ExonSkipDB Logo

Home

Download

Statistics

Landscape

Help

Contact

Center for Computational Systems Medicine
leaf

Gene summary

leaf

Gene structures and expression levels

leaf

Exon skipping events with PSIs in TCGA

leaf

Exon skipping events with PSIs in GTEx

leaf

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

leaf

Exon skipping events in the canonical protein sequence

leaf

SNVs in the skipped exons with depth of coverage

leaf

Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

leaf

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

leaf

Related drugs with this gene

leaf

Related diseases with this gene

Gene summary for APP

check button Gene summary
Gene informationGene symbol

APP

Gene ID

351

Gene nameamyloid beta precursor protein
SynonymsAAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4
Cytomap

21q21.3

Type of geneprotein-coding
Descriptionamyloid-beta A4 proteinalzheimer disease amyloid proteinamyloid beta (A4) precursor proteinamyloid beta A4 proteinamyloid precursor proteinbeta-amyloid peptidebeta-amyloid peptide(1-40)beta-amyloid peptide(1-42)beta-amyloid precursor proteincereb
Modification date20180527
UniProtAcc

P05067

ContextPubMed: APP [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
APP

GO:0001934

positive regulation of protein phosphorylation

11404397

APP

GO:0008285

negative regulation of cell proliferation

22944668


Top

Exon skipping events across known transcript of Ensembl for APP from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx 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.
all structure

Top

Gene isoform structures and expression levels for APP

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


Top

Exon skipping events with PSIs in TCGA for APP

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3614012127253824:27254082:27264033:27264180:27269884:2726998527264033:27264180ENSG00000142192.16ENST00000354192.3,ENST00000348990.5,ENST00000448388.2,ENST00000359726.3,ENST00000439274.2,ENST00000440126.3,ENST00000464867.1,ENST00000357903.3,ENST00000358918.3,ENST00000346798.3
exon_skip_3614102127264109:27264180:27269884:27269985:27277335:2727738927269884:27269985ENSG00000142192.16ENST00000354192.3,ENST00000348990.5,ENST00000448388.2,ENST00000359726.3,ENST00000439274.2,ENST00000440126.3,ENST00000357903.3,ENST00000346798.3
exon_skip_3614112127264109:27264180:27269884:27269985:27284052:2728427427269884:27269985ENSG00000142192.16ENST00000456209.2,ENST00000358918.3
exon_skip_3614182127269884:27269985:27277335:27277389:27284052:2728427427277335:27277389ENSG00000142192.16ENST00000354192.3,ENST00000348990.5,ENST00000448388.2,ENST00000359726.3,ENST00000439274.2,ENST00000440126.3,ENST00000357903.3,ENST00000346798.3
exon_skip_3614202127269884:27269985:27284052:27284274:27326903:2732700327284052:27284274ENSG00000142192.16ENST00000456209.2,ENST00000358918.3
exon_skip_3614222127277335:27277389:27284052:27284274:27326903:2732700327284052:27284274ENSG00000142192.16ENST00000354192.3,ENST00000348990.5,ENST00000448388.2,ENST00000359726.3,ENST00000439274.2,ENST00000440126.3,ENST00000357903.3,ENST00000346798.3
exon_skip_3614252127326903:27327003:27327940:27328069:27347382:2734753227327940:27328069ENSG00000142192.16ENST00000354192.3,ENST00000348990.5,ENST00000448388.2,ENST00000359726.3,ENST00000439274.2,ENST00000448850.1,ENST00000456209.2,ENST00000440126.3,ENST00000357903.3,ENST00000358918.3,ENST00000346798.3
exon_skip_3614302127347502:27347541:27348266:27348341:27354656:2735479027348266:27348341ENSG00000142192.16ENST00000354192.3,ENST00000348990.5,ENST00000448388.2,ENST00000359726.3,ENST00000439274.2,ENST00000448850.1,ENST00000440126.3,ENST00000415997.1,ENST00000357903.3,ENST00000358918.3,ENST00000346798.3
exon_skip_3614342127354656:27354790:27369674:27369731:27372329:2737234427369674:27369731ENSG00000142192.16ENST00000439274.2,ENST00000358918.3,ENST00000346798.3
exon_skip_3614352127354656:27354790:27369674:27369731:27394155:2739424327369674:27369731ENSG00000142192.16ENST00000359726.3,ENST00000415997.1
exon_skip_3614372127354656:27354790:27372329:27372497:27394155:2739424327372329:27372497ENSG00000142192.16ENST00000448850.1,ENST00000440126.3,ENST00000357903.3
exon_skip_3614402127369674:27369731:27372329:27372497:27394155:2739424327372329:27372497ENSG00000142192.16ENST00000439274.2,ENST00000491395.1,ENST00000358918.3,ENST00000346798.3
exon_skip_3614452127425551:27425664:27462258:27462388:27484295:2748440027462258:27462388ENSG00000142192.16ENST00000348990.5,ENST00000448388.2,ENST00000359726.3,ENST00000474136.1,ENST00000440126.3,ENST00000357903.3,ENST00000358918.3,ENST00000346798.3
exon_skip_3614462127425551:27425664:27462258:27462388:27542881:2754297227462258:27462388ENSG00000142192.16ENST00000354192.3,ENST00000439274.2
exon_skip_3614482127462258:27462388:27484295:27484463:27542881:2754297227484295:27484463ENSG00000142192.16ENST00000348990.5,ENST00000359726.3,ENST00000474136.1,ENST00000357903.3,ENST00000358918.3

check button PSI values of skipped exons in TCGA.
psi tcga

Top

Exon skipping events with PSIs in GTEx for APP

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3614012127253824:27254082:27264033:27264180:27269884:2726998527264033:27264180ENSG00000142192.16ENST00000346798.3,ENST00000354192.3,ENST00000348990.5,ENST00000357903.3,ENST00000358918.3,ENST00000359726.3,ENST00000448388.2,ENST00000440126.3,ENST00000439274.2,ENST00000464867.1
exon_skip_3614102127264109:27264180:27269884:27269985:27277335:2727738927269884:27269985ENSG00000142192.16ENST00000346798.3,ENST00000354192.3,ENST00000348990.5,ENST00000357903.3,ENST00000359726.3,ENST00000448388.2,ENST00000440126.3,ENST00000439274.2
exon_skip_3614112127264109:27264180:27269884:27269985:27284052:2728427427269884:27269985ENSG00000142192.16ENST00000358918.3,ENST00000456209.2
exon_skip_3614182127269884:27269985:27277335:27277389:27284052:2728427427277335:27277389ENSG00000142192.16ENST00000346798.3,ENST00000354192.3,ENST00000348990.5,ENST00000357903.3,ENST00000359726.3,ENST00000448388.2,ENST00000440126.3,ENST00000439274.2
exon_skip_3614202127269884:27269985:27284052:27284274:27326903:2732700327284052:27284274ENSG00000142192.16ENST00000358918.3,ENST00000456209.2
exon_skip_3614222127277335:27277389:27284052:27284274:27326903:2732700327284052:27284274ENSG00000142192.16ENST00000346798.3,ENST00000354192.3,ENST00000348990.5,ENST00000357903.3,ENST00000359726.3,ENST00000448388.2,ENST00000440126.3,ENST00000439274.2
exon_skip_3614252127326903:27327003:27327940:27328069:27347382:2734753227327940:27328069ENSG00000142192.16ENST00000346798.3,ENST00000354192.3,ENST00000348990.5,ENST00000357903.3,ENST00000358918.3,ENST00000359726.3,ENST00000448388.2,ENST00000440126.3,ENST00000439274.2,ENST00000456209.2,ENST00000448850.1
exon_skip_3614302127347502:27347541:27348266:27348341:27354656:2735479027348266:27348341ENSG00000142192.16ENST00000346798.3,ENST00000354192.3,ENST00000348990.5,ENST00000357903.3,ENST00000358918.3,ENST00000359726.3,ENST00000448388.2,ENST00000440126.3,ENST00000439274.2,ENST00000448850.1,ENST00000415997.1
exon_skip_3614342127354656:27354790:27369674:27369731:27372329:2737234427369674:27369731ENSG00000142192.16ENST00000346798.3,ENST00000358918.3,ENST00000439274.2
exon_skip_3614352127354656:27354790:27369674:27369731:27394155:2739424327369674:27369731ENSG00000142192.16ENST00000359726.3,ENST00000415997.1
exon_skip_3614372127354656:27354790:27372329:27372497:27394155:2739424327372329:27372497ENSG00000142192.16ENST00000357903.3,ENST00000440126.3,ENST00000448850.1
exon_skip_3614402127369674:27369731:27372329:27372497:27394155:2739424327372329:27372497ENSG00000142192.16ENST00000346798.3,ENST00000358918.3,ENST00000439274.2,ENST00000491395.1
exon_skip_3614452127425551:27425664:27462258:27462388:27484295:2748440027462258:27462388ENSG00000142192.16ENST00000346798.3,ENST00000348990.5,ENST00000357903.3,ENST00000358918.3,ENST00000359726.3,ENST00000448388.2,ENST00000440126.3,ENST00000474136.1
exon_skip_3614462127425551:27425664:27462258:27462388:27542881:2754297227462258:27462388ENSG00000142192.16ENST00000354192.3,ENST00000439274.2
exon_skip_3614482127462258:27462388:27484295:27484463:27542881:2754297227484295:27484463ENSG00000142192.16ENST00000348990.5,ENST00000357903.3,ENST00000358918.3,ENST00000359726.3,ENST00000474136.1

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

Top

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

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003467982726988427269985Frame-shift
ENST000003467982746225827462388Frame-shift
ENST000003467982726403327264180In-frame
ENST000003467982727733527277389In-frame
ENST000003467982728405227284274In-frame
ENST000003467982732794027328069In-frame
ENST000003467982734826627348341In-frame
ENST000003467982736967427369731In-frame
ENST000003467982737232927372497In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003467982726988427269985Frame-shift
ENST000003467982746225827462388Frame-shift
ENST000003467982726403327264180In-frame
ENST000003467982727733527277389In-frame
ENST000003467982728405227284274In-frame
ENST000003467982732794027328069In-frame
ENST000003467982734826627348341In-frame
ENST000003467982736967427369731In-frame
ENST000003467982737232927372497In-frame

Top

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

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000346798348477027372329273724979001067288344
ENST000003467983484770273696742736973110681124344363
ENST000003467983484770273482662734834112591333408433
ENST000003467983484770273279402732806914931621486529
ENST000003467983484770272840522728427417221943562636
ENST000003467983484770272773352727738919441997636654
ENST000003467983484770272640332726418020992245688737

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000346798348477027372329273724979001067288344
ENST000003467983484770273696742736973110681124344363
ENST000003467983484770273482662734834112591333408433
ENST000003467983484770273279402732806914931621486529
ENST000003467983484770272840522728427417221943562636
ENST000003467983484770272773352727738919441997636654
ENST000003467983484770272640332726418020992245688737

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature


Top

SNVs in the skipped exons for APP

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-AACI-01exon_skip_361425
27327941273280692732804427328044Frame_Shift_DelT-p.K495fs
LIHCTCGA-DD-A1EG-01exon_skip_361430
27348267273483412734829127348291Frame_Shift_DelT-p.K425fs
LUADTCGA-55-8507-01exon_skip_361430
27348267273483412734832027348320Frame_Shift_DelC-p.A416fs
LIHCTCGA-DD-A39Y-01exon_skip_361440
exon_skip_361437
27372330273724972737236127372361Frame_Shift_DelT-p.E335fs
KICHTCGA-KO-8407-01exon_skip_361440
exon_skip_361437
27372330273724972737238527372386Frame_Shift_Ins-Cp.G326fs
UCECTCGA-BG-A0W2-01exon_skip_361410
exon_skip_361411
27269885272699852726992927269929Nonsense_MutationCAp.E674*
UCECTCGA-B5-A0JY-01exon_skip_361430
27348267273483412734830327348303Nonsense_MutationCAp.E324*
COADTCGA-CM-4746-01exon_skip_361440
exon_skip_361437
27372330273724972737241527372415Nonsense_MutationATp.C316X
LUSCTCGA-46-3769-01exon_skip_361440
exon_skip_361437
27372330273724972737243927372439Nonsense_MutationGCp.Y308*

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
APP_27354656_27354790_27372329_27372497_27394155_27394243_TCGA-46-3769-01Sample: TCGA-46-3769-01
Cancer type: LUSC
ESID: exon_skip_361437
Skipped exon start: 27372330
Skipped exon end: 27372497
Mutation start: 27372439
Mutation end: 27372439
Mutation type: Nonsense_Mutation
Reference seq: G
Mutation seq: C
AAchange: p.Y308*
exon_skip_25126_LUSC_TCGA-46-3769-01.png
boxplot
exon_skip_361437_LUSC_TCGA-46-3769-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
SNU1040_LARGE_INTESTINE27264034272641802726404427264044Missense_MutationCTp.G734D
SNU81_LARGE_INTESTINE27269885272699852726994927269949Missense_MutationGAp.S667F
KARPAS1106P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE27269885272699852726995027269950Missense_MutationAGp.S667P
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE27327941273280692732795827327958Missense_MutationCTp.A524T
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE27327941273280692732796927327969Missense_MutationGTp.P520H
SKUT1_SOFT_TISSUE27327941273280692732798227327982Missense_MutationGAp.R516C
HSC39_STOMACH27327941273280692732799727327997Missense_MutationGAp.H511Y
KYM1_SOFT_TISSUE27327941273280692732799827327998Missense_MutationCGp.K510N
TE9_OESOPHAGUS27327941273280692732799827327998Missense_MutationCGp.K510N
JHH4_LIVER27327941273280692732799827327998Missense_MutationCGp.K510N
NCIH510_LUNG27348267273483412734828727348287Missense_MutationCGp.D427H
EPLC272H_LUNG27348267273483412734831727348317Missense_MutationCTp.E417K
COLO668_LUNG27369675273697312736969927369699Missense_MutationGCp.P356A
BICR18_UPPER_AERODIGESTIVE_TRACT27372330273724972737241327372413Missense_MutationGAp.A317V
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE27372330273724972737241327372413Missense_MutationGAp.A317V
HCC1428_BREAST27372330273724972737244927372449Missense_MutationGAp.S305F
A2058_SKIN27462259274623882746230927462309Missense_MutationCGp.R102P
NUGC3_STOMACH27462259274623882746231527462315Missense_MutationCTp.R100Q
LNCAPCLONEFGC_PROSTATE27462259274623882746234327462343Missense_MutationGTp.P91T
SNU1040_LARGE_INTESTINE27269885272699852726992327269923Nonsense_MutationGAp.R676*
MDAMB361_BREAST27372330273724972737244327372443Nonsense_MutationCTp.W307*
CCK81_LARGE_INTESTINE27277336272773892727733727277337Splice_SiteTCp.P654P
SNU626_CENTRAL_NERVOUS_SYSTEM27484296274844632748446327484463Splice_SiteCTp.V20I

Top

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

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

Top

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for APP


Top

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for APP


Top

RelatedDrugs for APP

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
P05067DB06782DimercaprolAmyloid-beta A4 proteinsmall moleculeapproved
P05067DB09148Florbetaben (18F)Amyloid-beta A4 proteinsmall moleculeapproved
P05067DB00746DeferoxamineAmyloid-beta A4 proteinsmall moleculeapproved|investigational
P05067DB01593ZincAmyloid-beta A4 proteinsmall moleculeapproved|investigational
P05067DB09149Florbetapir (18F)Amyloid-beta A4 proteinsmall moleculeapproved|investigational
P05067DB09151Flutemetamol (18F)Amyloid-beta A4 proteinsmall moleculeapproved|investigational
P05067DB14487Zinc acetateAmyloid-beta A4 proteinsmall moleculeapproved|investigational
P05067DB14517Aluminium phosphateAmyloid-beta A4 proteinsmall moleculeapproved|investigational
P05067DB14533Zinc chlorideAmyloid-beta A4 proteinsmall moleculeapproved|investigational

Top

RelatedDiseases for APP

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
APPC0002395Alzheimer's Disease55CTD_human;HPO;ORPHANET;UNIPROT
APPC0025261Memory Disorders12CTD_human
APPC0027746Nerve Degeneration11CTD_human
APPC0023186Learning Disorders6CTD_human
APPC0011570Mental Depression5PSYGENET
APPC0011581Depressive disorder5PSYGENET
APPC2751536CEREBRAL AMYLOID ANGIOPATHY, APP-RELATED5ORPHANET;UNIPROT
APPC0009241Cognition Disorders4CTD_human
APPC0522224Paralysed4CTD_human
APPC0524851Neurodegenerative Disorders2CTD_human
APPC0600467Neurogenic Inflammation2CTD_human
APPC2931672Cerebral hemorrhage with amyloidosis, hereditary, Dutch type2CTD_human;ORPHANET
APPC0002622Amnesia1CTD_human
APPC0002726Amyloidosis1CTD_human
APPC0003469Anxiety Disorders1CTD_human
APPC0005586Bipolar Disorder1PSYGENET
APPC0006111Brain Diseases1CTD_human
APPC0011573Endogenous depression1PSYGENET
APPC0016667Fragile X Syndrome1CTD_human
APPC0023893Liver Cirrhosis, Experimental1CTD_human
APPC0027540Necrosis1CTD_human
APPC0037928Spinal Cord Diseases1CTD_human
APPC0038002Splenomegaly1CTD_human
APPC0043094Weight Gain1CTD_human
APPC0085220Cerebral Amyloid Angiopathy1CTD_human;HPO
APPC0231341Premature aging syndrome1CTD_human
APPC0338656Impaired cognition1CTD_human
APPC0497327Dementia1CTD_human;HPO
APPC2936349Plaque, Amyloid1CTD_human