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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 PACSIN2

check button Gene summary
Gene informationGene symbol

PACSIN2

Gene ID

11252

Gene nameprotein kinase C and casein kinase substrate in neurons 2
SynonymsSDPII
Cytomap

22q13.2

Type of geneprotein-coding
Descriptionprotein kinase C and casein kinase substrate in neurons protein 2cytoplasmic phosphoprotein PACSIN2syndapin-2syndapin-IIsyndapin2
Modification date20200313
UniProtAcc

A0A024R4X1,

A0A0U1RR22,

B0QYG7,

B0QYG8,

B0QYG9,

H0Y923,

Q6FIA3,

Q9UNF0,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
PACSIN2

GO:0097320

plasma membrane tubulation

23596323


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Gene structures and expression levels for PACSIN2

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

ENSG00000100266
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.
Tissue typeDEG directionENSTTranscript info.Base mean exp.log2FC(AD/control)P-valueAdjc. p-value

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 PACSIN2

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_137394chr2242893574:42893613:42912021:42912157:42959799:4295988142912021:42912157
exon_skip_167320chr2242893574:42893613:42912021:42912157:42959572:4295989942912021:42912157
exon_skip_195151chr2242893574:42893613:42912021:42912157:43015021:4301509842912021:42912157
exon_skip_228415chr2242879048:42879169:42880617:42880622:42882184:4288230442880617:42880622
exon_skip_242328chr2242879061:42879169:42880617:42880622:42882184:4288230442880617:42880622
exon_skip_257801chr2242884386:42884561:42888643:42888798:42890947:4289118242888643:42888798
exon_skip_294448chr2242888643:42888798:42890947:42891182:42893457:4289361342890947:42891182
exon_skip_35614chr2242879048:42879169:42882184:42882304:42884386:4288456142882184:42882304
exon_skip_77069chr2242876137:42876333:42876888:42877010:42879048:4287916942876888:42877010
exon_skip_79561chr2242893457:42893613:42909427:42909565:42912021:4291215742909427:42909565
exon_skip_9542chr2242876137:42876333:42876888:42877010:42879048:4287916642876888:42877010

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_228415ROSMAP_DLPFC2.944651e-014.032759e-01-1.088107e-016.573803e-04
exon_skip_77069ROSMAP_PCC5.855385e-014.852941e-011.002443e-019.286202e-04
exon_skip_228415ROSMAP_PCC3.974615e-014.994118e-01-1.019502e-019.517514e-04
exon_skip_77069MSBB_STG3.137255e-012.134783e-011.002472e-014.882265e-03
exon_skip_228415MSBB_STG5.318644e-016.485714e-01-1.167070e-014.851011e-02
exon_skip_228415MSBB_FL4.842149e-016.077551e-01-1.235402e-019.024261e-03
exon_skip_228415Mayo_TC2.351220e-013.432468e-01-1.081248e-015.667294e-03


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Open reading frame (ORF) annotation in the exon skipping event for PACSIN2

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
ENST0000026324642912021429121573UTR-3CDS
ENST000002632464288218442882304Frame-shift
ENST000004022294288218442882304Frame-shift
ENST000004037444288218442882304Frame-shift
ENST000002632464289094742891182Frame-shift
ENST000004022294289094742891182Frame-shift
ENST000004037444289094742891182Frame-shift
ENST000002632464287688842877010In-frame
ENST000004022294287688842877010In-frame
ENST000004037444287688842877010In-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
ENST0000026324642912021429121573UTR-3CDS
ENST000002632464288218442882304Frame-shift
ENST000004022294288218442882304Frame-shift
ENST000004037444288218442882304Frame-shift
ENST000002632464289094742891182Frame-shift
ENST000004022294289094742891182Frame-shift
ENST000004037444289094742891182Frame-shift
ENST000002632464287688842877010In-frame
ENST000004022294287688842877010In-frame
ENST000004037444287688842877010In-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
ENST0000026324642912021429121573UTR-3CDS
ENST000002632464289094742891182Frame-shift
ENST000004022294289094742891182Frame-shift
ENST000004037444289094742891182Frame-shift
ENST000002632464287688842877010In-frame
ENST000004022294287688842877010In-frame
ENST000004037444287688842877010In-frame
ENST000002632464288864342888798In-frame
ENST000004022294288864342888798In-frame
ENST000004037444288864342888798In-frame

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Infer the effects of exon skipping event on protein functional features for PACSIN2

p-ENSG00000100266_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
ENST000002632463266486428768884287701012311352343383
ENST000004022291900486428768884287701012221343343383
ENST000004037442127486428768884287701012511372343383

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
ENST000002632463266486428768884287701012311352343383
ENST000004022291900486428768884287701012221343343383
ENST000004037442127486428768884287701012511372343383

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
ENST0000026324632664864288864342888798656810151202
ENST0000040222919004864288864342888798647801151202
ENST0000040374421274864288864342888798676830151202
ENST000002632463266486428768884287701012311352343383
ENST000004022291900486428768884287701012221343343383
ENST000004037442127486428768884287701012511372343383

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
Q9UNF0343383344384Alternative sequenceID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|Ref.6;Dbxref=PMID:11230166
Q9UNF0343383344384Alternative sequenceID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|Ref.6;Dbxref=PMID:11230166
Q9UNF0343383344384Alternative sequenceID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|Ref.6;Dbxref=PMID:11230166
Q9UNF03433831486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF03433831486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF03433831486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF0343383362364MotifNote=NPF1
Q9UNF0343383362364MotifNote=NPF1
Q9UNF0343383362364MotifNote=NPF1
Q9UNF0343383378380Sequence conflictNote=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0343383378380Sequence conflictNote=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0343383378380Sequence conflictNote=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
Q9UNF0343383344384Alternative sequenceID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|Ref.6;Dbxref=PMID:11230166
Q9UNF0343383344384Alternative sequenceID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|Ref.6;Dbxref=PMID:11230166
Q9UNF0343383344384Alternative sequenceID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|Ref.6;Dbxref=PMID:11230166
Q9UNF03433831486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF03433831486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF03433831486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF0343383362364MotifNote=NPF1
Q9UNF0343383362364MotifNote=NPF1
Q9UNF0343383362364MotifNote=NPF1
Q9UNF0343383378380Sequence conflictNote=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0343383378380Sequence conflictNote=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0343383378380Sequence conflictNote=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
Q9UNF01512021486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF01512021486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF01512021486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF015120225274Coiled coil.
Q9UNF015120225274Coiled coil.
Q9UNF015120225274Coiled coil.
Q9UNF015120211282DomainNote=F-BAR;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01077
Q9UNF015120211282DomainNote=F-BAR;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01077
Q9UNF015120211282DomainNote=F-BAR;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01077
Q9UNF0151202129169HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202129169HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202129169HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202172177HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202172177HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202172177HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202185188HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202185188HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202185188HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202189191HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202189191HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202189191HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202197255HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202197255HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202197255HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202175175Natural variantID=VAR_053555;Note=N->S;Dbxref=dbSNP:rs35383004
Q9UNF0151202175175Natural variantID=VAR_053555;Note=N->S;Dbxref=dbSNP:rs35383004
Q9UNF0151202175175Natural variantID=VAR_053555;Note=N->S;Dbxref=dbSNP:rs35383004
Q9UNF0151202182182Sequence conflictNote=L->F;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0151202182182Sequence conflictNote=L->F;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0151202182182Sequence conflictNote=L->F;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0151202192195TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202192195TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0151202192195TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3ABH
Q9UNF0343383344384Alternative sequenceID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|Ref.6;Dbxref=PMID:11230166
Q9UNF0343383344384Alternative sequenceID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|Ref.6;Dbxref=PMID:11230166
Q9UNF0343383344384Alternative sequenceID=VSP_004517;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11230166,ECO:0000303|Ref.6;Dbxref=PMID:11230166
Q9UNF03433831486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF03433831486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF03433831486ChainID=PRO_0000161795;Note=Protein kinase C and casein kinase substrate in neurons protein 2
Q9UNF0343383362364MotifNote=NPF1
Q9UNF0343383362364MotifNote=NPF1
Q9UNF0343383362364MotifNote=NPF1
Q9UNF0343383378380Sequence conflictNote=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0343383378380Sequence conflictNote=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UNF0343383378380Sequence conflictNote=DDT->EDI;Ontology_term=ECO:0000305;evidence=ECO:0000305


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3'-UTR located exon skipping events that lost miRNA binding sites in PACSIN2

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 PACSIN2

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 PACSIN2

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 PACSIN2

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 PACSIN2

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
CBPCBP2exon_skip_77069-4.805550e-011.449007e-10
CBG3BP2exon_skip_77069-4.624373e-018.432840e-10
CBTARDBPexon_skip_2284154.229270e-012.797260e-08
CBG3BP2exon_skip_2284156.098603e-011.436230e-17
CBSRSF9exon_skip_2284156.043786e-013.314479e-17
CBSRSF4exon_skip_195151-5.047999e-011.567890e-11
CBHNRNPFexon_skip_195151-4.400928e-018.052704e-09
DLPFCG3BP2exon_skip_2284157.174605e-011.340871e-53
FLSRSF2exon_skip_77069-4.941964e-013.645187e-12
FLHNRNPKexon_skip_77069-4.966044e-012.760063e-12
FLG3BP2exon_skip_77069-6.452256e-015.540391e-22
FLKHDRBS2exon_skip_77069-4.490083e-014.596040e-10
FLEIF4G2exon_skip_77069-4.103617e-011.699699e-08
FLCELF1exon_skip_77069-4.031763e-013.167530e-08
FLSRSF1exon_skip_77069-4.120427e-011.466231e-08
FLSRSF9exon_skip_77069-5.387213e-011.469692e-14
FLG3BP2exon_skip_2284156.823159e-011.246292e-24
FLSRSF9exon_skip_2284155.221577e-012.823462e-13
HCCRBM6exon_skip_770694.391535e-012.678535e-14
HCCRBM5exon_skip_770694.196709e-014.511303e-13
HCCPCBP4exon_skip_770694.241084e-012.409101e-13
HCCG3BP2exon_skip_77069-4.040240e-013.833423e-12
HCCG3BP2exon_skip_2284154.608470e-019.262038e-16
IFGG3BP2exon_skip_77069-7.129160e-012.069970e-05
IFGKHDRBS2exon_skip_77069-5.072672e-015.865611e-03
IFGNUP42exon_skip_77069-4.277496e-012.317010e-02
IFGG3BP2exon_skip_2284156.195658e-014.383136e-04
IFGRALYLexon_skip_195151-4.417337e-011.860377e-02
PCCRBM6exon_skip_770695.087245e-011.490166e-15
PCCPCBP4exon_skip_770694.021094e-019.235697e-10
PCCG3BP2exon_skip_77069-7.142937e-017.361867e-35
PCCG3BP2exon_skip_2284157.851512e-013.285436e-46
PGSRSF2exon_skip_77069-5.741176e-011.583285e-14
PGSRSF11exon_skip_77069-5.464981e-014.684243e-13
PGPCBP1exon_skip_77069-5.392417e-011.084455e-12
PGHNRNPKexon_skip_77069-6.161249e-014.775236e-17
PGPCBP2exon_skip_77069-4.753125e-017.938740e-10
PGG3BP2exon_skip_77069-8.238552e-012.549876e-38
PGKHDRBS2exon_skip_77069-7.065003e-015.532760e-24
PGNUP42exon_skip_77069-6.072419e-011.750512e-16
PGEIF4G2exon_skip_77069-6.078666e-011.599796e-16
PGCELF1exon_skip_77069-6.510225e-011.902639e-19
PGSRSF1exon_skip_77069-5.627534e-016.627790e-14
PGSRSF9exon_skip_77069-5.530607e-012.154243e-13
STGG3BP2exon_skip_77069-4.738890e-012.000997e-05
STGKHDRBS2exon_skip_77069-4.228849e-011.743232e-04
STGG3BP2exon_skip_2284154.941437e-013.188254e-06
TCSRSF2exon_skip_77069-4.182975e-013.710679e-08
TCG3BP2exon_skip_77069-6.582895e-013.106007e-21
TCKHDRBS2exon_skip_77069-7.719732e-016.629766e-33
TCNUP42exon_skip_77069-5.857782e-014.070952e-16
TCCELF1exon_skip_77069-5.361941e-012.728499e-13
TCG3BP2exon_skip_2284157.327397e-014.908393e-28

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RelatedDrugs for PACSIN2

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 PACSIN2

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