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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 AGAP1

check button Gene summary
Gene informationGene symbol

AGAP1

Gene ID

116987

Gene nameArfGAP with GTPase domain, ankyrin repeat and PH domain 1
SynonymsAGAP-1|CENTG2|GGAP1|cnt-g2
Cytomap

2q37.2

Type of geneprotein-coding
Descriptionarf-GAP with GTPase, ANK repeat and PH domain-containing protein 1Arf GAP with GTP-binding protein-like, ANK repeat and PH domains 1GTP-binding and GTPase-activating protein 1centaurin, gamma 2
Modification date20200313
UniProtAcc

A0A087X044,

A0A087X1U1,

A0A0U1RRF1,

B2RZG9,

C9J8Z2,

E7EUN2,

F5GXM9,

H7C0A7,

H7C211,

Q9UPQ3,

X5D293,

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 AGAP1

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

ENSG00000157985
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
PGUPENST00000453371.2AGAP1-209:lncRNA:AGAP11.389482e+016.991873e+002.198711e-061.631686e-04
CBUPENST00000409538.5AGAP1-205:protein_coding:AGAP19.345257e+019.768408e-012.139023e-101.200862e-08

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 AGAP1

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_117160chr2235930765:235930923:235968462:235968623:236014805:236014879235968462:235968623
exon_skip_134516chr2235968468:235968623:236014805:236014879:236036561:236036697236014805:236014879
exon_skip_14948chr2235908842:235908906:235930765:235930923:235968462:235968623235930765:235930923
exon_skip_182611chr2235968462:235968623:236014805:236014879:236036561:236036697236014805:236014879
exon_skip_19619chr2235908842:235908906:235968462:235968623:236036561:236036697235968462:235968623
exon_skip_202323chr2235908842:235908906:235968462:235968623:236014805:236014879235968462:235968623
exon_skip_204807chr2235807239:235807331:235883345:235883449:235908738:235908906235883345:235883449
exon_skip_257607chr2235709179:235709237:235717557:235717644:235740963:235741048235717557:235717644
exon_skip_32220chr2235797759:235797886:235799367:235799522:235807239:235807331235799367:235799522
exon_skip_52739chr2235744698:235744839:235750354:235750488:235797759:235797886235750354:235750488
exon_skip_73490chr2235883395:235883449:235908738:235908906:235930765:235930923235908738:235908906
exon_skip_88962chr2235930765:235930923:235968462:235968623:236036561:236036697235968462:235968623

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_125204ROSMAP_DLPFC6.875393e-017.927451e-01-1.052058e-013.325540e-05


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Open reading frame (ORF) annotation in the exon skipping event for AGAP1

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
ENST00000304032235717557235717644Frame-shift
ENST00000304032235750354235750488In-frame
ENST00000304032235799367235799522In-frame
ENST00000304032235883345235883449In-frame
ENST00000304032235930765235930923In-frame
ENST00000304032235968462235968623In-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
ENST00000304032235750354235750488In-frame
ENST00000304032235799367235799522In-frame
ENST00000304032235930765235930923In-frame
ENST00000304032235968462235968623In-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
ENST00000304032235717557235717644Frame-shift
ENST00000304032235908738235908906Frame-shift
ENST00000304032235750354235750488In-frame
ENST00000304032235799367235799522In-frame
ENST00000304032235883345235883449In-frame
ENST00000304032235930765235930923In-frame
ENST00000304032235968462235968623In-frame

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Infer the effects of exon skipping event on protein functional features for AGAP1

p-ENSG00000157985_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
ENST000003040321084985723575035423575048811201253180224
ENST000003040321084985723579936723579952213831537267319
ENST000003040321084985723588334523588344916321735350385
ENST000003040321084985723593076523593092319062063442494
ENST000003040321084985723596846223596862320652225495548

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
ENST000003040321084985723575035423575048811201253180224
ENST000003040321084985723579936723579952213831537267319
ENST000003040321084985723593076523593092319062063442494
ENST000003040321084985723596846223596862320652225495548

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
ENST000003040321084985723575035423575048811201253180224
ENST000003040321084985723579936723579952213831537267319
ENST000003040321084985723588334523588344916321735350385
ENST000003040321084985723593076523593092319062063442494
ENST000003040321084985723596846223596862320652225495548

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
Q9UPQ31802241857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ3180224178181Nucleotide bindingNote=GTP;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPQ318022466276RegionNote=Small GTPase-like
Q9UPQ32673191857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ326731966276RegionNote=Small GTPase-like
Q9UPQ3267319288288Sequence conflictNote=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UPQ3267319288288Sequence conflictNote=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UPQ3267319288288Sequence conflictNote=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UPQ3350385352405Alternative sequenceID=VSP_011181;Note=In isoform 3. MLLKRSGKSLNKEWKKKYVTLCDNGVLTYHPSLHDYMQNVHGKEIDLLRTTVKV->LPFFVLALTASTYLRPAGARARQSSPWPGPRGGQTSPHCAEGPQSAQLSGAMMN;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9UPQ33503851857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ3350385346588DomainNote=PH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00145
Q9UPQ3442494406857Alternative sequenceID=VSP_011182;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9UPQ3442494442494Alternative sequenceID=VSP_011183;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10470851,ECO:0000303|PubMed:12640130,ECO:0000303|Ref.2;Dbxref=PMID:10470851,PMID:12640130
Q9UPQ34424941857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ3442494346588DomainNote=PH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00145
Q9UPQ3495548406857Alternative sequenceID=VSP_011182;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9UPQ34955481857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ3495548346588DomainNote=PH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00145
Q9UPQ3495548521521Modified 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
Q9UPQ31802241857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ3180224178181Nucleotide bindingNote=GTP;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPQ318022466276RegionNote=Small GTPase-like
Q9UPQ32673191857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ326731966276RegionNote=Small GTPase-like
Q9UPQ3267319288288Sequence conflictNote=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UPQ3267319288288Sequence conflictNote=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UPQ3267319288288Sequence conflictNote=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UPQ3442494406857Alternative sequenceID=VSP_011182;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9UPQ3442494442494Alternative sequenceID=VSP_011183;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10470851,ECO:0000303|PubMed:12640130,ECO:0000303|Ref.2;Dbxref=PMID:10470851,PMID:12640130
Q9UPQ34424941857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ3442494346588DomainNote=PH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00145
Q9UPQ3495548406857Alternative sequenceID=VSP_011182;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9UPQ34955481857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ3495548346588DomainNote=PH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00145
Q9UPQ3495548521521Modified 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
Q9UPQ31802241857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ3180224178181Nucleotide bindingNote=GTP;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9UPQ318022466276RegionNote=Small GTPase-like
Q9UPQ32673191857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ326731966276RegionNote=Small GTPase-like
Q9UPQ3267319288288Sequence conflictNote=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UPQ3267319288288Sequence conflictNote=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UPQ3267319288288Sequence conflictNote=T->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UPQ3350385352405Alternative sequenceID=VSP_011181;Note=In isoform 3. MLLKRSGKSLNKEWKKKYVTLCDNGVLTYHPSLHDYMQNVHGKEIDLLRTTVKV->LPFFVLALTASTYLRPAGARARQSSPWPGPRGGQTSPHCAEGPQSAQLSGAMMN;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9UPQ33503851857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ3350385346588DomainNote=PH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00145
Q9UPQ3442494406857Alternative sequenceID=VSP_011182;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9UPQ3442494442494Alternative sequenceID=VSP_011183;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10470851,ECO:0000303|PubMed:12640130,ECO:0000303|Ref.2;Dbxref=PMID:10470851,PMID:12640130
Q9UPQ34424941857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ3442494346588DomainNote=PH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00145
Q9UPQ3495548406857Alternative sequenceID=VSP_011182;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q9UPQ34955481857ChainID=PRO_0000074218;Note=Arf-GAP with GTPase%2C ANK repeat and PH domain-containing protein 1
Q9UPQ3495548346588DomainNote=PH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00145
Q9UPQ3495548521521Modified 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 AGAP1

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 AGAP1

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 AGAP1

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 AGAP1

check button sQTL information located at the skipped exons.
Tissue typeExon skip IDSNP idLocationP-valueFDR
HCCexon_skip_14948rs7571708chr2:2359239292.615090e-042.017412e-02
HCCexon_skip_14948rs10182604chr2:2359251714.770980e-043.267102e-02
HCCexon_skip_14948rs7572513chr2:2359184474.822650e-043.297020e-02
HCCexon_skip_14948rs9653218chr2:2359037655.434118e-043.621826e-02
HCCexon_skip_14948rs6722180chr2:2359247145.543821e-043.680430e-02

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Correlation with RNA binding proteins (RBPs) for AGAP1

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
CBRBM4exon_skip_149485.384292e-014.179174e-13
CBSRSF11exon_skip_1345164.594665e-011.258936e-09
CBHNRNPKexon_skip_1345165.141649e-014.851517e-12
CBHNRNPDLexon_skip_1345164.424075e-015.885614e-09
CBHNRNPDexon_skip_1345164.619637e-019.973009e-10
CBHNRNPLexon_skip_1345164.084867e-019.923371e-08
CBSRSF9exon_skip_1345164.544974e-011.990315e-09
FLSRSF9exon_skip_1252044.008159e-014.872706e-09
HCCDAZAP1exon_skip_134516-5.706855e-011.207962e-24
HCCRBMS2exon_skip_134516-6.080752e-011.367981e-28
HCCRBMS1exon_skip_134516-4.109036e-012.211547e-12
HCCRBMS3exon_skip_134516-5.141290e-011.496624e-19
HCCZNF638exon_skip_134516-5.173767e-018.087875e-20
HCCSRSF11exon_skip_134516-5.352755e-012.411286e-21
HCCCNOT4exon_skip_134516-4.164816e-011.038115e-12
HCCKHDRBS3exon_skip_134516-5.842631e-015.103123e-26
HCCFUBP3exon_skip_134516-5.039170e-019.935447e-19
HCCSRSF5exon_skip_134516-4.918809e-018.539007e-18
IFGKHDRBS3exon_skip_1826114.685577e-011.190672e-02
PCCRBMS2exon_skip_134516-6.409931e-018.288824e-26
PCCRBMS1exon_skip_134516-5.433463e-011.326631e-17
PCCZNF638exon_skip_134516-4.326547e-014.903831e-11
PCCSRSF11exon_skip_134516-4.277891e-018.479618e-11
PCCFUBP3exon_skip_134516-4.223401e-011.549802e-10
STGSRSF2exon_skip_1826114.271324e-013.478975e-04
STGCNOT4exon_skip_1826114.105249e-016.178552e-04
STGHNRNPKexon_skip_1826114.733398e-015.973322e-05
STGKHDRBS3exon_skip_1826115.387291e-013.066987e-06
STGHNRNPDLexon_skip_1826114.087141e-016.566255e-04
STGHNRNPLexon_skip_1826114.506308e-011.465355e-04
TCCNOT4exon_skip_1345164.007218e-011.514728e-07
TCKHDRBS2exon_skip_1345167.523257e-011.930323e-30
TCKHDRBS3exon_skip_1345166.272835e-016.996470e-19
TCHNRNPDexon_skip_1345165.028878e-011.229895e-11

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RelatedDrugs for AGAP1

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 AGAP1

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