ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for ATXN1

Gene summary

Gene information	Gene symbol	ATXN1
	Gene ID	6310
	Gene name	ataxin 1
	Synonyms	ATX1\|D6S504E\|SCA1
	Cytomap	6p22.3
	Type of gene	protein-coding
	Description	ataxin-1alternative ataxin1spinocerebellar ataxia type 1 protein
	Modification date	20200313
	UniProtAcc	A0A024R005, A0A2R8YCF3, P54253, Q96C81, Q96FF1,
	Context	- 31442405(Loss of Ataxin-1 Potentiates Alzheimer's Pathogenesis by Elevating Cerebral BACE1 Transcription)

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

Gene	GO ID	GO term	PubMed ID
ATXN1	GO:0045892	negative regulation of transcription, DNA-templated	15016912
ATXN1	GO:0051168	nuclear export	15615787

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Gene structures and expression levels for ATXN1

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.

ENSG00000124788

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	ENST00000492857.1	ATXN1-208:lncRNA:ATXN1	2.100392e+00	8.986250e-01	3.908013e-03	1.604816e-02

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 ATXN1

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_105853	chr6	16485988:16486109:16522627:16522688:16585780:16585907	16522627:16522688
exon_skip_112954	chr6	16299112:16306859:16326394:16328470:16485972:16486109	16326394:16328470
exon_skip_118020	chr6	16306337:16306859:16326394:16328470:16485972:16486109	16326394:16328470
exon_skip_13102	chr6	16753233:16753347:16754043:16754091:16754640:16754746	16754043:16754091
exon_skip_134800	chr6	16486019:16486109:16522627:16522688:16585780:16585907	16522627:16522688
exon_skip_197746	chr6	16739602:16739918:16753233:16753347:16761298:16761370	16753233:16753347
exon_skip_204752	chr6	16657776:16657901:16753233:16753347:16761298:16761370	16753233:16753347
exon_skip_228513	chr6	16754043:16754091:16754640:16754746:16761298:16761370	16754640:16754746
exon_skip_229302	chr6	16738465:16739918:16753233:16753347:16761298:16761491	16753233:16753347
exon_skip_233498	chr6	16753233:16753347:16754043:16754091:16761298:16761370	16754043:16754091
exon_skip_239770	chr6	16522627:16522688:16585780:16585907:16657776:16657901	16585780:16585907
exon_skip_24944	chr6	16585786:16585907:16657776:16657901:16753233:16753308	16657776:16657901
exon_skip_268633	chr6	16485972:16486109:16522627:16522688:16585780:16585907	16522627:16522688
exon_skip_74052	chr6	16585780:16585907:16657776:16657901:16753233:16753308	16657776:16657901

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 ATXN1

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
ENST00000244769	16326394	16328470	3UTR-3CDS
ENST00000436367	16326394	16328470	3UTR-3CDS
ENST00000244769	16522627	16522688	3UTR-3UTR
ENST00000436367	16522627	16522688	3UTR-3UTR
ENST00000244769	16585780	16585907	3UTR-3UTR
ENST00000436367	16585780	16585907	3UTR-3UTR
ENST00000244769	16657776	16657901	3UTR-3UTR
ENST00000436367	16657776	16657901	3UTR-3UTR
ENST00000436367	16753233	16753347	3UTR-3UTR

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
ENST00000244769	16522627	16522688	3UTR-3UTR
ENST00000436367	16522627	16522688	3UTR-3UTR
ENST00000244769	16657776	16657901	3UTR-3UTR
ENST00000436367	16657776	16657901	3UTR-3UTR
ENST00000436367	16753233	16753347	3UTR-3UTR

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
ENST00000244769	16326394	16328470	3UTR-3CDS
ENST00000436367	16326394	16328470	3UTR-3CDS
ENST00000244769	16522627	16522688	3UTR-3UTR
ENST00000436367	16522627	16522688	3UTR-3UTR
ENST00000244769	16657776	16657901	3UTR-3UTR
ENST00000436367	16657776	16657901	3UTR-3UTR
ENST00000436367	16753233	16753347	3UTR-3UTR

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Infer the effects of exon skipping event on protein functional features for ATXN1

p-ENSG00000124788_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

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

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3'-UTR located exon skipping events that lost miRNA binding sites in ATXN1

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
Mayo	ENST00000436367	16753233	16753347	hsa-miR-3120-3p	chr6:16753277-16753284	8mer-1a	chr6:16753263-16753287	153.00	-22.52
Mayo	ENST00000436367	16753233	16753347	hsa-let-7a-2-3p	chr6:16753280-16753287	8mer-1a	chr6:16753263-16753287	153.00	-22.52
Mayo	ENST00000436367	16657776	16657901	hsa-miR-3167	chr6:16657814-16657821	8mer-1a	chr6:16657811-16657834	152.00	-23.49
Mayo	ENST00000436367	16522627	16522688	hsa-miR-6502-3p	chr6:16522667-16522674	8mer-1a	chr6:16522655-16522674	156.00	-16.46
Mayo	ENST00000436367	16657776	16657901	hsa-miR-127-5p	chr6:16657865-16657872	8mer-1a	chr6:16657845-16657872	149.00	-18.95
Mayo	ENST00000436367	16753233	16753347	hsa-miR-324-3p	chr6:16753261-16753268	8mer-1a	chr6:16753248-16753269	175.00	-29.62
Mayo	ENST00000436367	16753233	16753347	hsa-miR-4733-3p	chr6:16753323-16753330	8mer-1a	chr6:16753310-16753335	178.00	-34.34
Mayo	ENST00000436367	16657776	16657901	hsa-miR-512-3p	chr6:16657850-16657857	8mer-1a	chr6:16657836-16657857	156.00	-19.29
Mayo	ENST00000436367	16753233	16753347	hsa-miR-5193	chr6:16753267-16753274	8mer-1a	chr6:16753252-16753274	155.00	-27.28
Mayo	ENST00000436367	16753233	16753347	hsa-let-7g-3p	chr6:16753280-16753287	8mer-1a	chr6:16753263-16753287	153.00	-22.52
Mayo	ENST00000436367	16657776	16657901	hsa-miR-4473	chr6:16657851-16657858	8mer-1a	chr6:16657845-16657872	149.00	-18.95
Mayo	ENST00000436367	16657776	16657901	hsa-miR-876-5p	chr6:16657814-16657821	8mer-1a	chr6:16657811-16657834	152.00	-23.49
Mayo	ENST00000436367	16753233	16753347	hsa-miR-4536-3p	chr6:16753335-16753342	8mer-1a	chr6:16753322-16753342	154.00	-19.21
Mayo	ENST00000436367	16753233	16753347	hsa-miR-224-5p	chr6:16753328-16753335	8mer-1a	chr6:16753310-16753335	178.00	-34.34
MSBB	ENST00000436367	16753233	16753347	hsa-miR-3120-3p	chr6:16753277-16753284	8mer-1a	chr6:16753263-16753287	153.00	-22.52
MSBB	ENST00000436367	16753233	16753347	hsa-let-7a-2-3p	chr6:16753280-16753287	8mer-1a	chr6:16753263-16753287	153.00	-22.52
MSBB	ENST00000436367	16657776	16657901	hsa-miR-3167	chr6:16657814-16657821	8mer-1a	chr6:16657811-16657834	152.00	-23.49
MSBB	ENST00000436367	16522627	16522688	hsa-miR-6502-3p	chr6:16522667-16522674	8mer-1a	chr6:16522655-16522674	156.00	-16.46
MSBB	ENST00000436367	16657776	16657901	hsa-miR-127-5p	chr6:16657865-16657872	8mer-1a	chr6:16657845-16657872	149.00	-18.95
MSBB	ENST00000436367	16753233	16753347	hsa-miR-324-3p	chr6:16753261-16753268	8mer-1a	chr6:16753248-16753269	175.00	-29.62
MSBB	ENST00000436367	16753233	16753347	hsa-miR-4733-3p	chr6:16753323-16753330	8mer-1a	chr6:16753310-16753335	178.00	-34.34
MSBB	ENST00000436367	16657776	16657901	hsa-miR-512-3p	chr6:16657850-16657857	8mer-1a	chr6:16657836-16657857	156.00	-19.29
MSBB	ENST00000436367	16753233	16753347	hsa-miR-5193	chr6:16753267-16753274	8mer-1a	chr6:16753252-16753274	155.00	-27.28
MSBB	ENST00000436367	16753233	16753347	hsa-let-7g-3p	chr6:16753280-16753287	8mer-1a	chr6:16753263-16753287	153.00	-22.52
MSBB	ENST00000436367	16657776	16657901	hsa-miR-4473	chr6:16657851-16657858	8mer-1a	chr6:16657845-16657872	149.00	-18.95
MSBB	ENST00000436367	16657776	16657901	hsa-miR-876-5p	chr6:16657814-16657821	8mer-1a	chr6:16657811-16657834	152.00	-23.49
MSBB	ENST00000436367	16753233	16753347	hsa-miR-4536-3p	chr6:16753335-16753342	8mer-1a	chr6:16753322-16753342	154.00	-19.21
MSBB	ENST00000436367	16753233	16753347	hsa-miR-224-5p	chr6:16753328-16753335	8mer-1a	chr6:16753310-16753335	178.00	-34.34
ROSMAP	ENST00000436367	16753233	16753347	hsa-miR-3120-3p	chr6:16753277-16753284	8mer-1a	chr6:16753263-16753287	153.00	-22.52
ROSMAP	ENST00000436367	16753233	16753347	hsa-let-7a-2-3p	chr6:16753280-16753287	8mer-1a	chr6:16753263-16753287	153.00	-22.52
ROSMAP	ENST00000436367	16657776	16657901	hsa-miR-3167	chr6:16657814-16657821	8mer-1a	chr6:16657811-16657834	152.00	-23.49
ROSMAP	ENST00000436367	16522627	16522688	hsa-miR-6502-3p	chr6:16522667-16522674	8mer-1a	chr6:16522655-16522674	156.00	-16.46
ROSMAP	ENST00000436367	16657776	16657901	hsa-miR-127-5p	chr6:16657865-16657872	8mer-1a	chr6:16657845-16657872	149.00	-18.95
ROSMAP	ENST00000436367	16585780	16585907	hsa-miR-136-5p	chr6:16585802-16585809	8mer-1a	chr6:16585789-16585813	164.00	-25.18
ROSMAP	ENST00000436367	16585780	16585907	hsa-miR-324-3p	chr6:16585875-16585882	8mer-1a	chr6:16585860-16585883	163.00	-26.67
ROSMAP	ENST00000436367	16753233	16753347	hsa-miR-324-3p	chr6:16753261-16753268	8mer-1a	chr6:16753248-16753269	175.00	-29.62
ROSMAP	ENST00000436367	16753233	16753347	hsa-miR-4733-3p	chr6:16753323-16753330	8mer-1a	chr6:16753310-16753335	178.00	-34.34
ROSMAP	ENST00000436367	16585780	16585907	hsa-miR-21-5p	chr6:16585813-16585820	8mer-1a	chr6:16585805-16585831	156.00	-19.59
ROSMAP	ENST00000436367	16657776	16657901	hsa-miR-512-3p	chr6:16657850-16657857	8mer-1a	chr6:16657836-16657857	156.00	-19.29
ROSMAP	ENST00000436367	16753233	16753347	hsa-miR-5193	chr6:16753267-16753274	8mer-1a	chr6:16753252-16753274	155.00	-27.28
ROSMAP	ENST00000436367	16753233	16753347	hsa-let-7g-3p	chr6:16753280-16753287	8mer-1a	chr6:16753263-16753287	153.00	-22.52
ROSMAP	ENST00000436367	16585780	16585907	hsa-miR-584-5p	chr6:16585809-16585816	8mer-1a	chr6:16585805-16585831	156.00	-19.59
ROSMAP	ENST00000436367	16585780	16585907	hsa-miR-218-2-3p	chr6:16585808-16585815	8mer-1a	chr6:16585805-16585831	156.00	-19.59
ROSMAP	ENST00000436367	16585780	16585907	hsa-miR-590-5p	chr6:16585813-16585820	8mer-1a	chr6:16585805-16585831	156.00	-19.59
ROSMAP	ENST00000436367	16585780	16585907	hsa-miR-597-3p	chr6:16585806-16585813	8mer-1a	chr6:16585789-16585813	164.00	-25.18
ROSMAP	ENST00000436367	16657776	16657901	hsa-miR-4473	chr6:16657851-16657858	8mer-1a	chr6:16657845-16657872	149.00	-18.95
ROSMAP	ENST00000436367	16657776	16657901	hsa-miR-876-5p	chr6:16657814-16657821	8mer-1a	chr6:16657811-16657834	152.00	-23.49
ROSMAP	ENST00000436367	16753233	16753347	hsa-miR-4536-3p	chr6:16753335-16753342	8mer-1a	chr6:16753322-16753342	154.00	-19.21
ROSMAP	ENST00000436367	16753233	16753347	hsa-miR-224-5p	chr6:16753328-16753335	8mer-1a	chr6:16753310-16753335	178.00	-34.34

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SNVs in the skipped exons for ATXN1

- 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 ATXN1

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 ATXN1

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
TC	exon_skip_233498	rs6942123	chr6:16832875	8.560869e-06	2.178370e-03
HCC	exon_skip_233498	rs10434861	chr6:16722711	7.743771e-05	7.356760e-03
HCC	exon_skip_233498	rs10456788	chr6:16750625	1.058851e-04	9.601106e-03

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Correlation with RNA binding proteins (RBPs) for ATXN1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	NUP42	exon_skip_233498	4.605060e-01	1.322669e-08
IFG	RALYL	exon_skip_268633	4.617028e-01	1.338882e-02
IFG	RBM25	exon_skip_204752	4.570473e-01	1.654182e-02
IFG	ELAVL1	exon_skip_204752	4.670544e-01	1.404310e-02
IFG	RBM6	exon_skip_204752	4.750846e-01	1.227163e-02
IFG	TIA1	exon_skip_204752	5.469282e-01	3.155709e-03
IFG	RBM5	exon_skip_204752	6.040973e-01	8.473668e-04
IFG	FUBP1	exon_skip_204752	6.156557e-01	6.298888e-04
IFG	SNRNP70	exon_skip_204752	5.787228e-01	1.564327e-03
IFG	HNRNPF	exon_skip_204752	4.558244e-01	1.687082e-02
IFG	RBM5	exon_skip_233498	-6.965564e-01	4.515147e-04
IFG	IGF2BP3	exon_skip_233498	-4.910459e-01	2.379466e-02
IFG	PABPC1	exon_skip_233498	-6.252844e-01	2.436352e-03
PCC	ELAVL4	exon_skip_204752	-4.673302e-01	1.553782e-11
PCC	RALYL	exon_skip_204752	-4.273871e-01	1.057724e-09
PCC	NOVA1	exon_skip_204752	-4.438564e-01	1.982824e-10
PG	SRSF2	exon_skip_204752	-4.130489e-01	2.899503e-08
PG	ELAVL4	exon_skip_204752	-6.212974e-01	3.299705e-19
PG	ILF2	exon_skip_204752	-4.807155e-01	4.866752e-11
PG	NUP42	exon_skip_204752	-4.062646e-01	5.109611e-08
PG	RALYL	exon_skip_204752	-5.903225e-01	4.631504e-17
PG	HNRNPL	exon_skip_204752	-4.489893e-01	1.159113e-09
PG	CELF1	exon_skip_204752	-4.463816e-01	1.483020e-09
PG	NOVA1	exon_skip_204752	-4.855292e-01	2.922298e-11
TC	ELAVL4	exon_skip_204752	-6.880493e-01	1.733026e-23
TC	RBM6	exon_skip_204752	4.021119e-01	1.631129e-07
TC	NUP42	exon_skip_204752	-5.366953e-01	3.629564e-13
TC	RALYL	exon_skip_204752	-7.247524e-01	5.071836e-27
TC	ESRP1	exon_skip_204752	-5.354930e-01	4.188588e-13
TC	NOVA1	exon_skip_204752	-4.729030e-01	3.514657e-10
TC	NUP42	exon_skip_233498	5.362840e-01	2.549982e-12

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RelatedDrugs for ATXN1

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 ATXN1

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 ATXN1

Gene structures and expression levels for ATXN1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for ATXN1

Open reading frame (ORF) annotation in the exon skipping event for ATXN1

Infer the effects of exon skipping event on protein functional features for ATXN1

3'-UTR located exon skipping events that lost miRNA binding sites in ATXN1

SNVs in the skipped exons for ATXN1

AD stage-associated exon skippint events for ATXN1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ATXN1

Correlation with RNA binding proteins (RBPs) for ATXN1

RelatedDrugs for ATXN1

RelatedDiseases for ATXN1