ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SNX5

Gene summary

Gene information	Gene symbol	SNX5
	Gene ID	27131
	Gene name	sorting nexin 5
	Synonyms	-
	Cytomap	20p11.23
	Type of gene	protein-coding
	Description	sorting nexin-5
	Modification date	20200320
	UniProtAcc	A0A087WUY5, A0A0S2Z5F1, Q5QPE4, Q5QPE5, Q6P5V6, Q9Y5X3, U3KQL0, U3KQP5,
	Context

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

Gene	GO ID	GO term	PubMed ID
SNX5	GO:0006907	pinocytosis	18854019

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Gene structures and expression levels for SNX5

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.

ENSG00000089006

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	ENST00000484809.1	SNX5-212:retained_intron:SNX5	3.344064e+02	-1.253302e+00	4.121081e-15	1.734207e-12

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 SNX5

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_107815	chr20	17943110:17943195:17944122:17944144:17947486:17947621	17944122:17944144
exon_skip_141054	chr20	17948890:17948976:17949064:17949103:17950132:17950207	17949064:17949103
exon_skip_157985	chr20	17950322:17950396:17951021:17951327:17951500:17951595	17951021:17951327
exon_skip_158165	chr20	17947486:17947645:17948890:17948976:17949064:17949103	17948890:17948976
exon_skip_162510	chr20	17950132:17950207:17950291:17950396:17951500:17951537	17950291:17950396
exon_skip_199290	chr20	17952587:17952710:17953996:17954117:17955365:17955475	17953996:17954117
exon_skip_202011	chr20	17952587:17952710:17953996:17954223:17955365:17955475	17953996:17954223
exon_skip_225182	chr20	17950291:17950396:17951021:17951327:17951500:17951537	17951021:17951327
exon_skip_233080	chr20	17950322:17950396:17951021:17951327:17951500:17951537	17951021:17951327
exon_skip_52620	chr20	17953996:17954117:17955365:17955475:17956933:17957037	17955365:17955475
exon_skip_76586	chr20	17952587:17952710:17953996:17954231:17955365:17955475	17953996:17954231
exon_skip_83067	chr20	17951500:17951595:17952587:17952710:17953996:17954024	17952587:17952710

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 SNX5

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
ENST00000377759	17949064	17949103	Frame-shift
ENST00000377768	17949064	17949103	Frame-shift
ENST00000377759	17950291	17950396	Frame-shift
ENST00000377768	17950291	17950396	Frame-shift
ENST00000377759	17952587	17952710	Frame-shift
ENST00000377768	17952587	17952710	Frame-shift
ENST00000377759	17953996	17954117	Frame-shift
ENST00000377768	17953996	17954117	Frame-shift
ENST00000377759	17955365	17955475	In-frame
ENST00000377768	17955365	17955475	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
ENST00000377759	17949064	17949103	Frame-shift
ENST00000377768	17949064	17949103	Frame-shift
ENST00000377759	17953996	17954117	Frame-shift
ENST00000377768	17953996	17954117	Frame-shift
ENST00000377759	17955365	17955475	In-frame
ENST00000377768	17955365	17955475	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
ENST00000377759	17949064	17949103	Frame-shift
ENST00000377768	17949064	17949103	Frame-shift
ENST00000377759	17950291	17950396	Frame-shift
ENST00000377768	17950291	17950396	Frame-shift
ENST00000377759	17953996	17954117	Frame-shift
ENST00000377768	17953996	17954117	Frame-shift
ENST00000377759	17948890	17948976	In-frame
ENST00000377768	17948890	17948976	In-frame
ENST00000377759	17955365	17955475	In-frame
ENST00000377768	17955365	17955475	In-frame

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Infer the effects of exon skipping event on protein functional features for SNX5

p-ENSG00000089006_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
ENST00000377759	2287	404	17955365	17955475	452	561	52	88
ENST00000377768	2305	404	17955365	17955475	470	579	52	88

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
ENST00000377759	2287	404	17955365	17955475	452	561	52	88
ENST00000377768	2305	404	17955365	17955475	470	579	52	88

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
ENST00000377759	2287	404	17955365	17955475	452	561	52	88
ENST00000377768	2305	404	17955365	17955475	470	579	52	88
ENST00000377759	2287	404	17948890	17948976	1127	1212	277	305
ENST00000377768	2305	404	17948890	17948976	1145	1230	277	305

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
Q9Y5X3	52	88	18	126	Alternative sequence	ID=VSP_056386;Note=In isoform 2. LRSVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLIETTDYAGLIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQ->VRSSQPQTPGRAALRAPGSLHSFPCASIGRGCSPPSPAREAPVRPGRPLSLVFTEGCPGESLWMSRILLGQNQRRGTLAPAQAPVPSGLGEMISGDPGMFFLKLSSASW;O
Q9Y5X3	52	88	18	126	Alternative sequence	ID=VSP_056386;Note=In isoform 2. LRSVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLIETTDYAGLIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQ->VRSSQPQTPGRAALRAPGSLHSFPCASIGRGCSPPSPAREAPVRPGRPLSLVFTEGCPGESLWMSRILLGQNQRRGTLAPAQAPVPSGLGEMISGDPGMFFLKLSSASW;O
Q9Y5X3	52	88	44	53	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	44	53	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	56	59	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5TGH
Q9Y5X3	52	88	56	59	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5TGH
Q9Y5X3	52	88	61	68	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	61	68	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	2	404	Chain	ID=PRO_0000213844;Note=Sorting nexin-5
Q9Y5X3	52	88	2	404	Chain	ID=PRO_0000213844;Note=Sorting nexin-5
Q9Y5X3	52	88	25	172	Domain	Note=PX;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00147
Q9Y5X3	52	88	25	172	Domain	Note=PX;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00147
Q9Y5X3	52	88	69	80	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	69	80	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	83	85	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	83	85	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2

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
Q9Y5X3	52	88	18	126	Alternative sequence	ID=VSP_056386;Note=In isoform 2. LRSVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLIETTDYAGLIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQ->VRSSQPQTPGRAALRAPGSLHSFPCASIGRGCSPPSPAREAPVRPGRPLSLVFTEGCPGESLWMSRILLGQNQRRGTLAPAQAPVPSGLGEMISGDPGMFFLKLSSASW;O
Q9Y5X3	52	88	18	126	Alternative sequence	ID=VSP_056386;Note=In isoform 2. LRSVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLIETTDYAGLIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQ->VRSSQPQTPGRAALRAPGSLHSFPCASIGRGCSPPSPAREAPVRPGRPLSLVFTEGCPGESLWMSRILLGQNQRRGTLAPAQAPVPSGLGEMISGDPGMFFLKLSSASW;O
Q9Y5X3	52	88	44	53	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	44	53	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	56	59	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5TGH
Q9Y5X3	52	88	56	59	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5TGH
Q9Y5X3	52	88	61	68	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	61	68	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	2	404	Chain	ID=PRO_0000213844;Note=Sorting nexin-5
Q9Y5X3	52	88	2	404	Chain	ID=PRO_0000213844;Note=Sorting nexin-5
Q9Y5X3	52	88	25	172	Domain	Note=PX;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00147
Q9Y5X3	52	88	25	172	Domain	Note=PX;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00147
Q9Y5X3	52	88	69	80	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	69	80	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	83	85	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	83	85	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2

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
Q9Y5X3	52	88	18	126	Alternative sequence	ID=VSP_056386;Note=In isoform 2. LRSVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLIETTDYAGLIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQ->VRSSQPQTPGRAALRAPGSLHSFPCASIGRGCSPPSPAREAPVRPGRPLSLVFTEGCPGESLWMSRILLGQNQRRGTLAPAQAPVPSGLGEMISGDPGMFFLKLSSASW;O
Q9Y5X3	52	88	18	126	Alternative sequence	ID=VSP_056386;Note=In isoform 2. LRSVSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTLIETTDYAGLIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQ->VRSSQPQTPGRAALRAPGSLHSFPCASIGRGCSPPSPAREAPVRPGRPLSLVFTEGCPGESLWMSRILLGQNQRRGTLAPAQAPVPSGLGEMISGDPGMFFLKLSSASW;O
Q9Y5X3	52	88	44	53	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	44	53	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	56	59	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5TGH
Q9Y5X3	52	88	56	59	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5TGH
Q9Y5X3	52	88	61	68	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	61	68	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	2	404	Chain	ID=PRO_0000213844;Note=Sorting nexin-5
Q9Y5X3	52	88	2	404	Chain	ID=PRO_0000213844;Note=Sorting nexin-5
Q9Y5X3	52	88	25	172	Domain	Note=PX;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00147
Q9Y5X3	52	88	25	172	Domain	Note=PX;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00147
Q9Y5X3	52	88	69	80	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	69	80	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	83	85	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	52	88	83	85	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5WY2
Q9Y5X3	277	305	127	404	Alternative sequence	ID=VSP_056387;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|Ref.2;Dbxref=PMID:14702039
Q9Y5X3	277	305	127	404	Alternative sequence	ID=VSP_056387;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|Ref.2;Dbxref=PMID:14702039
Q9Y5X3	277	305	2	404	Chain	ID=PRO_0000213844;Note=Sorting nexin-5
Q9Y5X3	277	305	2	404	Chain	ID=PRO_0000213844;Note=Sorting nexin-5
Q9Y5X3	277	305	202	404	Domain	Note=BAR
Q9Y5X3	277	305	202	404	Domain	Note=BAR
Q9Y5X3	277	305	280	280	Mutagenesis	Note=Enables homodimerization%3B when associated with A-383. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23085988;Dbxref=PMID:23085988
Q9Y5X3	277	305	280	280	Mutagenesis	Note=Enables homodimerization%3B when associated with A-383. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23085988;Dbxref=PMID:23085988
Q9Y5X3	277	305	279	279	Sequence conflict	Note=V->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9Y5X3	277	305	279	279	Sequence conflict	Note=V->L;Ontology_term=ECO:0000305;evidence=ECO:0000305

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3'-UTR located exon skipping events that lost miRNA binding sites in SNX5

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 SNX5

- 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 SNX5

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 SNX5

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 SNX5

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for SNX5

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 SNX5

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 SNX5

Gene structures and expression levels for SNX5

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SNX5

Open reading frame (ORF) annotation in the exon skipping event for SNX5

Infer the effects of exon skipping event on protein functional features for SNX5

3'-UTR located exon skipping events that lost miRNA binding sites in SNX5

SNVs in the skipped exons for SNX5

AD stage-associated exon skippint events for SNX5

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SNX5

Correlation with RNA binding proteins (RBPs) for SNX5

RelatedDrugs for SNX5

RelatedDiseases for SNX5