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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: 34869

FusionGeneSummary for SMC6_PTPRA

check button Fusion gene summary
Fusion gene informationFusion gene name: SMC6_PTPRA
Fusion gene ID: 34869
HgeneTgene
Gene symbol

SMC6

PTPRA

Gene ID

79677

5786

Gene namestructural maintenance of chromosomes 6protein tyrosine phosphatase, receptor type A
SynonymsSMC-6|SMC6L1|hSMC6HEPTP|HLPR|HPTPA|HPTPalpha|LRP|PTPA|PTPRL2|R-PTP-alpha|RPTPA
Cytomap

2p24.2

20p13

Type of geneprotein-codingprotein-coding
Descriptionstructural maintenance of chromosomes protein 6SMC protein 6SMC6 structural maintenance of chromosomes 6-like 1receptor-type tyrosine-protein phosphatase alphaLeukocyte common antigen-related peptide (protein tyrosine phosphate)PTPLCA-related phosphatasePTPase-alphaprotein tyrosine phosphatase, receptor type, alpha polypeptideprotein-tyrosine phosphatase alph
Modification date2018051920180527
UniProtAcc

Q96SB8

P18433

Ensembl transtripts involved in fusion geneENST00000402989, ENST00000448223, 
ENST00000351948, ENST00000381272, 
ENST00000489535, 		ENST00000380393, 
ENST00000216877, ENST00000358719, 
ENST00000399903, ENST00000425918, 
ENST00000318266, ENST00000356147, 
Fusion gene scores* DoF score2 X 2 X 1=43 X 3 X 1=9
# samples 23
** MAII scorelog2(2/4*10)=2.32192809488736log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SMC6 [Title/Abstract] AND PTPRA [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
HgeneSMC6

GO:0006974

cellular response to DNA damage stimulus

11408570|25931565


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
ChiTaRS3.1DA756796SMC6chr2

17980902

-PTPRAchr20

2903852

+
* 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
5UTR-5UTRENST00000402989ENST00000380393SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000402989ENST00000216877SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000402989ENST00000358719SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000402989ENST00000399903SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000402989ENST00000425918SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000402989ENST00000318266SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000402989ENST00000356147SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000448223ENST00000380393SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000448223ENST00000216877SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000448223ENST00000358719SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000448223ENST00000399903SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000448223ENST00000425918SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000448223ENST00000318266SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000448223ENST00000356147SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000351948ENST00000380393SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000351948ENST00000216877SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000351948ENST00000358719SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000351948ENST00000399903SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000351948ENST00000425918SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000351948ENST00000318266SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000351948ENST00000356147SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000381272ENST00000380393SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000381272ENST00000216877SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000381272ENST00000358719SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000381272ENST00000399903SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000381272ENST00000425918SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000381272ENST00000318266SMC6chr2

17980902

-PTPRAchr20

2903852

+
intron-5UTRENST00000381272ENST00000356147SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000489535ENST00000380393SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000489535ENST00000216877SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000489535ENST00000358719SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000489535ENST00000399903SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000489535ENST00000425918SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000489535ENST00000318266SMC6chr2

17980902

-PTPRAchr20

2903852

+
5UTR-5UTRENST00000489535ENST00000356147SMC6chr2

17980902

-PTPRAchr20

2903852

+

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FusionProtFeatures for SMC6_PTPRA


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SMC6

Q96SB8

PTPRA

P18433

Core component of the SMC5-SMC6 complex, a complexinvolved in DNA double-strand breaks by homologous recombination.The complex may promote sister chromatid homologous recombinationby recruiting the SMC1-SMC3 cohesin complex to double-strandbreaks. The complex is required for telomere maintenance viarecombination in ALT (alternative lengthening of telomeres) celllines and mediates sumoylation of shelterin complex (telosome)components which is proposed to lead to shelterin complexdisassembly in ALT-associated PML bodies (APBs). Required forrecruitment of telomeres to PML nuclear bodies. SMC5-SMC6 complexmay prevent transcription of episomal DNA, such as circular viralDNA genome (PubMed:26983541). {ECO:0000269|PubMed:16810316,ECO:0000269|PubMed:17589526, ECO:0000269|PubMed:26983541}.

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 SMC6_PTPRA


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 SMC6_PTPRA


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


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


Top

RelatedDrugs for SMC6_PTPRA


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 SMC6_PTPRA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgenePTPRAC0036341Schizophrenia2PSYGENET
TgenePTPRAC0151744Myocardial Ischemia1CTD_human