	106	76	81	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	83	95	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	102	104	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	106	109	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	69	86	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	61	106	48	68	Transmembrane	Note=Helical%3B Name%3D1;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	61	106	87	108	Transmembrane	Note=Helical%3B Name%3D2;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	430	474	430	475	Alternative sequence	ID=VSP_043913;Note=In isoform 2. SITATAASIGAAGIPQAGLVTMVIVLTSVGLPTDDITLIIAVDWFL->R;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:16042756;Dbxref=PMID:16042756
P43003	430	474	1	542	Chain	ID=PRO_0000202057;Note=Excitatory amino acid transporter 1
P43003	430	474	424	439	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	446	449	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	451	456	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	462	464	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	465	473	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	426	459	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	430	474	443	447	Region	Note=Aspartate binding;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5LM4,ECO:0000269\|PubMed:28424515;Dbxref=PMID:28424515
P43003	430	474	460	472	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	430	474	473	494	Transmembrane	Note=Helical%3B Name%3D8;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515

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
P43003	61	106	1	542	Chain	ID=PRO_0000202057;Note=Excitatory amino acid transporter 1
P43003	61	106	76	81	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	83	95	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	102	104	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	106	109	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	61	106	69	86	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	61	106	48	68	Transmembrane	Note=Helical%3B Name%3D1;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	61	106	87	108	Transmembrane	Note=Helical%3B Name%3D2;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	1	542	Chain	ID=PRO_0000202057;Note=Excitatory amino acid transporter 1
P43003	287	364	283	300	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	287	364	316	328	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	287	364	332	335	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	287	364	347	351	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	287	364	353	362	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	287	364	346	376	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	363	363	Mutagenesis	Note=Loss of electrogenic glutamate transport. Strongly decreased L-aspartate and L-glutamate uptake combined with strongly increased permeability ot other ions%3B when associated with M-477. S->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:2047
P43003	287	364	290	290	Natural variant	ID=VAR_031733;Note=In EA6. P->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16116111;Dbxref=dbSNP:rs137852619,PMID:16116111
P43003	287	364	363	365	Region	Note=Aspartate binding;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5LM4,ECO:0000269\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	298	318	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	341	345	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	270	297	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	287	364	319	340	Transmembrane	Note=Helical%3B Name%3D6;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	402	402	Binding site	Note=Aspartate;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5LM4,ECO:0000269\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	1	542	Chain	ID=PRO_0000202057;Note=Excitatory amino acid transporter 1
P43003	365	429	369	377	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	387	396	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	400	407	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	411	414	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	424	439	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	346	376	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	426	459	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	394	394	Metal binding	Note=Sodium 1%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:O59010
P43003	365	429	396	396	Metal binding	Note=Sodium 2%3B via carbonyl oxygen;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5LM4,ECO:0000269\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	398	398	Metal binding	Note=Sodium 1;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:O59010
P43003	365	429	363	365	Region	Note=Aspartate binding;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5LM4,ECO:0000269\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	366	366	Sequence conflict	Note=S->CT;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43003	365	429	377	385	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	413	425	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	386	412	Transmembrane	Note=Helical%3B Name%3D7;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	365	429	365	367	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	365	429	378	380	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	430	475	Alternative sequence	ID=VSP_043913;Note=In isoform 2. SITATAASIGAAGIPQAGLVTMVIVLTSVGLPTDDITLIIAVDWFL->R;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:16042756;Dbxref=PMID:16042756
P43003	430	474	1	542	Chain	ID=PRO_0000202057;Note=Excitatory amino acid transporter 1
P43003	430	474	424	439	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	446	449	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	451	456	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	462	464	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	465	473	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5LM4
P43003	430	474	426	459	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	430	474	443	447	Region	Note=Aspartate binding;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5LM4,ECO:0000269\|PubMed:28424515;Dbxref=PMID:28424515
P43003	430	474	460	472	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515
P43003	430	474	473	494	Transmembrane	Note=Helical%3B Name%3D8;Ontology_term=ECO:0000305;evidence=ECO:0000305\|PubMed:28424515;Dbxref=PMID:28424515

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3'-UTR located exon skipping events that lost miRNA binding sites in SLC1A3

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

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SNVs in the skipped exons for SLC1A3

- 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 SLC1A3

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

CDR

MSBB

STG

exon_skip_198361

3.112726e-01

2.389183e-03

chr5

36606617

36606735

36607224

36607311

36608329

36608604

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC1A3

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for SLC1A3

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for SLC1A3

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P43003	approved\|nutraceutical	DB00142	Glutamic Acid	small molecule	P43003

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RelatedDiseases for SLC1A3

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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Gene summary for SLC1A3

Gene structures and expression levels for SLC1A3

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SLC1A3

Open reading frame (ORF) annotation in the exon skipping event for SLC1A3

Infer the effects of exon skipping event on protein functional features for SLC1A3

3'-UTR located exon skipping events that lost miRNA binding sites in SLC1A3

SNVs in the skipped exons for SLC1A3

AD stage-associated exon skippint events for SLC1A3

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC1A3

Correlation with RNA binding proteins (RBPs) for SLC1A3

RelatedDrugs for SLC1A3

RelatedDiseases for SLC1A3