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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 PPFIBP1

check button Gene summary
Gene informationGene symbol

PPFIBP1

Gene ID

8496

Gene namePPFIA binding protein 1
SynonymsL2|SGT2|hSGT2|hSgt2p
Cytomap

12p11.23-p11.22

Type of geneprotein-coding
Descriptionliprin-beta-1PTPRF interacting protein, binding protein 1 (liprin beta 1)PTPRF-interacting protein-binding protein 1liprin related proteinprotein-tyrosine phosphatase receptor-type f polypeptide-interacting protein-binding protein 1
Modification date20200313
UniProtAcc

A0A024RB02,

A0A087WVX8,

A0A0A0MTP2,

F5GZP6,

F5H0E0,

F5H495,

F5H6Q7,

F5H7K5,

H0YFE4,

H0YGH8,

Q05CN4,

Q86W92,

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 PPFIBP1

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

ENSG00000110841
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
CBUPENST00000542629.5PPFIBP1-215:protein_coding:PPFIBP12.223657e+011.445998e+002.316136e-031.040999e-02
CBUPENST00000537261.1PPFIBP1-206:protein_coding:PPFIBP13.394525e+008.394326e-017.090336e-032.621573e-02
TCUPENST00000542629.5PPFIBP1-215:protein_coding:PPFIBP11.213483e+011.646271e+009.621005e-062.515436e-04

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 PPFIBP1

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_133509chr1227673767:27673827:27674192:27674221:27676428:2767655727674192:27674221
exon_skip_134421chr1227654722:27654814:27655143:27655235:27656616:2765673027655143:27655235
exon_skip_152069chr1227656616:27656730:27658816:27658848:27660884:2766094527658816:27658848
exon_skip_152328chr1227682624:27682703:27687385:27687507:27688298:2768842327687385:27687507
exon_skip_166218chr1227646062:27646148:27647729:27647842:27650010:2765005227647729:27647842
exon_skip_171808chr1227646062:27646148:27647729:27647842:27650010:2765014127647729:27647842
exon_skip_216598chr1227647729:27647842:27650010:27650141:27654722:2765481427650010:27650141
exon_skip_229983chr1227676428:27676599:27677064:27677096:27679489:2767963927677064:27677096
exon_skip_84019chr1227676428:27676599:27677064:27677096:27679489:2767961727677064:27677096
exon_skip_89289chr1227656616:27656730:27660884:27660945:27664362:2766443727660884:27660945

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_134421ROSMAP_PCC4.563281e-015.663529e-01-1.100248e-014.533028e-03
exon_skip_134421MSBB_PG3.300000e-015.336170e-01-2.036170e-013.999252e-03


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Open reading frame (ORF) annotation in the exon skipping event for PPFIBP1

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
ENST000003183042766088427660945Frame-shift
ENST000003183042764772927647842In-frame
ENST000003183042765001027650141In-frame
ENST000003183042765514327655235In-frame
ENST000003183042767419227674221In-frame
ENST000003183042768738527687507In-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
ENST000003183042766088427660945Frame-shift
ENST000003183042765001027650141In-frame
ENST000003183042765514327655235In-frame
ENST000003183042767419227674221In-frame
ENST000003183042768738527687507In-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
ENST000003183042766088427660945Frame-shift
ENST000003183042765001027650141In-frame
ENST000003183042765514327655235In-frame
ENST000003183042767419227674221In-frame
ENST000003183042768738527687507In-frame

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Infer the effects of exon skipping event on protein functional features for PPFIBP1

p-ENSG00000110841_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
ENST00000318304601810112764772927647842642754119157
ENST00000318304601810112765001027650141756886157201
ENST000003183046018101127655143276552359811072232263
ENST0000031830460181011276741922767422117161744477487
ENST0000031830460181011276873852768750725502671755796

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
ENST00000318304601810112765001027650141756886157201
ENST000003183046018101127655143276552359811072232263
ENST0000031830460181011276741922767422117161744477487
ENST0000031830460181011276873852768750725502671755796

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
ENST00000318304601810112765001027650141756886157201
ENST000003183046018101127655143276552359811072232263
ENST0000031830460181011276741922767422117161744477487
ENST0000031830460181011276873852768750725502671755796

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
Q86W921191571153Alternative sequenceID=VSP_009394;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10574462;Dbxref=PMID:10574462
Q86W9211915711011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W92119157156405Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q86W92119157148148Natural variantID=VAR_017758;Note=V->L;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10574462,ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:9624153,ECO:0000269|Ref.4,ECO:0000269|Ref.5;Dbxref=dbSNP:rs2194816,PMID:1
Q86W92157201158170Alternative sequenceID=VSP_009395;Note=In isoform 5. ELLSRTSLETQKL->VCAEARTKMGFPC;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W921572011711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W9215720111011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W92157201156405Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q86W922322631711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W92232263233263Alternative sequenceID=VSP_009397;Note=In isoform 2 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:9624153;Dbxref=PMID:15489334,PMID:9624153
Q86W9223226311011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W92232263156405Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q86W924774871711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W9247748711011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W927557961711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W9275579611011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W92755796719782DomainNote=SAM 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00184
Q86W92755796794794Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:23186163,PMID:24275569

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
Q86W92157201158170Alternative sequenceID=VSP_009395;Note=In isoform 5. ELLSRTSLETQKL->VCAEARTKMGFPC;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W921572011711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W9215720111011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W92157201156405Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q86W922322631711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W92232263233263Alternative sequenceID=VSP_009397;Note=In isoform 2 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:9624153;Dbxref=PMID:15489334,PMID:9624153
Q86W9223226311011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W92232263156405Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q86W924774871711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W9247748711011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W927557961711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W9275579611011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W92755796719782DomainNote=SAM 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00184
Q86W92755796794794Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:23186163,PMID:24275569

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
Q86W92157201158170Alternative sequenceID=VSP_009395;Note=In isoform 5. ELLSRTSLETQKL->VCAEARTKMGFPC;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W921572011711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W9215720111011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W92157201156405Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q86W922322631711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W92232263233263Alternative sequenceID=VSP_009397;Note=In isoform 2 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:9624153;Dbxref=PMID:15489334,PMID:9624153
Q86W9223226311011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W92232263156405Coiled coilOntology_term=ECO:0000255;evidence=ECO:0000255
Q86W924774871711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W9247748711011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W927557961711011Alternative sequenceID=VSP_009396;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|Ref.4,ECO:0000303|Ref.5
Q86W9275579611011ChainID=PRO_0000191034;Note=Liprin-beta-1
Q86W92755796719782DomainNote=SAM 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00184
Q86W92755796794794Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:23186163,PMID:24275569


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3'-UTR located exon skipping events that lost miRNA binding sites in PPFIBP1

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 PPFIBP1

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 PPFIBP1

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
ADstageMSBBIFGexon_skip_1520693.808491e-014.555874e-02chr12+276566162765673027658816276588482766088427660945
CDRMSBBIFGexon_skip_1520693.983061e-013.579002e-02chr12+276566162765673027658816276588482766088427660945

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PPFIBP1

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 PPFIBP1

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
DLPFCG3BP2exon_skip_1344214.558912e-014.382887e-18
FLSRSF2exon_skip_1344215.430873e-014.048438e-14
FLILF2exon_skip_1344216.554655e-019.515496e-22
FLHNRNPKexon_skip_1344215.516401e-011.332490e-14
FLG3BP2exon_skip_1344217.231860e-013.723156e-28
FLRALYLexon_skip_1344216.019632e-019.660656e-18
FLPTBP1exon_skip_134421-4.976380e-019.037840e-12
FLSRSF9exon_skip_1344214.528446e-019.022800e-10
FLRBM3exon_skip_1335094.054013e-014.960350e-09
HCCSRSF11exon_skip_134421-5.015784e-011.519141e-18
HCCRBM5exon_skip_134421-6.151063e-012.160516e-29
HCCIGF2BP2exon_skip_134421-4.589615e-012.025178e-15
HCCPTBP1exon_skip_134421-6.802252e-016.871329e-38
HCCSNRNP70exon_skip_134421-5.729279e-017.235552e-25
HCCPABPC1exon_skip_134421-4.115945e-012.015325e-12
HCCHNRNPFexon_skip_134421-6.145803e-012.484415e-29
HCCZC3H10exon_skip_134421-6.025561e-015.641387e-28
HCCRBM3exon_skip_1335094.050329e-014.829141e-12
IFGKHDRBS3exon_skip_152069-6.176843e-014.615286e-04
PCCSRSF11exon_skip_134421-4.340164e-013.393605e-11
PCCIGF2BP2exon_skip_134421-4.028772e-011.021981e-09
PCCG3BP2exon_skip_1344217.141463e-011.580451e-34
PCCRALYLexon_skip_1344214.534079e-013.393197e-12
PCCPTBP1exon_skip_134421-7.582915e-014.490919e-41
PCCPABPC1exon_skip_134421-5.317748e-016.019638e-17
PCCHNRNPFexon_skip_134421-6.251327e-011.710197e-24
PCCRBM3exon_skip_1335095.358875e-017.371936e-17
PGRBM47exon_skip_134421-4.199662e-011.961263e-08
PGILF2exon_skip_1344215.181493e-011.019355e-12
PGHNRNPKexon_skip_1344215.182518e-011.007169e-12
PGG3BP2exon_skip_1344217.217328e-017.749587e-28
PGRALYLexon_skip_1344216.799961e-019.827531e-24
PGPTBP1exon_skip_134421-4.761151e-011.023126e-10
PGEWSR1exon_skip_1344214.868223e-013.354633e-11
PGSART3exon_skip_1344214.487855e-011.488420e-09
PGHNRNPA0exon_skip_229983-4.408389e-016.576658e-10
TCSRSF2exon_skip_1344215.300082e-011.565542e-12
TCSRSF11exon_skip_1344214.219699e-015.020597e-08
TCILF2exon_skip_1344216.015687e-011.579435e-16
TCHNRNPKexon_skip_1344215.174353e-016.362696e-12
TCG3BP2exon_skip_1344218.081972e-018.891048e-37
TCNUP42exon_skip_1344217.080123e-019.874657e-25
TCRALYLexon_skip_1344218.705982e-011.115779e-48
TCPTBP3exon_skip_1344215.778803e-014.263318e-15
TCEWSR1exon_skip_1344214.240758e-014.237473e-08
TCSRSF9exon_skip_1344214.683939e-019.016702e-10
TCSART3exon_skip_1344214.575137e-012.443054e-09
TCKHDRBS2exon_skip_152069-6.758306e-019.359329e-22
TCKHDRBS3exon_skip_152069-6.341426e-011.376753e-18
TCNUP42exon_skip_152069-4.672054e-011.142660e-09
TCYBX2exon_skip_152069-5.319233e-011.490368e-12
TCHNRNPA0exon_skip_84019-4.009660e-012.803853e-07
TCNUP42exon_skip_84019-4.095814e-011.462782e-07

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RelatedDrugs for PPFIBP1

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 PPFIBP1

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