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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo

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

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Exon skipping events in the canonical protein sequence

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

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SNVs in the skipped exons with depth of coverage

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AD stage-associated exon skipping events

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Correlation with RNA binding proteins (RBPs)

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Related drugs with this gene

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Related diseases with this gene

Gene summary for WDFY3

check button Gene summary
Gene informationGene symbol

WDFY3

Gene ID

23001

Gene nameWD repeat and FYVE domain containing 3
SynonymsALFY|BCHS|MCPH18|ZFYVE25
Cytomap

4q21.23

Type of geneprotein-coding
DescriptionWD repeat and FYVE domain-containing protein 3autophagy-linked FYVE protein
Modification date20200313
UniProtAcc

A0A024RDC2,

A0A1D5RMR8,

A7E1Z6,

A7E293,

D6RJE4,

H0Y9T6,

H0YAD8,

Q8IZQ1,

Context

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

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Gene structures and expression levels for WDFY3

check buttonSkipped 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.
all structure

ENSG00000163625
check button Differentially expressed gene analysis across multiple brain tissues between AD and control.
Tissue typeDEG directionBase mean exp.log2FC(AD/control)P-valueAdj. p-value

check button Differentially expressed isoform analysis across multiple brain tissues between AD and control.
gencode gene structure
Tissue typeDEG directionENSTTranscript info.Base mean exp.log2FC(AD/control)P-valueAdjc. p-value
CBUPENST00000505923.5WDFY3-207:lncRNA:WDFY39.444412e+008.423383e-011.878765e-041.261996e-03
CBUPENST00000504839.1WDFY3-205:retained_intron:WDFY32.014233e+009.337725e-012.296222e-041.496682e-03
CBUPENST00000514711.1WDFY3-212:protein_coding:WDFY31.850230e+028.794723e-017.780072e-044.184627e-03

check button Landscape of isoform expressions across multiple brain tissues between AD and control.
gencode gene structure

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for WDFY3

check button Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).
boxplot

check button All exon skipping events in AD cohorts.
Exon skip IDchrExons involved in exon skippingSkipped exon
exon_skip_105390chr484829004:84829190:84831413:84831605:84836929:8483709084831413:84831605
exon_skip_107541chr484755266:84755400:84756926:84757161:84765810:8476602784756926:84757161
exon_skip_126791chr484709293:84709347:84713159:84713239:84715298:8471538384713159:84713239
exon_skip_139318chr484829004:84829190:84831413:84831605:84836929:8483699684831413:84831605
exon_skip_164962chr484831413:84831605:84836929:84837090:84841154:8484126384836929:84837090
exon_skip_168367chr484672291:84672991:84677199:84677396:84678168:8467827984677199:84677396
exon_skip_19494chr484841192:84841263:84844456:84844509:84849902:8484996884844456:84844509
exon_skip_197214chr484794879:84794979:84796521:84796752:84797996:8479810884796521:84796752
exon_skip_202853chr484704338:84704444:84705394:84705511:84708909:8470902884705394:84705511
exon_skip_20700chr484778503:84778655:84780108:84780298:84782963:8478307084780108:84780298
exon_skip_211914chr484803290:84803467:84808334:84808417:84809887:8481010784808334:84808417
exon_skip_218311chr484696732:84696823:84702353:84702506:84704338:8470444484702353:84702506
exon_skip_232473chr484821084:84821551:84826815:84826981:84829004:8482919084826815:84826981
exon_skip_236096chr484809887:84810344:84817392:84817585:84820085:8482018684817392:84817585
exon_skip_272499chr484841192:84841263:84844456:84844509:84849902:8485001584844456:84844509
exon_skip_277942chr484724582:84724594:84726861:84726911:84733382:8473346284726861:84726911
exon_skip_283461chr484678919:84679242:84682374:84682470:84683943:8468412584682374:84682470
exon_skip_294376chr484678947:84679242:84682374:84682470:84683943:8468412584682374:84682470
exon_skip_35620chr484724426:84724594:84726861:84726911:84733382:8473346284726861:84726911
exon_skip_37513chr484740187:84740416:84741761:84741921:84743700:8474379984741761:84741921
exon_skip_76266chr484678168:84678279:84678919:84679242:84682374:8468247084678919:84679242

check button Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.
psi tcga
Exon skipping informationTissue typeAvg(PSIs) in ADAvg(PSIs) in controlDifference (PSI)Adj. p-value
exon_skip_277942MSBB_PG6.085714e-014.231481e-011.854233e-019.576916e-07
exon_skip_211914MSBB_PG3.889865e-014.915789e-01-1.025925e-011.267754e-04
exon_skip_211914Mayo_TC2.416667e-013.658333e-01-1.241667e-016.628920e-07


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Open reading frame (ORF) annotation in the exon skipping event for WDFY3

check button Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000002958888468237484682470Frame-shift
ENST000002958888470235384702506Frame-shift
ENST000002958888474176184741921Frame-shift
ENST000002958888479652184796752Frame-shift
ENST000002958888482681584826981Frame-shift
ENST000002958888483141384831605Frame-shift
ENST000002958888467719984677396In-frame
ENST000002958888471315984713239In-frame
ENST000002958888472686184726911In-frame
ENST000002958888480833484808417In-frame

check button Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000002958888474176184741921Frame-shift
ENST000002958888479652184796752Frame-shift
ENST000002958888481739284817585Frame-shift
ENST000002958888482681584826981Frame-shift
ENST000002958888483141384831605Frame-shift
ENST000002958888472686184726911In-frame
ENST000002958888480833484808417In-frame

check button Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000002958888468237484682470Frame-shift
ENST000002958888470235384702506Frame-shift
ENST000002958888470539484705511Frame-shift
ENST000002958888474176184741921Frame-shift
ENST000002958888475692684757161Frame-shift
ENST000002958888478010884780298Frame-shift
ENST000002958888479652184796752Frame-shift
ENST000002958888481739284817585Frame-shift
ENST000002958888482681584826981Frame-shift
ENST000002958888483141384831605Frame-shift
ENST000002958888467719984677396In-frame
ENST000002958888467891984679242In-frame
ENST000002958888471315984713239In-frame
ENST000002958888472686184726911In-frame
ENST000002958888480833484808417In-frame
ENST000002958888483692984837090In-frame

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Infer the effects of exon skipping event on protein functional features for WDFY3

p-ENSG00000163625_img4.png
boxplot

check button Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000295888142643526848083348480841727542836782809
ENST0000029588814264352684726861847269117630767924072423
ENST0000029588814264352684713159847132398370844926542680
ENST000002958881426435268467719984677396106681086434203485

check button Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000295888142643526848083348480841727542836782809
ENST0000029588814264352684726861847269117630767924072423

check button Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000002958881426435268483692984837090823983138191
ENST00000295888142643526848083348480841727542836782809
ENST0000029588814264352684726861847269117630767924072423
ENST0000029588814264352684713159847132398370844926542680
ENST000002958881426435268467891984679242102321055432743382
ENST000002958881426435268467719984677396106681086434203485

check button 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 featureDescription of feature
Q8IZQ178280913526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ12407242324082424Alternative sequenceID=VSP_019475;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q8IZQ12407242313526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ12407242322852981RegionNote=Sufficient for localization to p62 bodies/ALIS;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20168092;Dbxref=PMID:20168092
Q8IZQ12654268013526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ12654268025312656DomainNote=BEACH-type PH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01119
Q8IZQ12654268022852981RegionNote=Sufficient for localization to p62 bodies/ALIS;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20168092;Dbxref=PMID:20168092
Q8IZQ12654268025863526RegionNote=Interaction with SQSTM1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20168092;Dbxref=PMID:20168092
Q8IZQ13420348513526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ13420348525863526RegionNote=Interaction with SQSTM1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20168092;Dbxref=PMID:20168092
Q8IZQ13420348529813526RegionNote=Interaction with ATG5;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20417604;Dbxref=PMID:20417604
Q8IZQ13420348534083447RepeatNote=WD 5
Q8IZQ13420348534543514Zinc fingerNote=FYVE-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00091

check button 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 featureDescription of feature
Q8IZQ178280913526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ12407242324082424Alternative sequenceID=VSP_019475;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q8IZQ12407242313526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ12407242322852981RegionNote=Sufficient for localization to p62 bodies/ALIS;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20168092;Dbxref=PMID:20168092

check button 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 featureDescription of feature
Q8IZQ113819113526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ178280913526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ12407242324082424Alternative sequenceID=VSP_019475;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q8IZQ12407242313526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ12407242322852981RegionNote=Sufficient for localization to p62 bodies/ALIS;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20168092;Dbxref=PMID:20168092
Q8IZQ12654268013526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ12654268025312656DomainNote=BEACH-type PH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01119
Q8IZQ12654268022852981RegionNote=Sufficient for localization to p62 bodies/ALIS;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20168092;Dbxref=PMID:20168092
Q8IZQ12654268025863526RegionNote=Interaction with SQSTM1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20168092;Dbxref=PMID:20168092
Q8IZQ13274338233463348Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3WIM
Q8IZQ13274338213526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ13274338233353335Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6VNB8
Q8IZQ13274338233393339Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
Q8IZQ13274338233463349MotifNote=LC3-interacting region (LIR);Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:24668264;Dbxref=PMID:24668264
Q8IZQ13274338233433343MutagenesisNote=Decreased interaction with GABARAP%2C no effect on interaction with MAP1LC3B%3B when associated with A-3344 and A-3351. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24668264;Dbxref=PMID:24668264
Q8IZQ13274338233443344MutagenesisNote=Decreased interaction with GABARAP%2C no effect on interaction with MAP1LC3B%3B when associated with A-3343 and A-3351. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24668264;Dbxref=PMID:24668264
Q8IZQ13274338233463346MutagenesisNote=Abolishes interaction with GABARAP and MAP1LC3C. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24668264;Dbxref=PMID:24668264
Q8IZQ13274338233473347MutagenesisNote=Decreases interaction with GABARAP and MAP1LC3C. I->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24668264;Dbxref=PMID:24668264
Q8IZQ13274338233483348MutagenesisNote=Decreases interaction with GABARAP and MAP1LC3C. F->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24668264;Dbxref=PMID:24668264
Q8IZQ13274338233493349MutagenesisNote=Decreases interaction with GABARAP and MAP1LC3C. V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24668264;Dbxref=PMID:24668264
Q8IZQ13274338233513351MutagenesisNote=Decreased interaction with GABARAP%2C no effect on interaction with MAP1LC3B%3B when associated with A-3343 and A-3344. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24668264;Dbxref=PMID:24668264
Q8IZQ13274338225863526RegionNote=Interaction with SQSTM1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20168092;Dbxref=PMID:20168092
Q8IZQ13274338229813526RegionNote=Interaction with ATG5;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20417604;Dbxref=PMID:20417604
Q8IZQ13274338233133363RegionNote=Interaction with GABARAP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24668264;Dbxref=PMID:24668264
Q8IZQ13420348513526ChainID=PRO_0000242693;Note=WD repeat and FYVE domain-containing protein 3
Q8IZQ13420348525863526RegionNote=Interaction with SQSTM1;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20168092;Dbxref=PMID:20168092
Q8IZQ13420348529813526RegionNote=Interaction with ATG5;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20417604;Dbxref=PMID:20417604
Q8IZQ13420348534083447RepeatNote=WD 5
Q8IZQ13420348534543514Zinc fingerNote=FYVE-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00091


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3'-UTR located exon skipping events that lost miRNA binding sites in WDFY3

check button 3'-UTR exon skipping evnets lost miRNA binding.
Tissue typeENSTExon skip startExon skip endmicroRNABinding site by TargetScanBinding type by TargetScanBdinding site by miRandaScore of miRandaEnergy by miRanda

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SNVs in the skipped exons for WDFY3

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

check button - Depth of Coverage in the skipped exon of the mutated samples.

check button - Sashimi plot in the skipped exon of the mutated samples.

check button - Non-synonymous mutations located in the skipped exons.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

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AD stage-associated exon skippint events for WDFY3

check button Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).
AD stage infoCohortTissueSE idCoefficient P-valueChromosomeStrandE1 startE1 endSkipped startSkipped endE2 startE2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for WDFY3

check button sQTL information located at the skipped exons.
Tissue typeExon skip IDSNP idLocationP-valueFDR

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Correlation with RNA binding proteins (RBPs) for WDFY3

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
CBNUP42exon_skip_2119145.083613e-014.190855e-10
FLRBM45exon_skip_35620-4.016485e-015.389514e-09
FLILF2exon_skip_2119145.111740e-011.414593e-14
FLPUF60exon_skip_2119144.538508e-011.878092e-11
FLNUP42exon_skip_2119144.425322e-016.676744e-11
FLHNRNPLexon_skip_2119145.043867e-013.560615e-14
FLSRSF9exon_skip_2119144.852253e-014.331058e-13
HCCTRA2Aexon_skip_356204.438810e-011.641063e-14
HCCRBM45exon_skip_356206.371784e-012.849242e-32
IFGPABPN1Lexon_skip_356204.477033e-011.689440e-02
IFGTRA2Aexon_skip_356204.615175e-011.343090e-02
PCCHNRNPFexon_skip_211914-4.394185e-011.625171e-10
PGILF2exon_skip_2119144.561600e-016.264158e-12
PGPUF60exon_skip_2119144.135251e-017.153997e-10
PGHNRNPLexon_skip_2119144.653240e-012.070233e-12
STGHNRNPDLexon_skip_35620-4.258737e-013.171052e-05
STGILF2exon_skip_2119144.700848e-013.352256e-06
STGNUP42exon_skip_2119144.091638e-016.855963e-05
STGHNRNPLexon_skip_2119144.382936e-011.740313e-05
TCNUP42exon_skip_35620-4.793999e-012.775713e-10
TCPCBP4exon_skip_2119144.247430e-012.078022e-07
TCSRSF5exon_skip_2119144.187008e-013.209931e-07

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RelatedDrugs for WDFY3

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for WDFY3

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource