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	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

Gene summary for RPH3A

Gene summary

Gene information	Gene symbol	RPH3A
	Gene ID	22895
	Gene name	rabphilin 3A
	Synonyms	-
	Cytomap	12q24.13
	Type of gene	protein-coding
	Description	rabphilin-3Aexophilin-1rabphilin 3A homolog
	Modification date	20200313
	UniProtAcc	A0A024RBK6, F8VNP7, F8VNU2, F8VNW3, F8VP47, F8VR41, F8VRJ1, F8VTR7, F8VV58, F8VVK8, F8VZS2, F8W045, F8W116, F8W131, F8W1A3, F8W1K7, Q6PJY8, Q6PKD5, Q9Y2J0,
	Context	- 24200817(Decreased rabphilin 3A immunoreactivity in Alzheimer's disease is associated with Abeta burden)

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 RPH3A

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.

ENSG00000089169

Differentially expressed gene analysis across multiple brain tissues between AD and control.

***cutpoints = c(0, 0.0001, 0.001, 0.01, 1), symbols = c("****", "***", "**", "ns")

Tissue type	DEG direction	Base mean exp.	log2FC(AD/control)	P-value	Adj. p-value
PG	DOWN	5.987724e+02	-1.079061e+00	7.349832e-16	1.551201e-12

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
PG	DOWN	ENST00000549913.6	RPH3A-217:lncRNA:RPH3A	2.278060e+01	-1.087074e+00	2.772119e-08	5.435961e-06
PG	DOWN	ENST00000551052.5	RPH3A-219:protein_coding:RPH3A	1.065789e+02	-1.070804e+00	1.889691e-05	8.039386e-04
PG	DOWN	ENST00000543106.6	RPH3A-203:protein_coding:RPH3A	1.376815e+02	-1.033732e+00	3.488810e-05	1.257050e-03
PG	DOWN	ENST00000547728.5	RPH3A-210:protein_coding:RPH3A	1.901796e+01	-1.662471e+00	7.365507e-05	2.189240e-03
PG	DOWN	ENST00000389385.9	RPH3A-201:protein_coding:RPH3A	1.858623e+02	-1.093083e+00	1.112998e-04	2.972231e-03
PG	DOWN	ENST00000546687.1	RPH3A-205:retained_intron:RPH3A	3.928541e+00	-9.154033e-01	3.482489e-04	6.823530e-03
CB	UP	ENST00000552667.5	RPH3A-224:protein_coding:RPH3A	8.658575e+00	1.043887e+00	5.774242e-05	4.645458e-04
CB	UP	ENST00000550901.5	RPH3A-218:protein_coding:RPH3A	3.267784e+00	9.471017e-01	1.228917e-03	6.142243e-03
CB	UP	ENST00000553114.5	RPH3A-227:protein_coding:RPH3A	1.413727e+00	1.011600e+00	4.396050e-03	1.770389e-02
TC	DOWN	ENST00000552667.5	RPH3A-224:protein_coding:RPH3A	3.910848e+00	-1.131974e+00	9.414208e-04	9.440700e-03
TC	DOWN	ENST00000549913.6	RPH3A-217:lncRNA:RPH3A	1.565069e+01	-8.136267e-01	2.556683e-03	2.021190e-02
TC	DOWN	ENST00000552755.1	RPH3A-226:lncRNA:RPH3A	1.100716e+00	-1.012490e+00	5.503845e-03	3.601060e-02
TC	DOWN	ENST00000551052.5	RPH3A-219:protein_coding:RPH3A	3.413005e+00	-1.010709e+00	7.155673e-03	4.375324e-02
TC	DOWN	ENST00000549324.1	RPH3A-214:retained_intron:RPH3A	1.308164e+02	-9.449717e-01	7.411554e-03	4.489030e-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 RPH3A

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_110639	chr12	112828301:112828389:112836491:112836502:112847696:112847731	112836491:112836502
exon_skip_115034	chr12	112894578:112894659:112895777:112895873:112896650:112896914	112895777:112895873
exon_skip_12216	chr12	112649414:112649463:112651767:112651827:112718006:112718087	112651767:112651827
exon_skip_135825	chr12	112651767:112651827:112792143:112792263:112828301:112828355	112792143:112792263
exon_skip_139356	chr12	112879119:112879198:112881772:112881846:112883293:112883343	112881772:112881846
exon_skip_14149	chr12	112792247:112792263:112828301:112828389:112847696:112847731	112828301:112828389
exon_skip_142443	chr12	112792247:112792263:112813322:112813385:112828301:112828355	112813322:112813385
exon_skip_144955	chr12	112792143:112792263:112828301:112828389:112836491:112836502	112828301:112828389
exon_skip_208753	chr12	112651767:112651827:112718006:112718087:112828301:112828355	112718006:112718087
exon_skip_211687	chr12	112575265:112575319:112617725:112617842:112649414:112649463	112617725:112617842
exon_skip_221364	chr12	112792247:112792263:112836491:112836502:112847696:112847731	112836491:112836502
exon_skip_232558	chr12	112651767:112651827:112792143:112792263:112828301:112828388	112792143:112792263
exon_skip_237953	chr12	112887797:112887923:112890024:112890080:112890849:112891003	112890024:112890080
exon_skip_242510	chr12	112792185:112792263:112813322:112813385:112828301:112828388	112813322:112813385
exon_skip_264440	chr12	112792185:112792263:112813322:112813385:112828301:112828389	112813322:112813385
exon_skip_281403	chr12	112649414:112649463:112651767:112651827:112792143:112792263	112651767:112651827
exon_skip_28225	chr12	112651767:112651827:112718006:112718087:112828301:112828389	112718006:112718087
exon_skip_39815	chr12	112792247:112792263:112828301:112828389:112836491:112836502	112828301:112828389
exon_skip_45244	chr12	112575265:112575319:112792143:112792263:112828301:112828355	112792143:112792263
exon_skip_56065	chr12	112651767:112651827:112718006:112718087:112828301:112828388	112718006:112718087
exon_skip_70430	chr12	112575265:112575319:112617725:112617842:112792143:112792169	112617725:112617842
exon_skip_79027	chr12	112651767:112651827:112792143:112792263:112828301:112828389	112792143:112792263
exon_skip_93939	chr12	112836499:112836502:112847696:112847842:112865414:112865432	112847696:112847842
exon_skip_9910	chr12	112575265:112575319:112617725:112617842:112792143:112792263	112617725:112617842

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 RPH3A

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
ENST00000389385	112828301	112828389	5CDS-5UTR
ENST00000415485	112828301	112828389	5CDS-5UTR
ENST00000543106	112828301	112828389	5CDS-5UTR
ENST00000543106	112792143	112792263	5UTR-5UTR
ENST00000389385	112895777	112895873	Frame-shift
ENST00000415485	112895777	112895873	Frame-shift
ENST00000543106	112895777	112895873	Frame-shift
ENST00000389385	112836491	112836502	In-frame
ENST00000415485	112836491	112836502	In-frame
ENST00000543106	112836491	112836502	In-frame
ENST00000389385	112847696	112847842	In-frame
ENST00000415485	112847696	112847842	In-frame
ENST00000543106	112847696	112847842	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
ENST00000543106	112792143	112792263	5UTR-5UTR
ENST00000389385	112836491	112836502	In-frame
ENST00000415485	112836491	112836502	In-frame
ENST00000543106	112836491	112836502	In-frame
ENST00000389385	112847696	112847842	In-frame
ENST00000415485	112847696	112847842	In-frame
ENST00000543106	112847696	112847842	In-frame
ENST00000389385	112881772	112881846	In-frame
ENST00000415485	112881772	112881846	In-frame
ENST00000543106	112881772	112881846	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
ENST00000389385	112828301	112828389	5CDS-5UTR
ENST00000415485	112828301	112828389	5CDS-5UTR
ENST00000543106	112828301	112828389	5CDS-5UTR
ENST00000543106	112792143	112792263	5UTR-5UTR
ENST00000389385	112895777	112895873	Frame-shift
ENST00000415485	112895777	112895873	Frame-shift
ENST00000543106	112895777	112895873	Frame-shift
ENST00000389385	112836491	112836502	In-frame
ENST00000415485	112836491	112836502	In-frame
ENST00000543106	112836491	112836502	In-frame
ENST00000389385	112847696	112847842	In-frame
ENST00000415485	112847696	112847842	In-frame
ENST00000543106	112847696	112847842	In-frame
ENST00000389385	112890024	112890080	In-frame
ENST00000415485	112890024	112890080	In-frame
ENST00000543106	112890024	112890080	In-frame

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Infer the effects of exon skipping event on protein functional features for RPH3A

p-ENSG00000089169_img4.png

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
ENST00000389385	4696	694	112847696	112847842	582	727	28	76
ENST00000415485	4469	694	112847696	112847842	351	496	28	76
ENST00000543106	2598	694	112847696	112847842	447	592	28	76

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
ENST00000389385	4696	694	112847696	112847842	582	727	28	76
ENST00000415485	4469	694	112847696	112847842	351	496	28	76
ENST00000543106	2598	694	112847696	112847842	447	592	28	76
ENST00000389385	4696	694	112881772	112881846	1750	1823	417	442
ENST00000415485	4469	694	112881772	112881846	1519	1592	417	442
ENST00000543106	2598	694	112881772	112881846	1615	1688	417	442

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
ENST00000389385	4696	694	112847696	112847842	582	727	28	76
ENST00000415485	4469	694	112847696	112847842	351	496	28	76
ENST00000543106	2598	694	112847696	112847842	447	592	28	76
ENST00000389385	4696	694	112890024	112890080	2062	2117	521	540
ENST00000415485	4469	694	112890024	112890080	1831	1886	521	540
ENST00000543106	2598	694	112890024	112890080	1927	1982	521	540

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
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00234
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00234
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00234

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
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00234
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00234
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00234
Q9Y2J0	417	442	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	417	442	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	417	442	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	417	442	394	498	Domain	Note=C2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00041
Q9Y2J0	417	442	394	498	Domain	Note=C2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00041
Q9Y2J0	417	442	394	498	Domain	Note=C2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00041
Q9Y2J0	417	442	422	422	Metal binding	Note=Calcium 1%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708
Q9Y2J0	417	442	422	422	Metal binding	Note=Calcium 1%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708
Q9Y2J0	417	442	422	422	Metal binding	Note=Calcium 1%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708
Q9Y2J0	417	442	423	423	Metal binding	Note=Calcium 1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708
Q9Y2J0	417	442	423	423	Metal binding	Note=Calcium 1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708
Q9Y2J0	417	442	423	423	Metal binding	Note=Calcium 1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708
Q9Y2J0	417	442	423	423	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708
Q9Y2J0	417	442	423	423	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708
Q9Y2J0	417	442	423	423	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708
Q9Y2J0	417	442	429	429	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708
Q9Y2J0	417	442	429	429	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708
Q9Y2J0	417	442	429	429	Metal binding	Note=Calcium 2;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47708

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
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	24	28	Alternative sequence	ID=VSP_021016;Note=In isoform 2. NDKEQ->K;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00234
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00234
Q9Y2J0	28	76	44	160	Domain	Note=RabBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00234
Q9Y2J0	521	540	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	521	540	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	521	540	1	694	Chain	ID=PRO_0000190227;Note=Rabphilin-3A
Q9Y2J0	521	540	539	539	Metal binding	Note=Calcium 3%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47709
Q9Y2J0	521	540	539	539	Metal binding	Note=Calcium 3%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47709
Q9Y2J0	521	540	539	539	Metal binding	Note=Calcium 3%3B via carbonyl oxygen;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P47709

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3'-UTR located exon skipping events that lost miRNA binding sites in RPH3A

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 RPH3A

- 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 RPH3A

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 RPH3A

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 RPH3A

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for RPH3A

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 RPH3A

Diseases associated with this gene. (DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

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