ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for GABRG2

Gene summary

Gene information	Gene symbol	GABRG2
	Gene ID	2566
	Gene name	gamma-aminobutyric acid type A receptor subunit gamma2
	Synonyms	CAE2\|ECA2\|EIEE74\|FEB8\|GEFSP3
	Cytomap	5q34
	Type of gene	protein-coding
	Description	gamma-aminobutyric acid receptor subunit gamma-2GABA(A) receptor subunit gamma-2GABA(A) receptor, gamma 2gamma-aminobutyric acid (GABA) A receptor, gamma 2gamma-aminobutyric acid type A receptor gamma2 subunit
	Modification date	20200313
	UniProtAcc	A0A1W2PP56, A0A1W2PPN5, A0A1W2PPS4, A0A1W2PQ81, A0A1W2PQA6, A0A1W2PQR9, A0A1W2PQX1, A0A1W2PR49, A0A1W2PRM8, A0A1W2PRN4, A0A1W2PRU1, A0A1W2PRY3, A0A1W2PSF4, A0A1X7SBS5, A0A1X7SBZ8, A0A286YFI6, A8MWU7, E5RGJ0, E5RIG3, P18507,
	Context	- 32400971(MAPT Haplotype-Stratified GWAS Reveals Differential Association for AD Risk Variants)

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

Gene	GO ID	GO term	PubMed ID
GABRG2	GO:1904862	inhibitory synapse assembly	23909897\|25489750

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Gene structures and expression levels for GABRG2

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.

ENSG00000113327

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
STG	UP	ENST00000640985.1	GABRG2-228:protein_coding:GABRG2	2.596493e+01	2.056407e+01	1.786279e-29	4.437820e-26
STG	UP	ENST00000522990.5	GABRG2-205:nonsense_mediated_decay:GABRG2	2.273084e+01	2.154890e+01	4.322305e-25	8.859104e-22
PG	DOWN	ENST00000639111.1	GABRG2-214:protein_coding:GABRG2	1.971090e+02	-9.054822e-01	2.535815e-06	1.808430e-04
PG	DOWN	ENST00000638772.1	GABRG2-210:protein_coding:GABRG2	1.001777e+02	-8.195237e-01	4.921880e-04	8.745671e-03
CB	UP	ENST00000639975.1	GABRG2-222:protein_coding:GABRG2	2.543056e+02	1.563584e+00	6.215174e-04	3.464607e-03

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 GABRG2

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_17231	chr5	162142164:162142316:162149108:162149313:162153093:162153426	162149108:162149313
exon_skip_192995	chr5	162103889:162104026:162142164:162142316:162149108:162149166	162142164:162142316
exon_skip_205218	chr5	162149108:162149313:162151730:162151753:162153093:162153106	162151730:162151753
exon_skip_214257	chr5	162149108:162149313:162150995:162151753:162153093:162153223	162150995:162151753
exon_skip_217209	chr5	162149108:162149313:162150995:162151753:162153093:162153372	162150995:162151753
exon_skip_218944	chr5	162149108:162149313:162151730:162151753:162153093:162153223	162151730:162151753
exon_skip_232175	chr5	162103889:162104026:162129223:162129261:162142164:162142316	162129223:162129261
exon_skip_237840	chr5	162142164:162142316:162149108:162151753:162153093:162153426	162149108:162151753
exon_skip_258435	chr5	162149108:162149313:162151730:162151753:162153093:162153426	162151730:162151753
exon_skip_296616	chr5	162067521:162067641:162068063:162068106:162093828:162093979	162068063:162068106
exon_skip_51652	chr5	162101235:162101317:162102554:162102673:162103889:162104026	162102554:162102673
exon_skip_66293	chr5	162149108:162149313:162151730:162151753:162153093:162153372	162151730:162151753
exon_skip_76227	chr5	162149108:162149313:162150995:162151753:162153093:162153426	162150995:162151753

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 GABRG2

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
ENST00000639213	162149108	162149313	Frame-shift

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

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
ENST00000639213	162142164	162142316	In-frame

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Infer the effects of exon skipping event on protein functional features for GABRG2

p-ENSG00000113327_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

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

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
ENST00000639213	9977	467	162142164	162142316	1306	1457	257	307

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

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

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
P18507	257	307	40	467	Chain	ID=PRO_0000000477;Note=Gamma-aminobutyric acid receptor subunit gamma-2
P18507	257	307	274	274	Natural variant	ID=VAR_078226;Note=Probable disease-associated mutation found in a patient with generalized epilepsy with myoclonic atonic seizures%2C cognitive impairment and behavioral disorder. Y->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:27864847;Dbxref
P18507	257	307	40	273	Topological domain	Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P18507	257	307	274	296	Transmembrane	Note=Helical;Ontology_term=ECO:0000305;evidence=ECO:0000305
P18507	257	307	300	322	Transmembrane	Note=Helical;Ontology_term=ECO:0000305;evidence=ECO:0000305

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3'-UTR located exon skipping events that lost miRNA binding sites in GABRG2

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 GABRG2

- 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 GABRG2

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 GABRG2

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
PCC	exon_skip_218944	rs211000	chr5:162188424	2.489854e-04	3.557054e-02

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Correlation with RNA binding proteins (RBPs) for GABRG2

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
FL	RALYL	exon_skip_258435	5.954603e-01	1.184072e-18

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RelatedDrugs for GABRG2

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P18507	approved\|investigational	DB00231	Temazepam	small molecule	P18507
P18507	approved	DB00395	Carisoprodol	small molecule	P18507
P18507	approved	DB00425	Zolpidem	small molecule	P18507
P18507	approved\|illicit\|investigational	DB00690	Flurazepam	small molecule	P18507
P18507	approved\|illicit\|withdrawn	DB00801	Halazepam	small molecule	P18507
P18507	approved\|illicit\|investigational\|vet_approved	DB00829	Diazepam	small molecule	P18507
P18507	approved	DB00842	Oxazepam	small molecule	P18507
P18507	approved\|investigational	DB00897	Triazolam	small molecule	P18507
P18507	approved	DB01205	Flumazenil	small molecule	P18507
P18507	approved\|illicit	DB01215	Estazolam	small molecule	P18507
P18507	approved\|investigational\|nutraceutical	DB01381	Ginkgo biloba	biotech	P18507
P18507	approved\|illicit	DB01544	Flunitrazepam	small molecule	P18507
P18507	approved\|illicit\|investigational	DB01558	Bromazepam	small molecule	P18507
P18507	approved\|illicit	DB01559	Clotiazepam	small molecule	P18507
P18507	approved\|illicit	DB01588	Prazepam	small molecule	P18507
P18507	approved\|illicit	DB01589	Quazepam	small molecule	P18507
P18507	approved	DB01595	Nitrazepam	small molecule	P18507
P18507	approved	DB13872	Lormetazepam	small molecule	P18507

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RelatedDiseases for GABRG2

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 GABRG2

Gene structures and expression levels for GABRG2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for GABRG2

Open reading frame (ORF) annotation in the exon skipping event for GABRG2

Infer the effects of exon skipping event on protein functional features for GABRG2

3'-UTR located exon skipping events that lost miRNA binding sites in GABRG2

SNVs in the skipped exons for GABRG2

AD stage-associated exon skippint events for GABRG2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GABRG2

Correlation with RNA binding proteins (RBPs) for GABRG2

RelatedDrugs for GABRG2

RelatedDiseases for GABRG2