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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: 29469

FusionGeneSummary for PTPN9_BUB3

check button Fusion gene summary
Fusion gene informationFusion gene name: PTPN9_BUB3
Fusion gene ID: 29469
HgeneTgene
Gene symbol

PTPN9

BUB3

Gene ID

5780

9184

Gene nameprotein tyrosine phosphatase, non-receptor type 9BUB3, mitotic checkpoint protein
SynonymsMEG2|PTPMEG2BUB3L|hBUB3
Cytomap

15q24.2

10q26.13

Type of geneprotein-codingprotein-coding
Descriptiontyrosine-protein phosphatase non-receptor type 9PTPase-MEG2protein-tyrosine phosphatase MEG2mitotic checkpoint protein BUB3BUB3 budding uninhibited by benzimidazoles 3 homologbudding uninhibited by benomylbudding uninhibited by benzimidazoles 3 homologmitotic checkpoint componenttesticular tissue protein Li 27
Modification date2018052020180523
UniProtAcc

P43378

O43684

Ensembl transtripts involved in fusion geneENST00000306726, ENST00000564970, 
ENST00000368865, ENST00000538238, 
ENST00000368859, ENST00000368858, 
ENST00000481952, 
Fusion gene scores* DoF score8 X 6 X 7=3361 X 1 X 1=1
# samples 136
** MAII scorelog2(13/336*10)=-1.36994960975031
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/1*10)=5.90689059560852
Context

PubMed: PTPN9 [Title/Abstract] AND BUB3 [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
HgenePTPN9

GO:0010977

negative regulation of neuron projection development

27655914

HgenePTPN9

GO:0035335

peptidyl-tyrosine dephosphorylation

27655914

HgenePTPN9

GO:1903078

positive regulation of protein localization to plasma membrane

27655914

TgeneBUB3

GO:0008608

attachment of spindle microtubules to kinetochore

18199686


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
ChiTaRS3.1BG212872PTPN9chr15

75816548

-BUB3chr10

124924563

+
ChiTaRS3.1BG198840PTPN9chr15

75816548

-BUB3chr10

124924563

+
ChiTaRS3.1BG220202PTPN9chr15

75816548

-BUB3chr10

124924563

+
ChiTaRS3.1BG186971PTPN9chr15

75816548

-BUB3chr10

124924563

+
ChiTaRS3.1BG204496PTPN9chr15

75816548

-BUB3chr10

124924563

+
ChiTaRS3.1BG459834PTPN9chr15

75816548

-BUB3chr10

124924563

+
* 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
5CDS-3UTRENST00000306726ENST00000368865PTPN9chr15

75816548

-BUB3chr10

124924563

+
5CDS-intronENST00000306726ENST00000538238PTPN9chr15

75816548

-BUB3chr10

124924563

+
5CDS-intronENST00000306726ENST00000368859PTPN9chr15

75816548

-BUB3chr10

124924563

+
5CDS-intronENST00000306726ENST00000368858PTPN9chr15

75816548

-BUB3chr10

124924563

+
5CDS-intronENST00000306726ENST00000481952PTPN9chr15

75816548

-BUB3chr10

124924563

+
intron-3UTRENST00000564970ENST00000368865PTPN9chr15

75816548

-BUB3chr10

124924563

+
intron-intronENST00000564970ENST00000538238PTPN9chr15

75816548

-BUB3chr10

124924563

+
intron-intronENST00000564970ENST00000368859PTPN9chr15

75816548

-BUB3chr10

124924563

+
intron-intronENST00000564970ENST00000368858PTPN9chr15

75816548

-BUB3chr10

124924563

+
intron-intronENST00000564970ENST00000481952PTPN9chr15

75816548

-BUB3chr10

124924563

+

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FusionProtFeatures for PTPN9_BUB3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PTPN9

P43378

BUB3

O43684

Protein-tyrosine phosphatase that could participate inthe transfer of hydrophobic ligands or in functions of the Golgiapparatus. {ECO:0000269|PubMed:19167335}. Has a dual function in spindle-assembly checkpointsignaling and in promoting the establishment of correctkinetochore-microtubule (K-MT) attachments. Promotes the formationof stable end-on bipolar attachments. Necessary for kinetochorelocalization of BUB1. Regulates chromosome segregation duringoocyte meiosis. The BUB1/BUB3 complex plays a role in theinhibition of anaphase-promoting complex or cyclosome (APC/C) whenspindle-assembly checkpoint is activated and inhibits theubiquitin ligase activity of APC/C by phosphorylating itsactivator CDC20. This complex can also phosphorylate MAD1L1.{ECO:0000269|PubMed:10198256, ECO:0000269|PubMed:15525512,ECO:0000269|PubMed:18199686}.

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 PTPN9_BUB3


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 PTPN9_BUB3


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
PTPN9RTN3, GHR, MYC, TP53BP1, VCP, AGTRAP, REEP6, MAL2, CMTM5, ENO1, MOV10, NXF1, NTRK1, CREB3, LZTR1, PC, EYA1, RAD51C, FAM26D, VSIG8, C5AR2, MDK, PDCD1, PTPN9, GEMIN8, FSIP1, SMN1, DDX20, GEMIN4, PMPCA, SLC39A7, STRAP, TUBA3C, AAR2, SMN2, TUBA3D, LMNABUB3HDAC1, HDAC2, PARP1, BUB1B, APC, USP11, USP7, CDC20, CDC27, HDGF, ANAPC4, ELAVL1, SF3A2, CUL3, COPS5, BUB1, MAD2L1, SMAD2, SMAD3, TOP1, ZNF207, SEPT2, FN1, VCAM1, NKAP, ITGA4, EGFR, SUGT1, CPNE1, UBA1, RPL37A, THRA, EXOC3, WBP4, CLIP1, RPA3, RPA2, RPA1, HUWE1, PSTPIP1, CCT7, CCT2, BTBD10, KCTD20, ZFC3H1, ANAPC16, UBR5, APEX1, METTL13, HK2, NTRK1, XPO1, HIST1H3E, DNM2, RNPS1, CCT4, CCT5, INTS7, RASIP1, KIAA1109, KPNB1, YBX1, MCM2, GLI1, SNW1, CDC5L, BOP1, PES1, CCT6B, CCT3, CASC5, CDC23, TCP1, CCT6A, ACTBL2, CCT8, ACTA2, LZTFL1, DLD, DNM1L, HSD17B10, UBE2A, BRCA1


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 PTPN9_BUB3


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 PTPN9_BUB3


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