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Open reading frame (ORF) annotation in the exon skipping event | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon | |
Gene summary for PAPPA |
Gene summary |
Gene information | Gene symbol | PAPPA | Gene ID | 5069 |
Gene name | pappalysin 1 | |
Synonyms | ASBABP2|DIPLA1|IGFBP-4ase|PAPA|PAPP-A|PAPPA1 | |
Cytomap | 9q33.1 | |
Type of gene | protein-coding | |
Description | pappalysin-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 date | 20180519 | |
UniProtAcc | Q13219 | |
Context | PubMed: PAPPA [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
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Exon skipping events across known transcript of Ensembl for PAPPA from UCSC genome browser |
Skipped 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. |
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Gene isoform structures and expression levels for PAPPA |
Expression levels of gene isoforms across TCGA. |
Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for PAPPA |
Information of exkip skipping event in TCGA. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_498483 | 9 | 118969734:118969880:118973917:118974211:118982215:118982408 | 118973917:118974211 | ENSG00000182752.8 | ENST00000328252.3 |
exon_skip_498484 | 9 | 118989709:118989831:118997417:118997916:119028135:119028264 | 118997417:118997916 | ENSG00000182752.8 | ENST00000328252.3 |
exon_skip_498485 | 9 | 119028135:119028264:119033603:119033695:119065035:119065229 | 119033603:119033695 | ENSG00000182752.8 | ENST00000534838.1,ENST00000328252.3 |
exon_skip_498486 | 9 | 119065035:119065229:119093522:119093636:119094611:119094747 | 119093522:119093636 | ENSG00000182752.8 | ENST00000534838.1,ENST00000328252.3 |
exon_skip_498487 | 9 | 119094710:119094747:119095022:119095125:119097139:119097353 | 119095022:119095125 | ENSG00000182752.8 | ENST00000460463.1 |
exon_skip_498488 | 9 | 119114984:119115195:119115900:119116072:119124870:119125018 | 119115900:119116072 | ENSG00000182752.8 | ENST00000534838.1,ENST00000328252.3 |
PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PAPPA |
Information of exkip skipping event in GTEx |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
exon_skip_498483 | 9 | 118969734:118969880:118973917:118974211:118982215:118982408 | 118973917:118974211 | ENSG00000182752.8 | ENST00000328252.3 |
exon_skip_498484 | 9 | 118989709:118989831:118997417:118997916:119028135:119028264 | 118997417:118997916 | ENSG00000182752.8 | ENST00000328252.3 |
exon_skip_498485 | 9 | 119028135:119028264:119033603:119033695:119065035:119065229 | 119033603:119033695 | ENSG00000182752.8 | ENST00000328252.3,ENST00000534838.1 |
exon_skip_498486 | 9 | 119065035:119065229:119093522:119093636:119094611:119094747 | 119093522:119093636 | ENSG00000182752.8 | ENST00000328252.3,ENST00000534838.1 |
exon_skip_498487 | 9 | 119094710:119094747:119095022:119095125:119097139:119097353 | 119095022:119095125 | ENSG00000182752.8 | ENST00000460463.1 |
exon_skip_498488 | 9 | 119114984:119115195:119115900:119116072:119124870:119125018 | 119115900:119116072 | ENSG00000182752.8 | ENST00000328252.3,ENST00000534838.1 |
PSI values of skipped exons in GTEx. |
* Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for PAPPA |
Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000328252 | 118997417 | 118997916 | Frame-shift |
ENST00000328252 | 119033603 | 119033695 | Frame-shift |
ENST00000328252 | 119115900 | 119116072 | Frame-shift |
ENST00000328252 | 118973917 | 118974211 | In-frame |
ENST00000328252 | 119093522 | 119093636 | In-frame |
Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000328252 | 118997417 | 118997916 | Frame-shift |
ENST00000328252 | 119033603 | 119033695 | Frame-shift |
ENST00000328252 | 119115900 | 119116072 | Frame-shift |
ENST00000328252 | 118973917 | 118974211 | In-frame |
ENST00000328252 | 119093522 | 119093636 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PAPPA |
Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000328252 | 10976 | 1627 | 118973917 | 118974211 | 1994 | 2287 | 541 | 639 |
ENST00000328252 | 10976 | 1627 | 119093522 | 119093636 | 3517 | 3630 | 1049 | 1087 |
Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases. |
ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
ENST00000328252 | 10976 | 1627 | 118973917 | 118974211 | 1994 | 2287 | 541 | 639 |
ENST00000328252 | 10976 | 1627 | 119093522 | 119093636 | 3517 | 3630 | 1049 | 1087 |
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 feature | Description of feature |
Q13219 | 541 | 639 | 563 | 563 | Active site | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095 |
Q13219 | 541 | 639 | 81 | 1627 | Chain | ID=PRO_0000029246;Note=Pappalysin-1 |
Q13219 | 541 | 639 | 327 | 622 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832 |
Q13219 | 541 | 639 | 332 | 657 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832 |
Q13219 | 541 | 639 | 583 | 600 | Disulfide bond | Note=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 |
Q13219 | 541 | 639 | 587 | 612 | Disulfide bond | Note=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 |
Q13219 | 541 | 639 | 601 | 601 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832 |
Q13219 | 541 | 639 | 619 | 619 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832 |
Q13219 | 541 | 639 | 562 | 562 | Metal binding | Note=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095 |
Q13219 | 541 | 639 | 566 | 566 | Metal binding | Note=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095 |
Q13219 | 541 | 639 | 572 | 572 | Metal binding | Note=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095 |
Q13219 | 541 | 639 | 272 | 583 | Region | Note=Metalloprotease |
Q13219 | 1049 | 1087 | 81 | 1627 | Chain | ID=PRO_0000029246;Note=Pappalysin-1 |
Q13219 | 1049 | 1087 | 1036 | 1070 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832 |
Q13219 | 1049 | 1087 | 1051 | 1139 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832 |
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 feature | Description of feature |
Q13219 | 541 | 639 | 563 | 563 | Active site | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095 |
Q13219 | 541 | 639 | 81 | 1627 | Chain | ID=PRO_0000029246;Note=Pappalysin-1 |
Q13219 | 541 | 639 | 327 | 622 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832 |
Q13219 | 541 | 639 | 332 | 657 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832 |
Q13219 | 541 | 639 | 583 | 600 | Disulfide bond | Note=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 |
Q13219 | 541 | 639 | 587 | 612 | Disulfide bond | Note=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 |
Q13219 | 541 | 639 | 601 | 601 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832 |
Q13219 | 541 | 639 | 619 | 619 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832 |
Q13219 | 541 | 639 | 562 | 562 | Metal binding | Note=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095 |
Q13219 | 541 | 639 | 566 | 566 | Metal binding | Note=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095 |
Q13219 | 541 | 639 | 572 | 572 | Metal binding | Note=Zinc%3B catalytic;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU10095 |
Q13219 | 541 | 639 | 272 | 583 | Region | Note=Metalloprotease |
Q13219 | 1049 | 1087 | 81 | 1627 | Chain | ID=PRO_0000029246;Note=Pappalysin-1 |
Q13219 | 1049 | 1087 | 1036 | 1070 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00302,ECO:0000269|PubMed:12421832;Dbxref=PMID:12421832 |
Q13219 | 1049 | 1087 | 1051 | 1139 | Disulfide bond | Ontology_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 |
- Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
- Differential PSIs between mutated versus non-mutated samples. |
- Non-synonymous mutations located in the skipped exons in TCGA. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
LIHC | TCGA-DD-A3A0-01 | exon_skip_498483 | 118973918 | 118974211 | 118974110 | 118974110 | Frame_Shift_Del | C | - | p.A606fs |
LIHC | TCGA-DD-A39Y-01 | exon_skip_498484 | 118997418 | 118997916 | 118997604 | 118997604 | Frame_Shift_Del | G | - | p.W807fs |
LIHC | TCGA-G3-A3CJ-01 | exon_skip_498484 | 118997418 | 118997916 | 118997624 | 118997624 | Frame_Shift_Del | A | - | p.N814fs |
LIHC | TCGA-G3-A3CJ-01 | exon_skip_498485 | 119033604 | 119033695 | 119033660 | 119033660 | Frame_Shift_Del | T | - | p.L973fs |
LIHC | TCGA-G3-A3CJ-01 | exon_skip_498488 | 119115901 | 119116072 | 119115959 | 119115959 | Frame_Shift_Del | C | - | p.P1412fs |
HNSC | TCGA-CR-7399-01 | exon_skip_498483 | 118973918 | 118974211 | 118973930 | 118973930 | Nonsense_Mutation | T | A | p.L546* |
STAD | TCGA-MX-A5UJ-01 | exon_skip_498483 | 118973918 | 118974211 | 118974016 | 118974016 | Nonsense_Mutation | C | T | p.R575* |
STAD | TCGA-MX-A5UJ-01 | exon_skip_498483 | 118973918 | 118974211 | 118974016 | 118974016 | Nonsense_Mutation | C | T | p.R575X |
STAD | TCGA-CG-4465-01 | exon_skip_498483 | 118973918 | 118974211 | 118974189 | 118974189 | Nonsense_Mutation | C | G | p.Y632* |
STAD | TCGA-CG-4465-01 | exon_skip_498483 | 118973918 | 118974211 | 118974189 | 118974189 | Nonsense_Mutation | C | G | p.Y632X |
READ | TCGA-CL-5917-01 | exon_skip_498485 | 119033604 | 119033695 | 119033668 | 119033668 | Nonsense_Mutation | C | T | p.R976X |
READ | TCGA-F5-6814-01 | exon_skip_498485 | 119033604 | 119033695 | 119033674 | 119033674 | Nonsense_Mutation | G | T | p.E978X |
SKCM | TCGA-DA-A95X-06 | exon_skip_498486 | 119093523 | 119093636 | 119093607 | 119093607 | Nonsense_Mutation | C | T | p.Q1078* |
SKCM | TCGA-GF-A3OT-06 | exon_skip_498488 | 119115901 | 119116072 | 119115986 | 119115986 | Nonsense_Mutation | A | T | p.K1421* |
SKCM | TCGA-GF-A3OT-06 | exon_skip_498488 | 119115901 | 119116072 | 119115986 | 119115986 | Nonsense_Mutation | A | T | p.K1421X |
SKCM | TCGA-D3-A8GQ-06 | exon_skip_498488 | 119115901 | 119116072 | 119116022 | 119116022 | Nonsense_Mutation | C | T | p.Q1433* |
HNSC | TCGA-CV-6933-01 | exon_skip_498484 | 118997418 | 118997916 | 118997917 | 118997917 | Splice_Site | G | T | p.M911_splice |
SKCM | TCGA-DA-A3F8-06 | exon_skip_498485 | 119033604 | 119033695 | 119033603 | 119033603 | Splice_Site | G | A | . |
PAAD | TCGA-IB-7651-01 | exon_skip_498486 | 119093523 | 119093636 | 119093522 | 119093522 | Splice_Site | G | A | . |
- Depth of coverage in the three exons composing exon skipping event |
Depth of coverage in three exons | Mutation description |
- Non-synonymous mutations located in the skipped exons in CCLE. |
Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
BICR18_UPPER_AERODIGESTIVE_TRACT | 119033604 | 119033695 | 119033668 | 119033669 | Frame_Shift_Del | CG | - | p.R976fs |
ACCS_URINARY_TRACT | 118997418 | 118997916 | 118997596 | 118997597 | Frame_Shift_Ins | - | ACTG | p.-806fs |
BICR18_UPPER_AERODIGESTIVE_TRACT | 119033604 | 119033695 | 119033670 | 119033671 | Frame_Shift_Ins | - | AG | p.Q977fs |
NCIH630_LARGE_INTESTINE | 118973918 | 118974211 | 118974095 | 118974097 | In_Frame_Del | ATG | - | p.D602del |
LOUCY_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118973918 | 118974211 | 118973943 | 118973943 | Missense_Mutation | C | A | p.F550L |
HCC2450_LUNG | 118973918 | 118974211 | 118973989 | 118973989 | Missense_Mutation | C | T | p.H566Y |
EN_ENDOMETRIUM | 118973918 | 118974211 | 118974014 | 118974014 | Missense_Mutation | T | C | p.F574S |
HCC202_BREAST | 118973918 | 118974211 | 118974109 | 118974109 | Missense_Mutation | G | C | p.A606P |
AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118973918 | 118974211 | 118974157 | 118974157 | Missense_Mutation | T | C | p.C622R |
NCIH810_LUNG | 118997418 | 118997916 | 118997456 | 118997456 | Missense_Mutation | C | T | p.R758C |
NCIH2227_LUNG | 118997418 | 118997916 | 118997519 | 118997519 | Missense_Mutation | C | G | p.Q779E |
NCIH720_LUNG | 118997418 | 118997916 | 118997613 | 118997613 | Missense_Mutation | G | T | p.S810I |
SLVL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118997418 | 118997916 | 118997618 | 118997618 | Missense_Mutation | G | T | p.A812S |
RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 118997418 | 118997916 | 118997619 | 118997619 | Missense_Mutation | C | T | p.A812V |
GP2D_LARGE_INTESTINE | 118997418 | 118997916 | 118997660 | 118997660 | Missense_Mutation | A | G | p.I826V |
HCC202_BREAST | 118997418 | 118997916 | 118997667 | 118997667 | Missense_Mutation | T | C | p.L828P |
LXF289_LUNG | 118997418 | 118997916 | 118997670 | 118997670 | Missense_Mutation | G | C | p.G829A |
SNU1040_LARGE_INTESTINE | 118997418 | 118997916 | 118997870 | 118997870 | Missense_Mutation | A | G | p.M896V |
RKO_LARGE_INTESTINE | 118997418 | 118997916 | 118997909 | 118997909 | Missense_Mutation | G | A | p.V909I |
HT115_LARGE_INTESTINE | 119033604 | 119033695 | 119033623 | 119033623 | Missense_Mutation | G | A | p.D961N |
CALU3_LUNG | 119033604 | 119033695 | 119033626 | 119033626 | Missense_Mutation | G | A | p.D962N |
CW2_LARGE_INTESTINE | 119033604 | 119033695 | 119033641 | 119033641 | Missense_Mutation | A | G | p.N967D |
PANC0813_PANCREAS | 119033604 | 119033695 | 119033660 | 119033660 | Missense_Mutation | T | C | p.L973P |
NCIH187_LUNG | 119033604 | 119033695 | 119033669 | 119033669 | Missense_Mutation | G | A | p.R976Q |
JHUEM7_ENDOMETRIUM | 119093523 | 119093636 | 119093530 | 119093530 | Missense_Mutation | G | A | p.R1052Q |
KYSE30_OESOPHAGUS | 119093523 | 119093636 | 119093530 | 119093530 | Missense_Mutation | G | T | p.R1052L |
BCPAP_THYROID | 119093523 | 119093636 | 119093551 | 119093551 | Missense_Mutation | G | C | p.S1059T |
HEC59_ENDOMETRIUM | 119093523 | 119093636 | 119093577 | 119093577 | Missense_Mutation | T | C | p.Y1068H |
HCC44_LUNG | 119093523 | 119093636 | 119093605 | 119093605 | Missense_Mutation | C | T | p.S1077F |
FLO1_OESOPHAGUS | 119093523 | 119093636 | 119093625 | 119093625 | Missense_Mutation | T | G | p.F1084V |
HCC202_BREAST | 119093523 | 119093636 | 119093627 | 119093627 | Missense_Mutation | T | G | p.F1084L |
HCC15_LUNG | 119115901 | 119116072 | 119115917 | 119115917 | Missense_Mutation | C | G | p.Q1398E |
EMCBAC1_LUNG | 119115901 | 119116072 | 119115928 | 119115928 | Missense_Mutation | G | T | p.Q1401H |
KYSE140_OESOPHAGUS | 119115901 | 119116072 | 119115984 | 119115984 | Missense_Mutation | C | G | p.P1420R |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PAPPA |
sQTL information located at the skipped exons. |
Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA 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 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for PAPPA |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |
PAPPA | C0002965 | Angina, Unstable | 1 | CTD_human |
PAPPA | C0014175 | Endometriosis | 1 | CTD_human |
PAPPA | C0021361 | Female infertility | 1 | CTD_human |
PAPPA | C0027051 | Myocardial Infarction | 1 | CTD_human |
PAPPA | C0948089 | Acute Coronary Syndrome | 1 | CTD_human |
PAPPA | C1956346 | Coronary Artery Disease | 1 | CTD_human |