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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 PTCH2

check button Gene summary
Gene informationGene symbol

PTCH2

Gene ID

8643

Gene namepatched 2
SynonymsPTC2
Cytomap

1p34.1

Type of geneprotein-coding
Descriptionprotein patched homolog 2patched homolog 2
Modification date20180523
UniProtAcc

Q9Y6C5

ContextPubMed: PTCH2 [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 PTCH2 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 PTCH2

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 PTCH2

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_26002145285515:45286376:45287513:45287576:45288273:4528834145287513:45287576ENSG00000117425.9ENST00000438067.1
exon_skip_26003145285515:45286376:45288273:45288341:45288740:4528884045288273:45288341ENSG00000117425.9ENST00000447098.2
exon_skip_26004145288919:45289057:45291921:45292059:45292159:4529244045291921:45292059ENSG00000117425.9ENST00000372192.3,ENST00000447098.2
exon_skip_26006145291921:45292059:45292159:45292440:45292573:4529275445292159:45292440ENSG00000117425.9ENST00000372192.3,ENST00000447098.2
exon_skip_26014145294653:45294746:45294828:45294984:45295073:4529520545294828:45294984ENSG00000117425.9ENST00000372192.3,ENST00000447098.2
exon_skip_26020145294828:45294984:45295073:45295205:45295285:4529543345295073:45295205ENSG00000117425.9ENST00000372192.3,ENST00000447098.2
exon_skip_26022145295285:45295433:45295580:45295702:45296519:4529671545295580:45295702ENSG00000117425.9ENST00000372192.3,ENST00000447098.2
exon_skip_26025145295580:45295702:45296519:45296715:45297377:4529746945296519:45296715ENSG00000117425.9ENST00000372192.3,ENST00000447098.2
exon_skip_26030145297823:45298013:45307518:45307711:45308532:4530861645307518:45307711ENSG00000117425.9ENST00000372192.3,ENST00000447098.2

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

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Exon skipping events with PSIs in GTEx for PTCH2

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_26003145285515:45286376:45288273:45288341:45288740:4528884045288273:45288341ENSG00000117425.9ENST00000447098.2
exon_skip_26004145288919:45289057:45291921:45292059:45292159:4529244045291921:45292059ENSG00000117425.9ENST00000447098.2,ENST00000372192.3
exon_skip_26006145291921:45292059:45292159:45292440:45292573:4529275445292159:45292440ENSG00000117425.9ENST00000447098.2,ENST00000372192.3
exon_skip_26014145294653:45294746:45294828:45294984:45295073:4529520545294828:45294984ENSG00000117425.9ENST00000447098.2,ENST00000372192.3
exon_skip_26020145294828:45294984:45295073:45295205:45295285:4529543345295073:45295205ENSG00000117425.9ENST00000447098.2,ENST00000372192.3
exon_skip_26022145295285:45295433:45295580:45295702:45296519:4529671545295580:45295702ENSG00000117425.9ENST00000447098.2,ENST00000372192.3
exon_skip_26025145295580:45295702:45296519:45296715:45297377:4529746945296519:45296715ENSG00000117425.9ENST00000447098.2,ENST00000372192.3
exon_skip_26030145297823:45298013:45307518:45307711:45308532:4530861645307518:45307711ENSG00000117425.9ENST00000447098.2,ENST00000372192.3

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 PTCH2

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
ENST000003721924529215945292440Frame-shift
ENST000003721924529558045295702Frame-shift
ENST000003721924529651945296715Frame-shift
ENST000003721924530751845307711Frame-shift
ENST000003721924529192145292059In-frame
ENST000003721924529482845294984In-frame
ENST000003721924529507345295205In-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
ENST000003721924529215945292440Frame-shift
ENST000003721924529558045295702Frame-shift
ENST000003721924529651945296715Frame-shift
ENST000003721924530751845307711Frame-shift
ENST000003721924529192145292059In-frame
ENST000003721924529482845294984In-frame
ENST000003721924529507345295205In-frame

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Infer the effects of exon skipping event on protein functional features for PTCH2

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
ENST0000037219242421203452950734529520512151346361405
ENST0000037219242421203452948284529498413471502405457
ENST00000372192424212034529192145292059310832459921038

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
ENST0000037219242421203452950734529520512151346361405
ENST0000037219242421203452948284529498413471502405457
ENST00000372192424212034529192145292059310832459921038

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
Q9Y6C536140511203ChainID=PRO_0000205970;Note=Protein patched homolog 2
Q9Y6C5361405394552DomainNote=SSD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00199
Q9Y6C5361405370370GlycosylationNote=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C536140579392Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5361405393413TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C540545711203ChainID=PRO_0000205970;Note=Protein patched homolog 2
Q9Y6C5405457394552DomainNote=SSD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00199
Q9Y6C5405457414428Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5405457450457Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5405457393413TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5405457429449TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5992103811203ChainID=PRO_0000205970;Note=Protein patched homolog 2
Q9Y6C59921038995995Natural variantID=VAR_050466;Note=V->M;Dbxref=dbSNP:rs11573591
Q9Y6C5992103810191019Natural variantID=VAR_018939;Note=V->M;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.5;Dbxref=dbSNP:rs11573591
Q9Y6C5992103810131013Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5992103810351064Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C599210389921012TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5992103810141034TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255


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
Q9Y6C536140511203ChainID=PRO_0000205970;Note=Protein patched homolog 2
Q9Y6C5361405394552DomainNote=SSD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00199
Q9Y6C5361405370370GlycosylationNote=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C536140579392Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5361405393413TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C540545711203ChainID=PRO_0000205970;Note=Protein patched homolog 2
Q9Y6C5405457394552DomainNote=SSD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00199
Q9Y6C5405457414428Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5405457450457Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5405457393413TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5405457429449TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5992103811203ChainID=PRO_0000205970;Note=Protein patched homolog 2
Q9Y6C59921038995995Natural variantID=VAR_050466;Note=V->M;Dbxref=dbSNP:rs11573591
Q9Y6C5992103810191019Natural variantID=VAR_018939;Note=V->M;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.5;Dbxref=dbSNP:rs11573591
Q9Y6C5992103810131013Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5992103810351064Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C599210389921012TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9Y6C5992103810141034TransmembraneNote=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255


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SNVs in the skipped exons for PTCH2

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
STADTCGA-BR-8588-01exon_skip_26006
45292160452924404529228645292286Frame_Shift_DelG-p.F951fs
ESCATCGA-IG-A3QL-01exon_skip_26014
45294829452949844529490845294908Frame_Shift_DelA-p.L431fs
ESCATCGA-IG-A3QL-01exon_skip_26014
45294829452949844529490845294908Frame_Shift_DelA-p.L432fs
HNSCTCGA-CV-A6JZ-01exon_skip_26020
45295074452952054529517545295184Frame_Shift_DelAAGCGTTCTC-p.ENAS369fs
LIHCTCGA-G3-A3CJ-01exon_skip_26025
45296520452967154529653845296538Frame_Shift_DelG-p.N266fs
LIHCTCGA-G3-A3CJ-01exon_skip_26025
45296520452967154529653845296538Frame_Shift_DelG-p.P265fs
LIHCTCGA-DD-A39Y-01exon_skip_26025
45296520452967154529655145296551Frame_Shift_DelG-p.P262fs
LIHCTCGA-DD-A1EG-01exon_skip_26025
45296520452967154529663545296635Frame_Shift_DelC-p.G233fs
PCPGTCGA-QR-A703-01exon_skip_26003
45288274452883414528833545288335Nonsense_MutationGAp.Q1122*

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
NCIH2126_LUNG45307519453077114530758245307582Frame_Shift_DelC-p.A68fs
SN12C_KIDNEY45295581452957024529559645295597Frame_Shift_Ins-Gp.Q307fs
SARC9371_BONE45288274452883414528826945288269Missense_MutationCTp.G1144R
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45288274452883414528831745288317Missense_MutationGAp.P1128S
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45288274452883414528831745288317Missense_MutationGAp.P1128S
HEC265_ENDOMETRIUM45288274452883414528832545288325Missense_MutationTCp.K1125R
IGROV1_OVARY45291922452920594529193045291930Missense_MutationCTp.V1036M
SNUC2A_LARGE_INTESTINE45291922452920594529201845292018Missense_MutationGCp.I1006M
SNUC2B_LARGE_INTESTINE45291922452920594529201845292018Missense_MutationGCp.I1006M
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45292160452924404529225545292255Missense_MutationGAp.R961W
EVSAT_BREAST45292160452924404529228545292285Missense_MutationACp.F951V
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45292160452924404529230945292309Missense_MutationGAp.H943Y
SNUC4_LARGE_INTESTINE45292160452924404529232645292326Missense_MutationGAp.A937V
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45292160452924404529233245292332Missense_MutationGAp.A935V
SW48_LARGE_INTESTINE45292160452924404529234445292344Missense_MutationCTp.R931Q
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45292160452924404529234445292344Missense_MutationCAp.R931L
HEC265_ENDOMETRIUM45292160452924404529239345292393Missense_MutationGAp.R915C
SNU1040_LARGE_INTESTINE45292160452924404529239345292393Missense_MutationGAp.R915C
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45292160452924404529241345292413Missense_MutationGTp.A908D
IGROV1_OVARY45294829452949844529484345294843Missense_MutationCTp.A453T
HCC515_LUNG45294829452949844529494445294944Missense_MutationGCp.A419G
NCIH1048_LUNG45294829452949844529495445294954Missense_MutationAGp.W416R
HCC2998_LARGE_INTESTINE45295074452952054529507945295079Missense_MutationGAp.L404F
SNU81_LARGE_INTESTINE45295074452952054529511945295119Missense_MutationGTp.F390L
MEWO_SKIN45295581452957024529559345295593Missense_MutationCTp.G308E
NCIH1436_LUNG45295581452957024529560845295608Missense_MutationGCp.A303G
HEC251_ENDOMETRIUM45295581452957024529562445295624Missense_MutationGTp.L298M
HELA_CERVIX45295581452957024529568445295684Missense_MutationCTp.E278K
BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45295581452957024529568445295684Missense_MutationCTp.E278K
SNUC2A_LARGE_INTESTINE45296520452967154529654345296543Missense_MutationCTp.A264T
SNUC2B_LARGE_INTESTINE45296520452967154529654345296543Missense_MutationCTp.A264T
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45296520452967154529655845296558Missense_MutationGAp.H259Y
HUO3N1_BONE45296520452967154529671145296711Missense_MutationGTp.R208S
C125PM_LARGE_INTESTINE45307519453077114530754545307545Missense_MutationGTp.T80K
L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45307519453077114530754745307547Missense_MutationCGp.E79D
LU134A_LUNG45307519453077114530754945307549Missense_MutationCGp.E79Q
HEC1B_ENDOMETRIUM45307519453077114530755745307557Missense_MutationGAp.A76V
TE9_OESOPHAGUS45307519453077114530763645307636Missense_MutationCTp.G50R
KP4_PANCREAS45307519453077114530766845307668Missense_MutationTAp.Y39F
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45295074452952054529516945295169Nonsense_MutationGAp.Q374*
BE13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE45296520452967154529659245296592Nonsense_MutationGTp.Y247*
HEC59_ENDOMETRIUM45295074452952054529520545295205Splice_SiteGAp.L362L

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTCH2

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 PTCH2


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PTCH2


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RelatedDrugs for PTCH2

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 PTCH2

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