ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for RBSN

Gene summary

Gene information	Gene symbol	RBSN
	Gene ID	64145
	Gene name	rabenosyn, RAB effector
	Synonyms	Rabenosyn-5\|ZFYVE20
	Cytomap	3p25.1
	Type of gene	protein-coding
	Description	rabenosyn-5110 kDa proteinFYVE finger-containing Rab5 effector protein rabenosyn-5RAB effector RBSNzinc finger, FYVE domain containing 20
	Modification date	20200313
	UniProtAcc	C9JZZ1, D6RD50, F8WE50, H7C204, Q9H1K0,
	Context

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 RBSN

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.

ENSG00000131381

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	ENST00000507357.1	RBSN-209:protein_coding:RBSN	1.654215e+00	1.033839e+00	9.181978e-05	6.892567e-04
CB	UP	ENST00000449964.6	RBSN-205:lncRNA:RBSN	2.286933e+01	1.073582e+00	4.688568e-04	2.728461e-03

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 RBSN

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_108055	chr3	15080732:15080802:15082367:15082608:15084735:15084896	15082367:15082608
exon_skip_114522	chr3	15096552:15096710:15098119:15098274:15099035:15099133	15098119:15098274
exon_skip_139668	chr3	15078157:15078161:15080732:15080802:15084735:15084896	15080732:15080802
exon_skip_143127	chr3	15090399:15090539:15091339:15091493:15095973:15096288	15091339:15091493
exon_skip_158710	chr3	15085861:15085961:15090399:15090539:15095973:15096288	15090399:15090539
exon_skip_182307	chr3	15096659:15096710:15098119:15098274:15099035:15099133	15098119:15098274
exon_skip_206947	chr3	15096692:15096710:15098119:15098274:15099035:15099133	15098119:15098274
exon_skip_228030	chr3	15080732:15080802:15082367:15082608:15084735:15084890	15082367:15082608
exon_skip_229965	chr3	15078157:15078161:15080732:15080802:15084735:15084890	15080732:15080802
exon_skip_257678	chr3	15085871:15085961:15090399:15090539:15095973:15096288	15090399:15090539
exon_skip_258491	chr3	15074905:15074930:15075606:15075710:15077062:15077164	15075606:15075710
exon_skip_290828	chr3	15096698:15096710:15098119:15098274:15099035:15099133	15098119:15098274
exon_skip_294330	chr3	15095998:15096288:15096535:15096710:15099035:15099133	15096535:15096710
exon_skip_71471	chr3	15085861:15085961:15090399:15090539:15091339:15091493	15090399:15090539
exon_skip_75705	chr3	15078157:15078161:15080732:15080802:15082367:15082440	15080732:15080802

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 RBSN

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
ENST00000476527	15096535	15096710	3UTR-3UTR
ENST00000253699	15082367	15082608	Frame-shift
ENST00000476527	15082367	15082608	Frame-shift
ENST00000253699	15090399	15090539	In-frame
ENST00000476527	15090399	15090539	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
ENST00000253699	15082367	15082608	Frame-shift
ENST00000476527	15082367	15082608	Frame-shift
ENST00000253699	15090399	15090539	In-frame
ENST00000476527	15090399	15090539	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
ENST00000476527	15096535	15096710	3UTR-3UTR
ENST00000253699	15080732	15080802	Frame-shift
ENST00000476527	15080732	15080802	Frame-shift
ENST00000253699	15082367	15082608	Frame-shift
ENST00000476527	15082367	15082608	Frame-shift
ENST00000253699	15075606	15075710	In-frame
ENST00000476527	15075606	15075710	In-frame
ENST00000253699	15090399	15090539	In-frame
ENST00000476527	15090399	15090539	In-frame

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

p-ENSG00000131381_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
ENST00000253699	6695	784	15090399	15090539	763	902	49	96
ENST00000476527	3022	784	15090399	15090539	622	761	49	96

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
ENST00000253699	6695	784	15090399	15090539	763	902	49	96
ENST00000476527	3022	784	15090399	15090539	622	761	49	96

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
ENST00000253699	6695	784	15090399	15090539	763	902	49	96
ENST00000476527	3022	784	15090399	15090539	622	761	49	96
ENST00000253699	6695	784	15075606	15075710	1716	1819	367	401
ENST00000476527	3022	784	15075606	15075710	1575	1678	367	401

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
Q9H1K0	49	96	2	784	Chain	ID=PRO_0000098711;Note=Rabenosyn-5
Q9H1K0	49	96	2	784	Chain	ID=PRO_0000098711;Note=Rabenosyn-5

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
Q9H1K0	49	96	2	784	Chain	ID=PRO_0000098711;Note=Rabenosyn-5
Q9H1K0	49	96	2	784	Chain	ID=PRO_0000098711;Note=Rabenosyn-5

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
Q9H1K0	49	96	2	784	Chain	ID=PRO_0000098711;Note=Rabenosyn-5
Q9H1K0	49	96	2	784	Chain	ID=PRO_0000098711;Note=Rabenosyn-5
Q9H1K0	367	401	209	784	Alternative sequence	ID=VSP_056004;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9H1K0	367	401	209	784	Alternative sequence	ID=VSP_056004;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9H1K0	367	401	2	784	Chain	ID=PRO_0000098711;Note=Rabenosyn-5
Q9H1K0	367	401	2	784	Chain	ID=PRO_0000098711;Note=Rabenosyn-5
Q9H1K0	367	401	378	414	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9H1K0	367	401	378	414	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9H1K0	367	401	264	784	Region	Note=Necessary for interaction with EHD1;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15020713;Dbxref=PMID:15020713
Q9H1K0	367	401	264	784	Region	Note=Necessary for interaction with EHD1;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15020713;Dbxref=PMID:15020713
Q9H1K0	367	401	264	500	Region	Note=Necessary for interaction with RAB4A
Q9H1K0	367	401	264	500	Region	Note=Necessary for interaction with RAB4A

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

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	ENST00000476527	15096535	15096710	hsa-miR-3161	chr3:15096620-15096627	8mer-1a	chr3:15096604-15096627	148.00	-14.73
Mayo	ENST00000476527	15096535	15096710	hsa-miR-200c-5p	chr3:15096702-15096709	8mer-1a	chr3:15096687-15096709	147.00	-17.51
Mayo	ENST00000476527	15096535	15096710	hsa-miR-548x-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
Mayo	ENST00000476527	15096535	15096710	hsa-miR-1276	chr3:15096650-15096657	8mer-1a	chr3:15096636-15096657	149.00	-18.29
Mayo	ENST00000476527	15096535	15096710	hsa-miR-548ae-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
Mayo	ENST00000476527	15096535	15096710	hsa-miR-548j-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
Mayo	ENST00000476527	15096535	15096710	hsa-miR-4795-5p	chr3:15096588-15096595	8mer-1a	chr3:15096573-15096596	161.00	-16.97
Mayo	ENST00000476527	15096535	15096710	hsa-miR-548aq-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
Mayo	ENST00000476527	15096535	15096710	hsa-miR-548ah-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
Mayo	ENST00000476527	15096535	15096710	hsa-miR-548aj-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
Mayo	ENST00000476527	15096535	15096710	hsa-miR-550a-3p	chr3:15096702-15096709	8mer-1a	chr3:15096687-15096709	147.00	-17.51
Mayo	ENST00000476527	15096535	15096710	hsa-miR-548am-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
Mayo	ENST00000476527	15096535	15096710	hsa-miR-361-3p	chr3:15096600-15096607	8mer-1a	chr3:15096584-15096607	145.00	-21.22
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-3161	chr3:15096620-15096627	8mer-1a	chr3:15096604-15096627	148.00	-14.73
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-200c-5p	chr3:15096702-15096709	8mer-1a	chr3:15096687-15096709	147.00	-17.51
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-548x-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-1276	chr3:15096650-15096657	8mer-1a	chr3:15096636-15096657	149.00	-18.29
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-548ae-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-548j-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-4795-5p	chr3:15096588-15096595	8mer-1a	chr3:15096573-15096596	161.00	-16.97
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-548aq-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-548ah-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-548aj-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-550a-3p	chr3:15096702-15096709	8mer-1a	chr3:15096687-15096709	147.00	-17.51
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-548am-3p	chr3:15096636-15096643	8mer-1a	chr3:15096636-15096657	149.00	-18.29
ROSMAP	ENST00000476527	15096535	15096710	hsa-miR-361-3p	chr3:15096600-15096607	8mer-1a	chr3:15096584-15096607	145.00	-21.22

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SNVs in the skipped exons for RBSN

- 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 RBSN

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 RBSN

sQTL information located at the skipped exons.

Tissue type	Exon skip ID	SNP id	Location	P-value	FDR
DLPFC	exon_skip_143127	rs6798961	chr3:15118495	9.493926e-05	8.078930e-03

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Correlation with RNA binding proteins (RBPs) for RBSN

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	RBM6	exon_skip_228030	-4.932265e-01	1.241760e-10
CB	CNOT4	exon_skip_228030	-4.377290e-01	1.905066e-08
CB	PCBP1	exon_skip_228030	-4.406577e-01	1.493013e-08
HCC	ZNF326	exon_skip_108055	-4.013210e-01	8.587004e-12
HCC	RBM6	exon_skip_108055	-4.234163e-01	4.395785e-13
HCC	EIF4G2	exon_skip_108055	-4.557903e-01	3.744644e-15
HCC	SRSF4	exon_skip_108055	-4.049854e-01	5.324472e-12
HCC	RBMS2	exon_skip_114522	5.321336e-01	3.833018e-21
HCC	RBM6	exon_skip_114522	5.517222e-01	6.584839e-23
HCC	RBM5	exon_skip_114522	5.476522e-01	1.566142e-22
HCC	KHDRBS3	exon_skip_114522	4.153480e-01	1.100491e-12
HCC	RBM41	exon_skip_114522	4.005760e-01	7.910509e-12
HCC	HNRNPF	exon_skip_114522	4.496454e-01	7.649885e-15
IFG	MSI1	exon_skip_143127	4.012152e-01	3.433938e-02
IFG	RBM6	exon_skip_182307	4.270253e-01	2.342953e-02
IFG	PTBP3	exon_skip_182307	4.180377e-01	2.685043e-02
PCC	RBMS2	exon_skip_290828	4.673759e-01	1.103422e-12
TC	KHDRBS2	exon_skip_206947	-5.573672e-01	4.119323e-14
TC	HNRNPA0	exon_skip_206947	-4.769886e-01	3.071672e-10
TC	HNRNPD	exon_skip_206947	-4.640359e-01	1.052541e-09
TC	HNRNPH2	exon_skip_206947	-4.778911e-01	2.813624e-10

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RelatedDrugs for RBSN

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 RBSN

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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