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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 TCGA

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Exon skipping events with PSIs in GTEx

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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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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for PAPPA

check button Gene summary
Gene informationGene symbol

PAPPA

Gene ID

5069

Gene namepappalysin 1
SynonymsASBABP2|DIPLA1|IGFBP-4ase|PAPA|PAPP-A|PAPPA1
Cytomap

9q33.1

Type of geneprotein-coding
Descriptionpappalysin-1IGF-dependent IGFBP-4 proteaseaspecific BCL2 ARE-binding protein 2differentially placenta 1 expressed proteininsulin-like growth factor-dependent IGF binding protein-4 proteasepregnancy-associated plasma protein A, pappalysin 1
Modification date20180519
UniProtAcc

Q13219

ContextPubMed: PAPPA [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

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Exon skipping events across known transcript of Ensembl for PAPPA 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

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Gene isoform structures and expression levels for PAPPA

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

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


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Exon skipping events with PSIs in TCGA for PAPPA

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4984839118969734:118969880:118973917:118974211:118982215:118982408118973917:118974211ENSG00000182752.8ENST00000328252.3
exon_skip_4984849118989709:118989831:118997417:118997916:119028135:119028264118997417:118997916ENSG00000182752.8ENST00000328252.3
exon_skip_4984859119028135:119028264:119033603:119033695:119065035:119065229119033603:119033695ENSG00000182752.8ENST00000534838.1,ENST00000328252.3
exon_skip_4984869119065035:119065229:119093522:119093636:119094611:119094747119093522:119093636ENSG00000182752.8ENST00000534838.1,ENST00000328252.3
exon_skip_4984879119094710:119094747:119095022:119095125:119097139:119097353119095022:119095125ENSG00000182752.8ENST00000460463.1
exon_skip_4984889119114984:119115195:119115900:119116072:119124870:119125018119115900:119116072ENSG00000182752.8ENST00000534838.1,ENST00000328252.3

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

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Exon skipping events with PSIs in GTEx for PAPPA

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4984839118969734:118969880:118973917:118974211:118982215:118982408118973917:118974211ENSG00000182752.8ENST00000328252.3
exon_skip_4984849118989709:118989831:118997417:118997916:119028135:119028264118997417:118997916ENSG00000182752.8ENST00000328252.3
exon_skip_4984859119028135:119028264:119033603:119033695:119065035:119065229119033603:119033695ENSG00000182752.8ENST00000328252.3,ENST00000534838.1
exon_skip_4984869119065035:119065229:119093522:119093636:119094611:119094747119093522:119093636ENSG00000182752.8ENST00000328252.3,ENST00000534838.1
exon_skip_4984879119094710:119094747:119095022:119095125:119097139:119097353119095022:119095125ENSG00000182752.8ENST00000460463.1
exon_skip_4984889119114984:119115195:119115900:119116072:119124870:119125018119115900:119116072ENSG00000182752.8ENST00000328252.3,ENST00000534838.1

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

* Skipped exon sequences.

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

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
ENST00000328252118997417118997916Frame-shift
ENST00000328252119033603119033695Frame-shift
ENST00000328252119115900119116072Frame-shift
ENST00000328252118973917118974211In-frame
ENST00000328252119093522119093636In-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
ENST00000328252118997417118997916Frame-shift
ENST00000328252119033603119033695Frame-shift
ENST00000328252119115900119116072Frame-shift
ENST00000328252118973917118974211In-frame
ENST00000328252119093522119093636In-frame

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

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
ENST0000032825210976162711897391711897421119942287541639
ENST000003282521097616271190935221190936363517363010491087

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
ENST0000032825210976162711897391711897421119942287541639
ENST000003282521097616271190935221190936363517363010491087

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
Q13219541639563563Active siteOntology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095
Q13219541639811627ChainID=PRO_0000029246;Note=Pappalysin-1
Q13219541639327622Disulfide bondOntology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639332657Disulfide bondOntology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639583600Disulfide bondNote=Or C-583 with C-612;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639587612Disulfide bondNote=Or C-587 with C-600;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639601601GlycosylationNote=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639619619GlycosylationNote=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639562562Metal bindingNote=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095
Q13219541639566566Metal bindingNote=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095
Q13219541639572572Metal bindingNote=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095
Q13219541639272583RegionNote=Metalloprotease
Q1321910491087811627ChainID=PRO_0000029246;Note=Pappalysin-1
Q132191049108710361070Disulfide bondOntology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q132191049108710511139Disulfide bondOntology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832


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
Q13219541639563563Active siteOntology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095
Q13219541639811627ChainID=PRO_0000029246;Note=Pappalysin-1
Q13219541639327622Disulfide bondOntology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639332657Disulfide bondOntology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639583600Disulfide bondNote=Or C-583 with C-612;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639587612Disulfide bondNote=Or C-587 with C-600;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639601601GlycosylationNote=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639619619GlycosylationNote=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q13219541639562562Metal bindingNote=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095
Q13219541639566566Metal bindingNote=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095
Q13219541639572572Metal bindingNote=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095
Q13219541639272583RegionNote=Metalloprotease
Q1321910491087811627ChainID=PRO_0000029246;Note=Pappalysin-1
Q132191049108710361070Disulfide bondOntology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832
Q132191049108710511139Disulfide bondOntology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832


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SNVs in the skipped exons for PAPPA

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-A3A0-01exon_skip_498483
118973918118974211118974110118974110Frame_Shift_DelC-p.A606fs
LIHCTCGA-DD-A39Y-01exon_skip_498484
118997418118997916118997604118997604Frame_Shift_DelG-p.W807fs
LIHCTCGA-G3-A3CJ-01exon_skip_498484
118997418118997916118997624118997624Frame_Shift_DelA-p.N814fs
LIHCTCGA-G3-A3CJ-01exon_skip_498485
119033604119033695119033660119033660Frame_Shift_DelT-p.L973fs
LIHCTCGA-G3-A3CJ-01exon_skip_498488
119115901119116072119115959119115959Frame_Shift_DelC-p.P1412fs
HNSCTCGA-CR-7399-01exon_skip_498483
118973918118974211118973930118973930Nonsense_MutationTAp.L546*
STADTCGA-MX-A5UJ-01exon_skip_498483
118973918118974211118974016118974016Nonsense_MutationCTp.R575*
STADTCGA-MX-A5UJ-01exon_skip_498483
118973918118974211118974016118974016Nonsense_MutationCTp.R575X
STADTCGA-CG-4465-01exon_skip_498483
118973918118974211118974189118974189Nonsense_MutationCGp.Y632*
STADTCGA-CG-4465-01exon_skip_498483
118973918118974211118974189118974189Nonsense_MutationCGp.Y632X
READTCGA-CL-5917-01exon_skip_498485
119033604119033695119033668119033668Nonsense_MutationCTp.R976X
READTCGA-F5-6814-01exon_skip_498485
119033604119033695119033674119033674Nonsense_MutationGTp.E978X
SKCMTCGA-DA-A95X-06exon_skip_498486
119093523119093636119093607119093607Nonsense_MutationCTp.Q1078*
SKCMTCGA-GF-A3OT-06exon_skip_498488
119115901119116072119115986119115986Nonsense_MutationATp.K1421*
SKCMTCGA-GF-A3OT-06exon_skip_498488
119115901119116072119115986119115986Nonsense_MutationATp.K1421X
SKCMTCGA-D3-A8GQ-06exon_skip_498488
119115901119116072119116022119116022Nonsense_MutationCTp.Q1433*
HNSCTCGA-CV-6933-01exon_skip_498484
118997418118997916118997917118997917Splice_SiteGTp.M911_splice
SKCMTCGA-DA-A3F8-06exon_skip_498485
119033604119033695119033603119033603Splice_SiteGA.
PAADTCGA-IB-7651-01exon_skip_498486
119093523119093636119093522119093522Splice_SiteGA.

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
BICR18_UPPER_AERODIGESTIVE_TRACT119033604119033695119033668119033669Frame_Shift_DelCG-p.R976fs
ACCS_URINARY_TRACT118997418118997916118997596118997597Frame_Shift_Ins-ACTGp.-806fs
BICR18_UPPER_AERODIGESTIVE_TRACT119033604119033695119033670119033671Frame_Shift_Ins-AGp.Q977fs
NCIH630_LARGE_INTESTINE118973918118974211118974095118974097In_Frame_DelATG-p.D602del
LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE118973918118974211118973943118973943Missense_MutationCAp.F550L
HCC2450_LUNG118973918118974211118973989118973989Missense_MutationCTp.H566Y
EN_ENDOMETRIUM118973918118974211118974014118974014Missense_MutationTCp.F574S
HCC202_BREAST118973918118974211118974109118974109Missense_MutationGCp.A606P
AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE118973918118974211118974157118974157Missense_MutationTCp.C622R
NCIH810_LUNG118997418118997916118997456118997456Missense_MutationCTp.R758C
NCIH2227_LUNG118997418118997916118997519118997519Missense_MutationCGp.Q779E
NCIH720_LUNG118997418118997916118997613118997613Missense_MutationGTp.S810I
SLVL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE118997418118997916118997618118997618Missense_MutationGTp.A812S
RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE118997418118997916118997619118997619Missense_MutationCTp.A812V
GP2D_LARGE_INTESTINE118997418118997916118997660118997660Missense_MutationAGp.I826V
HCC202_BREAST118997418118997916118997667118997667Missense_MutationTCp.L828P
LXF289_LUNG118997418118997916118997670118997670Missense_MutationGCp.G829A
SNU1040_LARGE_INTESTINE118997418118997916118997870118997870Missense_MutationAGp.M896V
RKO_LARGE_INTESTINE118997418118997916118997909118997909Missense_MutationGAp.V909I
HT115_LARGE_INTESTINE119033604119033695119033623119033623Missense_MutationGAp.D961N
CALU3_LUNG119033604119033695119033626119033626Missense_MutationGAp.D962N
CW2_LARGE_INTESTINE119033604119033695119033641119033641Missense_MutationAGp.N967D
PANC0813_PANCREAS119033604119033695119033660119033660Missense_MutationTCp.L973P
NCIH187_LUNG119033604119033695119033669119033669Missense_MutationGAp.R976Q
JHUEM7_ENDOMETRIUM119093523119093636119093530119093530Missense_MutationGAp.R1052Q
KYSE30_OESOPHAGUS119093523119093636119093530119093530Missense_MutationGTp.R1052L
BCPAP_THYROID119093523119093636119093551119093551Missense_MutationGCp.S1059T
HEC59_ENDOMETRIUM119093523119093636119093577119093577Missense_MutationTCp.Y1068H
HCC44_LUNG119093523119093636119093605119093605Missense_MutationCTp.S1077F
FLO1_OESOPHAGUS119093523119093636119093625119093625Missense_MutationTGp.F1084V
HCC202_BREAST119093523119093636119093627119093627Missense_MutationTGp.F1084L
HCC15_LUNG119115901119116072119115917119115917Missense_MutationCGp.Q1398E
EMCBAC1_LUNG119115901119116072119115928119115928Missense_MutationGTp.Q1401H
KYSE140_OESOPHAGUS119115901119116072119115984119115984Missense_MutationCGp.P1420R

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

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

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


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


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RelatedDrugs for PAPPA

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

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RelatedDiseases for PAPPA

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
PAPPAC0002965Angina, Unstable1CTD_human
PAPPAC0014175Endometriosis1CTD_human
PAPPAC0021361Female infertility1CTD_human
PAPPAC0027051Myocardial Infarction1CTD_human
PAPPAC0948089Acute Coronary Syndrome1CTD_human
PAPPAC1956346Coronary Artery Disease1CTD_human