ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for HDAC9

Gene summary

Gene information	Gene symbol	HDAC9
	Gene ID	9734
	Gene name	histone deacetylase 9
	Synonyms	HD7\|HD7b\|HD9\|HDAC\|HDAC7\|HDAC7B\|HDAC9B\|HDAC9FL\|HDRP\|MITR
	Cytomap	7p21.1
	Type of gene	protein-coding
	Description	histone deacetylase 9MEF-2 interacting transcription repressor (MITR) proteinhistone deacetylase 4/5-related proteinhistone deacetylase 7B
	Modification date	20200322
	UniProtAcc	B5MCF1, B7Z3P7, C9IZS0, C9J1W4, C9J835, C9JD56, C9JLX1, F8WDS2, Q75N08, Q75N09, Q75N10, Q75N14, Q75N15, Q75N16, Q9Y6V1,
	Context	- 30887246(Circular HDAC9/microRNA-138/Sirtuin-1 Pathway Mediates Synaptic and Amyloid Precursor Protein Processing Deficits in Alzheimer's Disease)

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

Gene	GO ID	GO term	PubMed ID
HDAC9	GO:0000122	negative regulation of transcription by RNA polymerase II	10655483\|11535832
HDAC9	GO:0016575	histone deacetylation	11535832
HDAC9	GO:0032869	cellular response to insulin stimulus	19303849
HDAC9	GO:0034983	peptidyl-lysine deacetylation	11535832
HDAC9	GO:0042632	cholesterol homeostasis	28855441
HDAC9	GO:0045892	negative regulation of transcription, DNA-templated	11535832
HDAC9	GO:0050710	negative regulation of cytokine secretion	28855441
HDAC9	GO:0051005	negative regulation of lipoprotein lipase activity	28855441
HDAC9	GO:0070932	histone H3 deacetylation	12590135
HDAC9	GO:0070933	histone H4 deacetylation	12590135
HDAC9	GO:1990678	histone H4-K16 deacetylation	28855441

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Gene structures and expression levels for HDAC9

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.

ENSG00000048052

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	UP	ENST00000417496.6	HDAC9-208:protein_coding:HDAC9	2.323262e+01	8.091940e-01	2.525563e-05	2.305820e-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 HDAC9

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_104901	chr7	18593908:18594029:18629350:18629481:18634627:18634742	18629350:18629481
exon_skip_106477	chr7	18648466:18648683:18666213:18666476:18727580:18727757	18666213:18666476
exon_skip_130679	chr7	18290450:18290515:18395115:18395183:18496262:18496324	18395115:18395183
exon_skip_152599	chr7	18496303:18496324:18543169:18543674:18585281:18585326	18543169:18543674
exon_skip_185763	chr7	18593908:18594029:18634627:18634742:18644671:18644793	18634627:18634742
exon_skip_20761	chr7	18585292:18585522:18590345:18590486:18591516:18591533	18590345:18590486
exon_skip_264266	chr7	18496303:18496324:18502581:18502639:18585281:18585326	18502581:18502639
exon_skip_277128	chr7	18749005:18749138:18762157:18762277:18767106:18767155	18762157:18762277
exon_skip_47002	chr7	18585292:18585522:18590336:18590486:18591516:18591533	18590336:18590486
exon_skip_6389	chr7	18496262:18496324:18502581:18502639:18585281:18585522	18502581:18502639
exon_skip_99066	chr7	18496303:18496324:18543169:18543674:18585281:18585522	18543169:18543674

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 HDAC9

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
ENST00000432645	18590345	18590486	Frame-shift
ENST00000432645	18762157	18762277	Frame-shift
ENST00000432645	18629350	18629481	In-frame
ENST00000432645	18666213	18666476	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
ENST00000432645	18590345	18590486	Frame-shift
ENST00000432645	18629350	18629481	In-frame
ENST00000432645	18666213	18666476	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
ENST00000432645	18590345	18590486	Frame-shift
ENST00000432645	18629350	18629481	In-frame
ENST00000432645	18666213	18666476	In-frame

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Infer the effects of exon skipping event on protein functional features for HDAC9

p-ENSG00000048052_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
ENST00000432645	3116	1011	18629350	18629481	657	787	219	262
ENST00000432645	3116	1011	18666213	18666476	1460	1722	486	574

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
ENST00000432645	3116	1011	18629350	18629481	657	787	219	262
ENST00000432645	3116	1011	18666213	18666476	1460	1722	486	574

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
ENST00000432645	3116	1011	18629350	18629481	657	787	219	262
ENST00000432645	3116	1011	18666213	18666476	1460	1722	486	574

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
Q9UKV0	219	262	218	261	Alternative sequence	ID=VSP_023767;Note=In isoform 6%2C isoform 8%2C isoform 9 and isoform 11. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q9UKV0	219	262	1	1011	Chain	ID=PRO_0000114710;Note=Histone deacetylase 9
Q9UKV0	219	262	220	220	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99N13
Q9UKV0	219	262	240	240	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99N13
Q9UKV0	219	262	175	343	Region	Note=Interaction with MAPK10;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9UKV0	219	262	218	261	Region	Note=Interaction with ETV6;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12590135;Dbxref=PMID:12590135
Q9UKV0	486	574	487	574	Alternative sequence	ID=VSP_002082;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10523670;Dbxref=PMID:10523670
Q9UKV0	486	574	1	1011	Chain	ID=PRO_0000114710;Note=Histone deacetylase 9
Q9UKV0	486	574	554	554	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99N13

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
Q9UKV0	219	262	218	261	Alternative sequence	ID=VSP_023767;Note=In isoform 6%2C isoform 8%2C isoform 9 and isoform 11. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q9UKV0	219	262	1	1011	Chain	ID=PRO_0000114710;Note=Histone deacetylase 9
Q9UKV0	219	262	220	220	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99N13
Q9UKV0	219	262	240	240	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99N13
Q9UKV0	219	262	175	343	Region	Note=Interaction with MAPK10;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9UKV0	219	262	218	261	Region	Note=Interaction with ETV6;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12590135;Dbxref=PMID:12590135
Q9UKV0	486	574	487	574	Alternative sequence	ID=VSP_002082;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10523670;Dbxref=PMID:10523670
Q9UKV0	486	574	1	1011	Chain	ID=PRO_0000114710;Note=Histone deacetylase 9
Q9UKV0	486	574	554	554	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99N13

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
Q9UKV0	219	262	218	261	Alternative sequence	ID=VSP_023767;Note=In isoform 6%2C isoform 8%2C isoform 9 and isoform 11. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q9UKV0	219	262	1	1011	Chain	ID=PRO_0000114710;Note=Histone deacetylase 9
Q9UKV0	219	262	220	220	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99N13
Q9UKV0	219	262	240	240	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99N13
Q9UKV0	219	262	175	343	Region	Note=Interaction with MAPK10;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9UKV0	219	262	218	261	Region	Note=Interaction with ETV6;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12590135;Dbxref=PMID:12590135
Q9UKV0	486	574	487	574	Alternative sequence	ID=VSP_002082;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:10523670;Dbxref=PMID:10523670
Q9UKV0	486	574	1	1011	Chain	ID=PRO_0000114710;Note=Histone deacetylase 9
Q9UKV0	486	574	554	554	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q99N13

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3'-UTR located exon skipping events that lost miRNA binding sites in HDAC9

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 HDAC9

- 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 HDAC9

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 HDAC9

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 HDAC9

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
IFG	SRSF5	exon_skip_104901	-4.514863e-01	1.808168e-02

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RelatedDrugs for HDAC9

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 HDAC9

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 HDAC9

Gene structures and expression levels for HDAC9

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for HDAC9

Open reading frame (ORF) annotation in the exon skipping event for HDAC9

Infer the effects of exon skipping event on protein functional features for HDAC9

3'-UTR located exon skipping events that lost miRNA binding sites in HDAC9

SNVs in the skipped exons for HDAC9

AD stage-associated exon skippint events for HDAC9

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HDAC9

Correlation with RNA binding proteins (RBPs) for HDAC9

RelatedDrugs for HDAC9

RelatedDiseases for HDAC9