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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 PDCD10

check button Gene summary
Gene informationGene symbol

PDCD10

Gene ID

11235

Gene nameprogrammed cell death 10
SynonymsCCM3|TFAR15
Cytomap

3q26.1

Type of geneprotein-coding
Descriptionprogrammed cell death protein 10TF-1 cell apoptosis-related protein 15apoptosis-related protein 15cerebral cavernous malformations 3 protein
Modification date20180522
UniProtAcc

Q9BUL8

ContextPubMed: PDCD10 [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
PDCD10

GO:0008284

positive regulation of cell proliferation

17360971|23541896

PDCD10

GO:0030335

positive regulation of cell migration

23541896

PDCD10

GO:0032874

positive regulation of stress-activated MAPK cascade

22652780

PDCD10

GO:0042542

response to hydrogen peroxide

22291017

PDCD10

GO:0043066

negative regulation of apoptotic process

17360971

PDCD10

GO:0043406

positive regulation of MAP kinase activity

17360971


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Exon skipping events across known transcript of Ensembl for PDCD10 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 PDCD10

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 PDCD10

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3897923167402126:167402177:167405021:167405104:167405402:167405481167405021:167405104ENSG00000114209.10ENST00000470131.1,ENST00000492396.1,ENST00000497056.2,ENST00000461494.1,ENST00000475915.2,ENST00000392750.2,ENST00000473645.2
exon_skip_3897973167405025:167405104:167405402:167405481:167413383:167413510167405402:167405481ENSG00000114209.10ENST00000470131.1,ENST00000492396.1,ENST00000497056.2,ENST00000461494.1,ENST00000475915.2,ENST00000392750.2,ENST00000473645.2,ENST00000487947.2,ENST00000471885.1
exon_skip_3897983167414827:167414914:167415638:167415766:167422629:167422683167415638:167415766ENSG00000114209.10ENST00000494502.2
exon_skip_3897993167414827:167414914:167422629:167422683:167437849:167437886167422629:167422683ENSG00000114209.10ENST00000470131.1,ENST00000497056.2,ENST00000462725.2,ENST00000461494.1,ENST00000475915.2,ENST00000392750.2,ENST00000479121.1,ENST00000492139.1,ENST00000473645.2,ENST00000483451.1,ENST00000487947.2,ENST00000464360.1,ENST00000471885.1
exon_skip_3898113167422629:167422683:167437849:167438061:167443188:167443261167437849:167438061ENSG00000114209.10ENST00000462725.2,ENST00000475915.2,ENST00000494502.2,ENST00000473645.2,ENST00000464360.1
exon_skip_3898123167422629:167422683:167437849:167438061:167452593:167452620167437849:167438061ENSG00000114209.10ENST00000481136.1,ENST00000497056.2
exon_skip_3898233167437992:167438061:167443188:167443261:167452001:167452034167443188:167443261ENSG00000114209.10ENST00000464360.1
exon_skip_3898253167437992:167438061:167443188:167443261:167452219:167452305167443188:167443261ENSG00000114209.10ENST00000462725.2
exon_skip_3898263167437992:167438061:167443188:167443261:167452246:167452270167443188:167443261ENSG00000114209.10ENST00000475915.2
exon_skip_3898283167437992:167438061:167443188:167443261:167452593:167452620167443188:167443261ENSG00000114209.10ENST00000494502.2,ENST00000473645.2
exon_skip_3898323167437992:167438061:167452001:167452034:167452593:167452620167452001:167452034ENSG00000114209.10ENST00000471885.1
exon_skip_3898363167437992:167438061:167452001:167452133:167452593:167452620167452001:167452133ENSG00000114209.10ENST00000470131.1
exon_skip_3898383167437992:167438061:167452001:167452138:167452593:167452620167452001:167452138ENSG00000114209.10ENST00000492139.1
exon_skip_3898433167443188:167443261:167452001:167452133:167452593:167452620167452001:167452133ENSG00000114209.10ENST00000464360.1

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

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Exon skipping events with PSIs in GTEx for PDCD10

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3897923167402126:167402177:167405021:167405104:167405402:167405481167405021:167405104ENSG00000114209.10ENST00000392750.2,ENST00000473645.2,ENST00000497056.2,ENST00000492396.1,ENST00000461494.1,ENST00000470131.1,ENST00000475915.2
exon_skip_3897973167405025:167405104:167405402:167405481:167413383:167413510167405402:167405481ENSG00000114209.10ENST00000392750.2,ENST00000473645.2,ENST00000497056.2,ENST00000492396.1,ENST00000461494.1,ENST00000470131.1,ENST00000475915.2,ENST00000487947.2,ENST00000471885.1
exon_skip_3897983167414827:167414914:167415638:167415766:167422629:167422683167415638:167415766ENSG00000114209.10ENST00000494502.2
exon_skip_3897993167414827:167414914:167422629:167422683:167437849:167437886167422629:167422683ENSG00000114209.10ENST00000392750.2,ENST00000473645.2,ENST00000497056.2,ENST00000461494.1,ENST00000470131.1,ENST00000475915.2,ENST00000487947.2,ENST00000471885.1,ENST00000479121.1,ENST00000462725.2,ENST00000492139.1,ENST00000483451.1,ENST00000464360.1
exon_skip_3898113167422629:167422683:167437849:167438061:167443188:167443261167437849:167438061ENSG00000114209.10ENST00000473645.2,ENST00000475915.2,ENST00000462725.2,ENST00000494502.2,ENST00000464360.1
exon_skip_3898123167422629:167422683:167437849:167438061:167452593:167452620167437849:167438061ENSG00000114209.10ENST00000497056.2,ENST00000481136.1
exon_skip_3898233167437992:167438061:167443188:167443261:167452001:167452034167443188:167443261ENSG00000114209.10ENST00000464360.1
exon_skip_3898253167437992:167438061:167443188:167443261:167452219:167452305167443188:167443261ENSG00000114209.10ENST00000462725.2
exon_skip_3898263167437992:167438061:167443188:167443261:167452246:167452270167443188:167443261ENSG00000114209.10ENST00000475915.2
exon_skip_3898283167437992:167438061:167443188:167443261:167452593:167452620167443188:167443261ENSG00000114209.10ENST00000473645.2,ENST00000494502.2
exon_skip_3898323167437992:167438061:167452001:167452034:167452593:167452620167452001:167452034ENSG00000114209.10ENST00000471885.1
exon_skip_3898363167437992:167438061:167452001:167452133:167452593:167452620167452001:167452133ENSG00000114209.10ENST00000470131.1
exon_skip_3898383167437992:167438061:167452001:167452138:167452593:167452620167452001:167452138ENSG00000114209.10ENST00000492139.1
exon_skip_3898433167443188:167443261:167452001:167452133:167452593:167452620167452001:167452133ENSG00000114209.10ENST00000464360.1

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 PDCD10

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
ENST000004736451674378491674380613UTR-3CDS
ENST000004970561674378491674380613UTR-3CDS
ENST000004736451674431881674432613UTR-3UTR
ENST000004701311674520011674521333UTR-3UTR
ENST00000392750167405021167405104Frame-shift
ENST00000461494167405021167405104Frame-shift
ENST00000470131167405021167405104Frame-shift
ENST00000473645167405021167405104Frame-shift
ENST00000497056167405021167405104Frame-shift
ENST00000392750167405402167405481Frame-shift
ENST00000461494167405402167405481Frame-shift
ENST00000470131167405402167405481Frame-shift
ENST00000473645167405402167405481Frame-shift
ENST00000497056167405402167405481Frame-shift
ENST00000392750167422629167422683In-frame
ENST00000461494167422629167422683In-frame
ENST00000470131167422629167422683In-frame
ENST00000473645167422629167422683In-frame
ENST00000497056167422629167422683In-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
ENST000004736451674378491674380613UTR-3CDS
ENST000004970561674378491674380613UTR-3CDS
ENST000004736451674431881674432613UTR-3UTR
ENST000004701311674520011674521333UTR-3UTR
ENST00000392750167405021167405104Frame-shift
ENST00000461494167405021167405104Frame-shift
ENST00000470131167405021167405104Frame-shift
ENST00000473645167405021167405104Frame-shift
ENST00000497056167405021167405104Frame-shift
ENST00000392750167405402167405481Frame-shift
ENST00000461494167405402167405481Frame-shift
ENST00000470131167405402167405481Frame-shift
ENST00000473645167405402167405481Frame-shift
ENST00000497056167405402167405481Frame-shift
ENST00000392750167422629167422683In-frame
ENST00000461494167422629167422683In-frame
ENST00000470131167422629167422683In-frame
ENST00000473645167422629167422683In-frame
ENST00000497056167422629167422683In-frame

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Infer the effects of exon skipping event on protein functional features for PDCD10

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
ENST0000039275020842121674226291674226835155683250
ENST000004614949512121674226291674226833263793250
ENST0000047013110432121674226291674226834324853250
ENST0000047364513772121674226291674226834204733250
ENST0000049705612932121674226291674226833383913250

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
ENST0000039275020842121674226291674226835155683250
ENST000004614949512121674226291674226833263793250
ENST0000047013110432121674226291674226834324853250
ENST0000047364513772121674226291674226834204733250
ENST0000049705612932121674226291674226833383913250

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
Q9BUL832501212ChainID=PRO_0000187562;Note=Programmed cell death protein 10
Q9BUL832501212ChainID=PRO_0000187562;Note=Programmed cell death protein 10
Q9BUL832501212ChainID=PRO_0000187562;Note=Programmed cell death protein 10
Q9BUL832501212ChainID=PRO_0000187562;Note=Programmed cell death protein 10
Q9BUL832501212ChainID=PRO_0000187562;Note=Programmed cell death protein 10
Q9BUL832502634HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832502634HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832502634HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832502634HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832502634HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832503854HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832503854HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832503854HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832503854HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832503854HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH


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
Q9BUL832501212ChainID=PRO_0000187562;Note=Programmed cell death protein 10
Q9BUL832501212ChainID=PRO_0000187562;Note=Programmed cell death protein 10
Q9BUL832501212ChainID=PRO_0000187562;Note=Programmed cell death protein 10
Q9BUL832501212ChainID=PRO_0000187562;Note=Programmed cell death protein 10
Q9BUL832501212ChainID=PRO_0000187562;Note=Programmed cell death protein 10
Q9BUL832502634HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832502634HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832502634HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832502634HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832502634HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832503854HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832503854HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832503854HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832503854HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH
Q9BUL832503854HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4GEH


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SNVs in the skipped exons for PDCD10

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-A39Y-01exon_skip_389792
167405022167405104167405033167405033Frame_Shift_DelA-p.F182fs
LIHCTCGA-DD-A3A0-01exon_skip_389792
167405022167405104167405058167405058Frame_Shift_DelA-p.F174fs
LIHCTCGA-DD-A3A1-01exon_skip_389792
167405022167405104167405062167405062Frame_Shift_DelT-p.S173fs
LIHCTCGA-G3-A3CJ-01exon_skip_389811
exon_skip_389812
167437850167438061167437882167437882Frame_Shift_DelG-p.L22fs
SKCMTCGA-FW-A3TU-06exon_skip_389792
167405022167405104167405098167405098Nonsense_MutationCAp.E161*
LUSCTCGA-66-2800-01exon_skip_389799
167422630167422683167422680167422680Nonsense_MutationCAp.E34*
HNSCTCGA-BA-4078-01exon_skip_389811
exon_skip_389812
167437850167438061167437849167437849Splice_SiteCTp.E32_splice

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
PDCD10_167422629_167422683_167437849_167438061_167452593_167452620_TCGA-BA-4078-01Sample: TCGA-BA-4078-01
Cancer type: HNSC
ESID: exon_skip_389812
Skipped exon start: 167437850
Skipped exon end: 167438061
Mutation start: 167437849
Mutation end: 167437849
Mutation type: Splice_Site
Reference seq: C
Mutation seq: T
AAchange: p.E32_splice
exon_skip_351842_HNSC_TCGA-BA-4078-01.png
boxplot
exon_skip_389812_HNSC_TCGA-BA-4078-01.png
boxplot
exon_skip_73983_HNSC_TCGA-BA-4078-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
NCIH1694_LUNG167405403167405481167405431167405435Frame_Shift_DelAAGAC-p.VF148fs
NCIH1694_LUNG167405403167405481167405439167405439Frame_Shift_DelA-p.N147fs
NCIH1694_LUNG167405403167405481167405432167405437In_Frame_DelAGACAT-p.147_149NVF>I
JHU028_LUNG167405022167405104167405026167405026Missense_MutationCAp.G185C
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE167405022167405104167405049167405049Missense_MutationGAp.T177I
PEDS015T_SOFT_TISSUE167405022167405104167405101167405101Missense_MutationGCp.L160V
SNU349_KIDNEY167405403167405481167405407167405407Missense_MutationCTp.R157H
EW16_BONE167405403167405481167405420167405420Missense_MutationGTp.Q153K
CCK81_LARGE_INTESTINE167422630167422683167422649167422649Missense_MutationAGp.L44P
CAL12T_LUNG167422630167422683167422654167422654Missense_MutationCGp.Q42H
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE167437850167438061167437878167437878Missense_MutationTAp.Y23F
SNU81_LARGE_INTESTINE167405403167405481167405459167405459Nonsense_MutationCAp.E140*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PDCD10

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 PDCD10


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PDCD10


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RelatedDrugs for PDCD10

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 PDCD10

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