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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: 22641

FusionGeneSummary for MSI2_SMYD3

check button Fusion gene summary
Fusion gene informationFusion gene name: MSI2_SMYD3
Fusion gene ID: 22641
HgeneTgene
Gene symbol

MSI2

SMYD3

Gene ID

124540

64754

Gene namemusashi RNA binding protein 2SET and MYND domain containing 3
SynonymsMSI2HKMT3E|ZMYND1|ZNFN3A1|bA74P14.1
Cytomap

17q22

1q44

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein Musashi homolog 2musashi homolog 2musashi-2histone-lysine N-methyltransferase SMYD3SET and MYND domain-containing protein 3bA74P14.1 (novel protein)zinc finger MYND domain-containing protein 1zinc finger protein, subfamily 3A (MYND domain containing), 1zinc finger, MYND domain containing 1
Modification date2018052320180519
UniProtAcc

Q96DH6

Q9H7B4

Ensembl transtripts involved in fusion geneENST00000416426, ENST00000284073, 
ENST00000322684, ENST00000442934, 
ENST00000579180, ENST00000579505, 
ENST00000541742, ENST00000490107, 
ENST00000388985, ENST00000366517, 
ENST00000403792, 
Fusion gene scores* DoF score29 X 8 X 12=278417 X 9 X 13=1989
# samples 2931
** MAII scorelog2(29/2784*10)=-3.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(31/1989*10)=-2.68170315555951
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MSI2 [Title/Abstract] AND SMYD3 [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

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
TCGARVPRADTCGA-TP-A8TT-01AMSI2chr17

55607085

+SMYD3chr1

246518396

-
* 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-5UTRENST00000416426ENST00000541742MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000416426ENST00000490107MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000416426ENST00000388985MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-intronENST00000416426ENST00000366517MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-intronENST00000416426ENST00000403792MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000284073ENST00000541742MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000284073ENST00000490107MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000284073ENST00000388985MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-intronENST00000284073ENST00000366517MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-intronENST00000284073ENST00000403792MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000322684ENST00000541742MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000322684ENST00000490107MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000322684ENST00000388985MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-intronENST00000322684ENST00000366517MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-intronENST00000322684ENST00000403792MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000442934ENST00000541742MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000442934ENST00000490107MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000442934ENST00000388985MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-intronENST00000442934ENST00000366517MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-intronENST00000442934ENST00000403792MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000579180ENST00000541742MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000579180ENST00000490107MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-5UTRENST00000579180ENST00000388985MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-intronENST00000579180ENST00000366517MSI2chr17

55607085

+SMYD3chr1

246518396

-
5CDS-intronENST00000579180ENST00000403792MSI2chr17

55607085

+SMYD3chr1

246518396

-
3UTR-5UTRENST00000579505ENST00000541742MSI2chr17

55607085

+SMYD3chr1

246518396

-
3UTR-5UTRENST00000579505ENST00000490107MSI2chr17

55607085

+SMYD3chr1

246518396

-
3UTR-5UTRENST00000579505ENST00000388985MSI2chr17

55607085

+SMYD3chr1

246518396

-
3UTR-intronENST00000579505ENST00000366517MSI2chr17

55607085

+SMYD3chr1

246518396

-
3UTR-intronENST00000579505ENST00000403792MSI2chr17

55607085

+SMYD3chr1

246518396

-

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FusionProtFeatures for MSI2_SMYD3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
MSI2

Q96DH6

SMYD3

Q9H7B4

RNA binding protein that regulates the expression oftarget mRNAs at the translation level. May play a role in theproliferation and maintenance of stem cells in the central nervoussystem (By similarity). {ECO:0000250}. Histone methyltransferase. Specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but notmonomethylation (PubMed:15235609, PubMed:22419068). Alsomethylates 'Lys-5' of histone H4 (PubMed:22419068). Plays animportant role in transcriptional activation as a member of an RNApolymerase complex (PubMed:15235609). Binds DNA containing 5'-CCCTCC-3' or 5'-GAGGGG-3' sequences (PubMed:15235609).{ECO:0000269|PubMed:15235609, ECO:0000269|PubMed:22419068}.

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 MSI2_SMYD3


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 MSI2_SMYD3


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
MSI2GRB2, H2AFX, CUL3, VCAM1, SOX2, TARDBP, RPA3, RPA2, RPA1, HNRNPH2, MEOX2, SUZ12, RNF2, BMI1, MRPL4, ICK, ANXA13, TIMM10B, RBFOX2, FKBP1A, CRIP1, CTSB, EIF3G, HNRNPA1, PABPC1, PABPC4, PIN1, STIP1, UFM1, WDR1, RAB7A, UBE2L3, NTRK1, CDK1, KIF21A, RHOBTB2, MDM2, TP53, ANKRD40, LOXL3, G3BP1, RNF157SMYD3MEST, HELZ, POLR2A, HSP90AA1, HIST3H3, ESR1, EZH2, EED, APP, CAMK2B, NDUFAB1, NFYB, CYP39A1, VANGL1, H3F3C, TRIT1, ZNF557, CDC37, HSP90AB1, HSP90AB4P, HSP90AB3P, HSP90AA5P, MAGED4B, KDM3B, RCAN3, PLCB3, TRMT2A, KMT2E


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 MSI2_SMYD3


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 MSI2_SMYD3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneSMYD3C0236733Amphetamine-Related Disorders1CTD_human