ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for ATP6V1H

Gene summary

Gene information	Gene symbol	ATP6V1H
	Gene ID	51606
	Gene name	ATPase H+ transporting V1 subunit H
	Synonyms	CGI-11\|MSTP042\|NBP1\|SFD\|SFDalpha\|SFDbeta\|VMA13
	Cytomap	8q11.23
	Type of gene	protein-coding
	Description	V-type proton ATPase subunit HATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit HV-ATPase 50/57 kDa subunitsV-ATPase subunit Hnef-binding protein 1protein VMA13 homologvacuolar ATP synthase subunit Hvacuolar ATPase subunit Hvacuolar proton p
	Modification date	20200313
	UniProtAcc	A0A024R7U9, A0A024R7X3, E5RG49, E5RHH0, E5RJG1, E5RK31, G3V126, H0YB41, Q9UI12,
	Context	- 29751835(Genome-wide association study identified ATP6V1H locus influencing cerebrospinal fluid BACE activity)

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

Gene	GO ID	GO term	PubMed ID
ATP6V1H	GO:0006897	endocytosis	12032142

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Gene structures and expression levels for ATP6V1H

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.

ENSG00000047249

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
CB	DOWN	ENST00000521707.1	ATP6V1H-211:retained_intron:ATP6V1H	2.426319e+01	-1.209617e+00	3.623986e-10	1.888593e-08
CB	DOWN	ENST00000518072.1	ATP6V1H-204:retained_intron:ATP6V1H	1.727669e+02	-1.289418e+00	1.017405e-05	1.069503e-04

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 ATP6V1H

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_148472	chr8	53715900:53716024:53743577:53743690:53769618:53769688	53743577:53743690
exon_skip_162222	chr8	53743587:53743690:53756555:53756656:53769618:53769688	53756555:53756656
exon_skip_167597	chr8	53756555:53756656:53769618:53769743:53771989:53772065	53769618:53769743
exon_skip_181389	chr8	53801799:53801896:53806742:53806858:53811164:53811217	53806742:53806858
exon_skip_185712	chr8	53801799:53801896:53814662:53814766:53817417:53817465	53814662:53814766
exon_skip_192455	chr8	53715919:53716024:53743577:53743690:53769618:53769688	53743577:53743690
exon_skip_200950	chr8	53715999:53716024:53743577:53743690:53769618:53769688	53743577:53743690
exon_skip_208405	chr8	53771989:53772167:53795647:53795839:53801799:53801868	53795647:53795839
exon_skip_215151	chr8	53769654:53769743:53771989:53772167:53795647:53795761	53771989:53772167
exon_skip_216628	chr8	53743627:53743690:53756555:53756656:53795647:53795761	53756555:53756656
exon_skip_267257	chr8	53715900:53716024:53743577:53743690:53756555:53756656	53743577:53743690
exon_skip_267622	chr8	53715900:53716024:53743577:53743690:53756555:53756568	53743577:53743690
exon_skip_269766	chr8	53806742:53806858:53811164:53811217:53814662:53814766	53811164:53811217
exon_skip_27813	chr8	53743627:53743690:53756555:53756656:53769618:53769688	53756555:53756656
exon_skip_284962	chr8	53769654:53769743:53771989:53772167:53795647:53795758	53771989:53772167
exon_skip_292937	chr8	53814732:53814766:53817417:53817530:53829444:53829533	53817417:53817530
exon_skip_40239	chr8	53743587:53743690:53756555:53756656:53795647:53795761	53756555:53756656
exon_skip_46772	chr8	53801799:53801896:53811164:53811217:53814662:53814766	53811164:53811217
exon_skip_55136	chr8	53817417:53817530:53829444:53829533:53832984:53833009	53829444:53829533
exon_skip_72741	chr8	53801799:53801896:53811164:53811217:53814662:53814762	53811164:53811217
exon_skip_82153	chr8	53833061:53833086:53841578:53841725:53843034:53843245	53841578:53841725
exon_skip_84149	chr8	53743587:53743690:53756555:53756656:53795647:53795839	53756555:53756656
exon_skip_98261	chr8	53715999:53716024:53743577:53743690:53756555:53756656	53743577:53743690

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 ATP6V1H

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
ENST00000359530	53771989	53772167	Frame-shift
ENST00000396774	53771989	53772167	Frame-shift
ENST00000359530	53795647	53795839	Frame-shift
ENST00000396774	53795647	53795839	Frame-shift
ENST00000359530	53743577	53743690	In-frame
ENST00000396774	53743577	53743690	In-frame
ENST00000359530	53756555	53756656	In-frame
ENST00000396774	53756555	53756656	In-frame
ENST00000359530	53769618	53769743	In-frame
ENST00000396774	53769618	53769743	In-frame
ENST00000359530	53811164	53811217	In-frame
ENST00000396774	53811164	53811217	In-frame
ENST00000359530	53817417	53817530	In-frame
ENST00000396774	53817417	53817530	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
ENST00000359530	53771989	53772167	Frame-shift
ENST00000396774	53771989	53772167	Frame-shift
ENST00000359530	53795647	53795839	Frame-shift
ENST00000396774	53795647	53795839	Frame-shift
ENST00000359530	53743577	53743690	In-frame
ENST00000396774	53743577	53743690	In-frame
ENST00000359530	53756555	53756656	In-frame
ENST00000396774	53756555	53756656	In-frame
ENST00000359530	53811164	53811217	In-frame
ENST00000396774	53811164	53811217	In-frame
ENST00000359530	53817417	53817530	In-frame
ENST00000396774	53817417	53817530	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
ENST00000359530	53771989	53772167	Frame-shift
ENST00000396774	53771989	53772167	Frame-shift
ENST00000359530	53795647	53795839	Frame-shift
ENST00000396774	53795647	53795839	Frame-shift
ENST00000359530	53743577	53743690	In-frame
ENST00000396774	53743577	53743690	In-frame
ENST00000359530	53756555	53756656	In-frame
ENST00000396774	53756555	53756656	In-frame
ENST00000359530	53769618	53769743	In-frame
ENST00000396774	53769618	53769743	In-frame
ENST00000359530	53811164	53811217	In-frame
ENST00000396774	53811164	53811217	In-frame
ENST00000359530	53817417	53817530	In-frame
ENST00000396774	53817417	53817530	In-frame
ENST00000359530	53829444	53829533	In-frame
ENST00000396774	53829444	53829533	In-frame

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Infer the effects of exon skipping event on protein functional features for ATP6V1H

p-ENSG00000047249_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
ENST00000359530	2024	483	53817417	53817530	571	683	102	139
ENST00000396774	1909	483	53817417	53817530	514	626	102	139
ENST00000359530	2024	483	53811164	53811217	790	842	175	192
ENST00000396774	1909	483	53811164	53811217	733	785	175	192
ENST00000359530	2024	483	53769618	53769743	1314	1438	350	391
ENST00000396774	1909	483	53769618	53769743	1257	1381	350	391
ENST00000359530	2024	483	53756555	53756656	1440	1540	392	425
ENST00000396774	1909	483	53756555	53756656	1383	1483	392	425
ENST00000359530	2024	483	53743577	53743690	1542	1654	426	463
ENST00000396774	1909	483	53743577	53743690	1485	1597	426	463

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
ENST00000359530	2024	483	53817417	53817530	571	683	102	139
ENST00000396774	1909	483	53817417	53817530	514	626	102	139
ENST00000359530	2024	483	53811164	53811217	790	842	175	192
ENST00000396774	1909	483	53811164	53811217	733	785	175	192
ENST00000359530	2024	483	53756555	53756656	1440	1540	392	425
ENST00000396774	1909	483	53756555	53756656	1383	1483	392	425
ENST00000359530	2024	483	53743577	53743690	1542	1654	426	463
ENST00000396774	1909	483	53743577	53743690	1485	1597	426	463

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
ENST00000359530	2024	483	53829444	53829533	481	569	72	101
ENST00000396774	1909	483	53829444	53829533	424	512	72	101
ENST00000359530	2024	483	53817417	53817530	571	683	102	139
ENST00000396774	1909	483	53817417	53817530	514	626	102	139
ENST00000359530	2024	483	53811164	53811217	790	842	175	192
ENST00000396774	1909	483	53811164	53811217	733	785	175	192
ENST00000359530	2024	483	53769618	53769743	1314	1438	350	391
ENST00000396774	1909	483	53769618	53769743	1257	1381	350	391
ENST00000359530	2024	483	53756555	53756656	1440	1540	392	425
ENST00000396774	1909	483	53756555	53756656	1383	1483	392	425
ENST00000359530	2024	483	53743577	53743690	1542	1654	426	463
ENST00000396774	1909	483	53743577	53743690	1485	1597	426	463

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
Q9UI12	102	139	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	102	139	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	102	139	129	129	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UI12	102	139	129	129	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UI12	175	192	176	193	Alternative sequence	ID=VSP_012274;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.1
Q9UI12	175	192	176	193	Alternative sequence	ID=VSP_012274;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.1
Q9UI12	175	192	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	175	192	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	350	391	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	350	391	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	392	425	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	392	425	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	426	463	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	426	463	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H

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
Q9UI12	102	139	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	102	139	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	102	139	129	129	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UI12	102	139	129	129	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UI12	175	192	176	193	Alternative sequence	ID=VSP_012274;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.1
Q9UI12	175	192	176	193	Alternative sequence	ID=VSP_012274;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.1
Q9UI12	175	192	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	175	192	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	392	425	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	392	425	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	426	463	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	426	463	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H

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
Q9UI12	72	101	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	72	101	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	102	139	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	102	139	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	102	139	129	129	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UI12	102	139	129	129	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UI12	175	192	176	193	Alternative sequence	ID=VSP_012274;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.1
Q9UI12	175	192	176	193	Alternative sequence	ID=VSP_012274;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.1
Q9UI12	175	192	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	175	192	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	350	391	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	350	391	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	392	425	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	392	425	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	426	463	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H
Q9UI12	426	463	1	483	Chain	ID=PRO_0000124193;Note=V-type proton ATPase subunit H

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3'-UTR located exon skipping events that lost miRNA binding sites in ATP6V1H

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 ATP6V1H

- 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 ATP6V1H

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 ATP6V1H

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 ATP6V1H

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	TARDBP	exon_skip_46772	-5.207266e-01	2.325205e-12
CB	CNOT4	exon_skip_46772	-5.384214e-01	2.951906e-13
DLPFC	CNOT4	exon_skip_46772	-4.025703e-01	9.346454e-15
FL	MSI1	exon_skip_46772	4.503081e-01	3.152025e-11
HCC	MSI1	exon_skip_46772	4.878910e-01	1.131332e-17
TC	CNOT4	exon_skip_72741	-4.602923e-01	9.132530e-10
TC	SRSF9	exon_skip_72741	-4.080264e-01	8.525150e-08
TC	ESRP1	exon_skip_72741	-5.317428e-01	4.650966e-13

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RelatedDrugs for ATP6V1H

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 ATP6V1H

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 ATP6V1H

Gene structures and expression levels for ATP6V1H

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for ATP6V1H

Open reading frame (ORF) annotation in the exon skipping event for ATP6V1H

Infer the effects of exon skipping event on protein functional features for ATP6V1H

3'-UTR located exon skipping events that lost miRNA binding sites in ATP6V1H

SNVs in the skipped exons for ATP6V1H

AD stage-associated exon skippint events for ATP6V1H

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ATP6V1H

Correlation with RNA binding proteins (RBPs) for ATP6V1H

RelatedDrugs for ATP6V1H

RelatedDiseases for ATP6V1H