ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SLC1A2

Gene summary

Gene information	Gene symbol	SLC1A2
	Gene ID	6506
	Gene name	solute carrier family 1 member 2
	Synonyms	EAAT2\|EIEE41\|GLT-1\|HBGT
	Cytomap	11p13
	Type of gene	protein-coding
	Description	excitatory amino acid transporter 2excitotoxic amino acid transporter 2glutamate/aspartate transporter IIsodium-dependent glutamate/aspartate transporter 2solute carrier family 1 (glial high affinity glutamate transporter), member 2
	Modification date	20200313
	UniProtAcc	A0A163QEF0, A0A2R8Y4D1, A0A2R8Y4N0, A0A2R8Y4W1, A0A2R8Y5Y1, A0A2R8Y642, A0A2R8Y6B8, A0A2R8Y6J5, A0A2R8Y740, A0A2R8Y860, A0A2R8Y862, A0A2R8YCL7, A0A2R8YD46, A0A2R8YFE3, A0A2R8YG01, A0A2R8YH93, A0A2R8YHI4, A0A2U3TZS7, A0A2U3U0E3, A2A2U1, C9J9N5, H0YEB1, H0YEK4, P43004,
	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
SLC1A2	GO:0015813	L-glutamate transmembrane transport	26690923
SLC1A2	GO:0070207	protein homotrimerization	15265858\|15483603
SLC1A2	GO:0070779	D-aspartate import across plasma membrane	7521911
SLC1A2	GO:0098712	L-glutamate import across plasma membrane	7521911\|15265858\|26690923

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Gene structures and expression levels for SLC1A2

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.

ENSG00000110436

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	DOWN	ENST00000449068.2	SLC1A2-204:protein_coding:SLC1A2	4.483433e+01	-2.031248e+00	2.359811e-04	1.018646e-02
HCC	UP	ENST00000642769.1	SLC1A2-217:protein_coding:SLC1A2	6.095460e+03	9.429294e-01	3.177204e-04	1.578038e-02
PG	UP	ENST00000643522.1	SLC1A2-224:protein_coding:SLC1A2	3.004225e+01	2.311416e+01	8.359827e-42	3.094202e-37
PG	UP	ENST00000479543.2	SLC1A2-206:lncRNA:SLC1A2	7.778962e+02	1.149787e+00	7.617443e-04	1.196446e-02
TC	UP	ENST00000646585.1	SLC1A2-244:lncRNA:SLC1A2	9.995450e-01	2.205610e+00	1.467436e-06	5.476253e-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 SLC1A2

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_100270	chr11	35265698:35265758:35280867:35281001:35286757:35286918	35280867:35281001
exon_skip_100835	chr11	35260844:35260965:35261670:35261740:35265527:35265745	35261670:35261740
exon_skip_101487	chr11	35292506:35292520:35301519:35301645:35306074:35306242	35301519:35301645
exon_skip_111014	chr11	35317504:35317516:35380381:35380541:35418950:35418966	35380381:35380541
exon_skip_113952	chr11	35292287:35292520:35301519:35301645:35306074:35306242	35301519:35301645
exon_skip_128731	chr11	35265527:35265758:35280867:35281001:35286757:35286918	35280867:35281001
exon_skip_133811	chr11	35254584:35254808:35260844:35260965:35265527:35265745	35260844:35260965
exon_skip_138844	chr11	35317504:35317516:35322561:35322679:35418950:35418966	35322561:35322679
exon_skip_157354	chr11	35317504:35317516:35322561:35322679:35419908:35419952	35322561:35322679
exon_skip_161257	chr11	35254421:35254808:35260844:35260965:35265527:35265745	35260844:35260965
exon_skip_163553	chr11	35260844:35260965:35261670:35261862:35265527:35265745	35261670:35261862
exon_skip_170770	chr11	35260844:35260965:35261670:35261740:35265527:35265758	35261670:35261740
exon_skip_170920	chr11	35317504:35317516:35370941:35371096:35419908:35420063	35370941:35371096
exon_skip_182517	chr11	35265578:35265758:35280867:35281001:35286757:35286918	35280867:35281001
exon_skip_185856	chr11	35260844:35260965:35265527:35265758:35280867:35281001	35265527:35265758
exon_skip_198261	chr11	35254421:35254808:35260844:35260965:35265527:35265668	35260844:35260965
exon_skip_199769	chr11	35317504:35317516:35399575:35399681:35404319:35404490	35399575:35399681
exon_skip_211968	chr11	35292288:35292520:35301519:35301645:35306074:35306163	35301519:35301645
exon_skip_217255	chr11	35292287:35292520:35301519:35301645:35306074:35306163	35301519:35301645
exon_skip_229667	chr11	35317504:35317516:35322561:35322679:35419936:35419985	35322561:35322679
exon_skip_230742	chr11	35260844:35260965:35261670:35261862:35265527:35265547	35261670:35261862
exon_skip_246106	chr11	35317504:35317516:35391540:35391608:35419920:35419965	35391540:35391608
exon_skip_248083	chr11	35317504:35317516:35418950:35419007:35419908:35419952	35418950:35419007
exon_skip_259901	chr11	35317504:35317516:35322561:35322679:35419908:35419955	35322561:35322679
exon_skip_264262	chr11	35254696:35254808:35260844:35260965:35265527:35265745	35260844:35260965
exon_skip_268194	chr11	35260854:35260965:35261670:35261740:35265527:35265745	35261670:35261740
exon_skip_270875	chr11	35260894:35260965:35261670:35261862:35265527:35265745	35261670:35261862
exon_skip_274239	chr11	35286851:35286951:35292287:35292520:35301519:35301641	35292287:35292520
exon_skip_279300	chr11	35306074:35306242:35312198:35312448:35315023:35315175	35312198:35312448
exon_skip_293715	chr11	35265527:35265758:35280867:35281001:35286757:35286807	35280867:35281001
exon_skip_294054	chr11	35317504:35317516:35370941:35371096:35419908:35419952	35370941:35371096
exon_skip_45658	chr11	35260844:35260965:35261670:35261740:35265527:35265547	35261670:35261740
exon_skip_51354	chr11	35260894:35260965:35261670:35261740:35265527:35265745	35261670:35261740
exon_skip_60706	chr11	35260854:35260965:35265527:35265758:35280867:35281001	35265527:35265758
exon_skip_73840	chr11	35286874:35286951:35292287:35292520:35301519:35301641	35292287:35292520
exon_skip_8886	chr11	35312198:35312448:35315023:35315175:35317377:35317381	35315023:35315175

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 SLC1A2

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
ENST00000278379	35265527	35265758	Frame-shift
ENST00000278379	35301519	35301645	Frame-shift
ENST00000278379	35312198	35312448	Frame-shift
ENST00000278379	35280867	35281001	In-frame
ENST00000278379	35292287	35292520	In-frame
ENST00000278379	35315023	35315175	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
ENST00000278379	35265527	35265758	Frame-shift
ENST00000278379	35301519	35301645	Frame-shift
ENST00000278379	35280867	35281001	In-frame
ENST00000278379	35292287	35292520	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
ENST00000278379	35301519	35301645	Frame-shift
ENST00000278379	35312198	35312448	Frame-shift
ENST00000278379	35280867	35281001	In-frame
ENST00000278379	35292287	35292520	In-frame

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Infer the effects of exon skipping event on protein functional features for SLC1A2

p-ENSG00000110436_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
ENST00000278379	12058	574	35315023	35315175	785	936	52	103
ENST00000278379	12058	574	35292287	35292520	1485	1717	286	363
ENST00000278379	12058	574	35280867	35281001	1914	2047	429	473

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
ENST00000278379	12058	574	35292287	35292520	1485	1717	286	363
ENST00000278379	12058	574	35280867	35281001	1914	2047	429	473

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
ENST00000278379	12058	574	35292287	35292520	1485	1717	286	363
ENST00000278379	12058	574	35280867	35281001	1914	2047	429	473

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
P43004	52	103	1	574	Chain	ID=PRO_0000202061;Note=Excitatory amino acid transporter 2
P43004	52	103	82	82	Natural variant	ID=VAR_077083;Note=In EIEE41. G->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:27476654,ECO:0000269\|PubMed:28777935;Dbxref=dbSNP:rs886037942,PMID:27476654,PMID:28777935
P43004	52	103	85	85	Natural variant	ID=VAR_077084;Note=In EIEE41. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27476654;Dbxref=dbSNP:rs886037943,PMID:27476654
P43004	52	103	58	58	Sequence conflict	Note=A->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	52	103	65	87	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	52	103	45	64	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
P43004	52	103	88	108	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
P43004	286	363	1	574	Chain	ID=PRO_0000202061;Note=Excitatory amino acid transporter 2
P43004	286	363	345	375	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	286	363	289	289	Natural variant	ID=VAR_080229;Note=In EIEE41. P->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28777935;Dbxref=PMID:28777935
P43004	286	363	362	364	Region	Note=Aspartate binding;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	286	363	263	289	Sequence conflict	Note=AKLMVDFFNILNEIVMKLVIMIMWYSP->GQADGGFLQHFERDCNEVSDHDHVVLS;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	347	347	Sequence conflict	Note=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	297	317	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	340	344	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	269	296	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	286	363	318	339	Transmembrane	Note=Helical%3B Name%3D6;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	429	473	1	574	Chain	ID=PRO_0000202061;Note=Excitatory amino acid transporter 2
P43004	429	473	425	458	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	429	473	442	446	Region	Note=Aspartate binding;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	429	473	459	471	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	429	473	472	493	Transmembrane	Note=Helical%3B Name%3D8;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003

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
P43004	286	363	1	574	Chain	ID=PRO_0000202061;Note=Excitatory amino acid transporter 2
P43004	286	363	345	375	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	286	363	289	289	Natural variant	ID=VAR_080229;Note=In EIEE41. P->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28777935;Dbxref=PMID:28777935
P43004	286	363	362	364	Region	Note=Aspartate binding;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	286	363	263	289	Sequence conflict	Note=AKLMVDFFNILNEIVMKLVIMIMWYSP->GQADGGFLQHFERDCNEVSDHDHVVLS;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	347	347	Sequence conflict	Note=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	297	317	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	340	344	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	269	296	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	286	363	318	339	Transmembrane	Note=Helical%3B Name%3D6;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	429	473	1	574	Chain	ID=PRO_0000202061;Note=Excitatory amino acid transporter 2
P43004	429	473	425	458	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	429	473	442	446	Region	Note=Aspartate binding;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	429	473	459	471	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	429	473	472	493	Transmembrane	Note=Helical%3B Name%3D8;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003

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
P43004	286	363	1	574	Chain	ID=PRO_0000202061;Note=Excitatory amino acid transporter 2
P43004	286	363	345	375	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	286	363	289	289	Natural variant	ID=VAR_080229;Note=In EIEE41. P->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28777935;Dbxref=PMID:28777935
P43004	286	363	362	364	Region	Note=Aspartate binding;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	286	363	263	289	Sequence conflict	Note=AKLMVDFFNILNEIVMKLVIMIMWYSP->GQADGGFLQHFERDCNEVSDHDHVVLS;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	347	347	Sequence conflict	Note=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	297	317	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	340	344	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	286	363	269	296	Transmembrane	Note=Helical%3B Name%3D5;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	286	363	318	339	Transmembrane	Note=Helical%3B Name%3D6;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	429	473	1	574	Chain	ID=PRO_0000202061;Note=Excitatory amino acid transporter 2
P43004	429	473	425	458	Intramembrane	Note=Discontinuously helical;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	429	473	442	446	Region	Note=Aspartate binding;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003
P43004	429	473	459	471	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P43004	429	473	472	493	Transmembrane	Note=Helical%3B Name%3D8;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P43003

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3'-UTR located exon skipping events that lost miRNA binding sites in SLC1A2

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 SLC1A2

- 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 SLC1A2

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 SLC1A2

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 SLC1A2

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for SLC1A2

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P43004	approved\|nutraceutical	DB00142	Glutamic Acid	small molecule	P43004

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RelatedDiseases for SLC1A2

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 SLC1A2

Gene structures and expression levels for SLC1A2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SLC1A2

Open reading frame (ORF) annotation in the exon skipping event for SLC1A2

Infer the effects of exon skipping event on protein functional features for SLC1A2

3'-UTR located exon skipping events that lost miRNA binding sites in SLC1A2

SNVs in the skipped exons for SLC1A2

AD stage-associated exon skippint events for SLC1A2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC1A2

Correlation with RNA binding proteins (RBPs) for SLC1A2

RelatedDrugs for SLC1A2

RelatedDiseases for SLC1A2