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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 29476

FusionGeneSummary for PTPRA_CDK5RAP1

check button Fusion gene summary
Fusion gene informationFusion gene name: PTPRA_CDK5RAP1
Fusion gene ID: 29476
HgeneTgene
Gene symbol

PTPRA

CDK5RAP1

Gene ID

5786

51654

Gene nameprotein tyrosine phosphatase, receptor type ACDK5 regulatory subunit associated protein 1
SynonymsHEPTP|HLPR|HPTPA|HPTPalpha|LRP|PTPA|PTPRL2|R-PTP-alpha|RPTPAC20orf34|C42|CGI-05|HSPC167
Cytomap

20p13

20q11.21

Type of geneprotein-codingprotein-coding
Descriptionreceptor-type tyrosine-protein phosphatase alphaLeukocyte common antigen-related peptide (protein tyrosine phosphate)PTPLCA-related phosphatasePTPase-alphaprotein tyrosine phosphatase, receptor type, alpha polypeptideprotein-tyrosine phosphatase alphCDK5 regulatory subunit-associated protein 1CDK5 activator-binding protein C42
Modification date2018052720180523
UniProtAcc

P18433

Q96SZ6

Ensembl transtripts involved in fusion geneENST00000380393, ENST00000216877, 
ENST00000358719, ENST00000399903, 
ENST00000425918, ENST00000318266, 
ENST00000356147, 
ENST00000473997, 
ENST00000346416, ENST00000339269, 
ENST00000357886, ENST00000544843, 
ENST00000477105, 
Fusion gene scores* DoF score13 X 10 X 8=10406 X 4 X 6=144
# samples 146
** MAII scorelog2(14/1040*10)=-2.89308479608349
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PTPRA [Title/Abstract] AND CDK5RAP1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneCDK5RAP1

GO:0045736

negative regulation of cyclin-dependent protein serine/threonine kinase activity

11882646


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVCOADTCGA-A6-2677-01BPTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-3CDSENST00000380393ENST00000473997PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
intron-3CDSENST00000380393ENST00000346416PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
intron-3CDSENST00000380393ENST00000339269PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
intron-3CDSENST00000380393ENST00000357886PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
intron-3CDSENST00000380393ENST00000544843PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
intron-5UTRENST00000380393ENST00000477105PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000216877ENST00000473997PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000216877ENST00000346416PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000216877ENST00000339269PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000216877ENST00000357886PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000216877ENST00000544843PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-5UTRENST00000216877ENST00000477105PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000358719ENST00000473997PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000358719ENST00000346416PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000358719ENST00000339269PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000358719ENST00000357886PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000358719ENST00000544843PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-5UTRENST00000358719ENST00000477105PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000399903ENST00000473997PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000399903ENST00000346416PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000399903ENST00000339269PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000399903ENST00000357886PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000399903ENST00000544843PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-5UTRENST00000399903ENST00000477105PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000425918ENST00000473997PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000425918ENST00000346416PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000425918ENST00000339269PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000425918ENST00000357886PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000425918ENST00000544843PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-5UTRENST00000425918ENST00000477105PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000318266ENST00000473997PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000318266ENST00000346416PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000318266ENST00000339269PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000318266ENST00000357886PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-3CDSENST00000318266ENST00000544843PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
5UTR-5UTRENST00000318266ENST00000477105PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
intron-3CDSENST00000356147ENST00000473997PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
intron-3CDSENST00000356147ENST00000346416PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
intron-3CDSENST00000356147ENST00000339269PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
intron-3CDSENST00000356147ENST00000357886PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
intron-3CDSENST00000356147ENST00000544843PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-
intron-5UTRENST00000356147ENST00000477105PTPRAchr20

2854406

+CDK5RAP1chr20

31975339

-

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FusionProtFeatures for PTPRA_CDK5RAP1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PTPRA

P18433

CDK5RAP1

Q96SZ6


check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for PTPRA_CDK5RAP1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for PTPRA_CDK5RAP1


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
PTPRAGRB2, KCNA2, SRC, FYN, UVRAG, GABARAPL2, CALM1, LGALS8, FCN1, HSPB1, YWHAZ, SMEK1, EGFR, ERBB2, ARL2, ATXN2, KCNMA1, NCBP1, PSAT1, PTPRE, VPS25, TMEM51, CCDC88A, EPB41L1, PSD3, BASP1, GPRIN3, EXOC3, BAIAP2, RAPH1, NF2, GAB1, ASNSD1, DENND4A, TPCN2, SP4, CYB561, GALNT12, LGALS1, PTPRA, TXNDC5, XPO5, TNPO3, SAAL1, XPO4, B4GAT1, XPO6, PDIA6, NCDN, CSE1L, TNPO1, XPOT, CANX, MBP, PTPRGCDK5RAP1CDK5R1, BAG3, EXOSC3, EXOSC5, KCTD17, C9orf41, WWP2, KIAA0930, ZMYND19, NDUFAF5, XRCC6, XRCC5, PDZK1, PLA2G10, ZZEF1, ARMC8, MATR3


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for PTPRA_CDK5RAP1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for PTPRA_CDK5RAP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePTPRAC0036341Schizophrenia2PSYGENET
HgenePTPRAC0151744Myocardial Ischemia1CTD_human