ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SPG7

Gene summary

Gene information	Gene symbol	SPG7
	Gene ID	6687
	Gene name	SPG7 matrix AAA peptidase subunit, paraplegin
	Synonyms	CAR\|CMAR\|PGN\|SPG5C
	Cytomap	16q24.3
	Type of gene	protein-coding
	Description	parapleginSPG7, paraplegin matrix AAA peptidase subunitcell matrix adhesion regulatorspastic paraplegia 7 (pure and complicated autosomal recessive)spastic paraplegia 7 protein
	Modification date	20200320
	UniProtAcc	A0A087X0F5, A0A2R8Y3M4, A0A2R8Y4L0, A0A2R8Y4L7, A0A2R8Y4M0, A0A2R8Y4M8, A0A2R8Y4Y7, A0A2R8Y4Z7, A0A2R8Y530, A0A2R8Y617, A0A2R8Y632, A0A2R8Y6E8, A0A2R8Y6K2, A0A2R8Y6Z7, A0A2R8Y726, A0A2R8Y729, A0A2R8Y7B8, A0A2R8Y7E2, A0A2R8Y7N2, A0A2R8Y856, A0A2R8YCU3, A0A2R8YDM8, A0A2R8YDQ1, A0A2R8YDS3, A0A2R8YDU1, A0A2R8YDW8, A0A2R8YEH4, A0A2R8YFF4, A0A2R8YFJ7, A0A2R8YFN9, A0A2R8YFQ9, A0A2R8YFW4, A0A2R8YG79, A0A2R8YG90, A0A2R8YGV4, A0A2R8YGZ0, A0A2U3TZH1, H3BMP1, H3BNE4, H3BTR8, H3BTY6, J3KRF6, Q9UQ90,
	Context	- 23176075(Retinal Nerve Fibre Layer Loss in Hereditary Spastic Paraplegias Is Restricted to Complex Phenotypes)

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

Gene

GO ID

GO term

PubMed ID

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Gene structures and expression levels for SPG7

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.

ENSG00000197912

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	ENST00000645742.1	SPG7-267:lncRNA:SPG7	6.592464e+02	-1.366799e+00	2.239290e-07	4.205513e-06
CB	UP	ENST00000646958.1	SPG7-288:retained_intron:SPG7	2.116731e+02	8.244302e-01	2.339732e-05	2.162235e-04
CB	DOWN	ENST00000645977.1	SPG7-274:retained_intron:SPG7	9.374651e+01	-1.165338e+00	5.402776e-04	3.076312e-03
CB	DOWN	ENST00000646399.1	SPG7-278:nonsense_mediated_decay:SPG7	3.523047e+01	-1.512312e+00	6.284156e-03	2.375039e-02
TC	DOWN	ENST00000642984.1	SPG7-231:retained_intron:SPG7	3.462347e+01	-1.049253e+00	1.443679e-03	1.306749e-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 SPG7

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

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 SPG7

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
ENST00000645818	89510490	89510592	Frame-shift
ENST00000645818	89526329	89526468	Frame-shift
ENST00000645818	89529477	89529579	Frame-shift
ENST00000645818	89544648	89544772	Frame-shift
ENST00000645818	89552979	89553135	Frame-shift
ENST00000645818	89548003	89548113	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
ENST00000645818	89529477	89529579	Frame-shift

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
ENST00000645818	89510490	89510592	Frame-shift
ENST00000645818	89526329	89526468	Frame-shift
ENST00000645818	89529477	89529579	Frame-shift
ENST00000645818	89531904	89532066	Frame-shift
ENST00000645818	89544648	89544772	Frame-shift
ENST00000645818	89546658	89546760	Frame-shift
ENST00000645818	89550494	89550609	Frame-shift
ENST00000645818	89552979	89553135	Frame-shift
ENST00000645818	89512948	89513037	In-frame
ENST00000645818	89548003	89548113	In-frame

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Infer the effects of exon skipping event on protein functional features for SPG7

p-ENSG00000197912_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
ENST00000645818	3376	795	89548003	89548113	1850	1959	518	554

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
ENST00000645818	3376	795	89512948	89513037	584	672	96	125
ENST00000645818	3376	795	89548003	89548113	1850	1959	518	554

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
Q9UQ90	518	554	490	795	Alternative sequence	ID=VSP_009193;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9UQ90	518	554	106	795	Chain	ID=PRO_0000084675;Note=Paraplegin
Q9UQ90	518	554	518	529	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QZ4
Q9UQ90	518	554	545	557	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QZ4
Q9UQ90	518	554	545	545	Natural variant	ID=VAR_063610;Note=F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16534102;Dbxref=dbSNP:rs758338586,PMID:16534102
Q9UQ90	518	554	270	795	Topological domain	Note=Mitochondrial matrix;Ontology_term=ECO:0000255;evidence=ECO:0000255

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
Q9UQ90	96	125	106	795	Chain	ID=PRO_0000084675;Note=Paraplegin
Q9UQ90	96	125	44	105	Propeptide	ID=PRO_0000442305;Note=Removed in mature form;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3ULF4
Q9UQ90	96	125	106	144	Topological domain	Note=Mitochondrial matrix;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UQ90	518	554	490	795	Alternative sequence	ID=VSP_009193;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9UQ90	518	554	106	795	Chain	ID=PRO_0000084675;Note=Paraplegin
Q9UQ90	518	554	518	529	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QZ4
Q9UQ90	518	554	545	557	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2QZ4
Q9UQ90	518	554	545	545	Natural variant	ID=VAR_063610;Note=F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16534102;Dbxref=dbSNP:rs758338586,PMID:16534102
Q9UQ90	518	554	270	795	Topological domain	Note=Mitochondrial matrix;Ontology_term=ECO:0000255;evidence=ECO:0000255

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3'-UTR located exon skipping events that lost miRNA binding sites in SPG7

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 SPG7

- 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 SPG7

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

ADstage

MSBB

IFG

exon_skip_43028

-3.806639e-01

4.567270e-02

chr16

89532581

89532636

89540944

89542279

89544648

89544745

CDR

MSBB

IFG

exon_skip_125143

3.825060e-01

4.454950e-02

chr16

89532581

89532636

89540944

89541384

89544648

89544745

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SPG7

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 SPG7

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	TARDBP	exon_skip_43028	-4.415029e-01	5.700187e-09
CB	ELAVL1	exon_skip_43028	-4.466918e-01	3.592364e-09
CB	U2AF2	exon_skip_43028	-6.334757e-01	3.228461e-19
CB	CNOT4	exon_skip_43028	-5.462091e-01	9.560258e-14
CB	PCBP1	exon_skip_43028	-4.996254e-01	2.023589e-11
CB	TRA2A	exon_skip_43028	-4.926748e-01	4.205799e-11
CB	KHSRP	exon_skip_43028	-4.253073e-01	2.293573e-08
CB	HNRNPA2B1	exon_skip_43028	-5.260701e-01	1.070384e-12
CB	HNRNPC	exon_skip_43028	-5.438519e-01	1.279060e-13
CB	SRSF4	exon_skip_43028	-4.814540e-01	1.324150e-10
CB	HNRNPF	exon_skip_43028	-4.400230e-01	6.493238e-09

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RelatedDrugs for SPG7

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 SPG7

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 SPG7

Gene structures and expression levels for SPG7

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SPG7

Open reading frame (ORF) annotation in the exon skipping event for SPG7

Infer the effects of exon skipping event on protein functional features for SPG7

3'-UTR located exon skipping events that lost miRNA binding sites in SPG7

SNVs in the skipped exons for SPG7

AD stage-associated exon skippint events for SPG7

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SPG7

Correlation with RNA binding proteins (RBPs) for SPG7

RelatedDrugs for SPG7

RelatedDiseases for SPG7