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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:SMYD2-PROX1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SMYD2-PROX1
FusionPDB ID: 84362
FusionGDB2.0 ID: 84362
HgeneTgene
Gene symbol

SMYD2

PROX1

Gene ID

56950

5629

Gene nameSET and MYND domain containing 2prospero homeobox 1
SynonymsHSKM-B|KMT3C|ZMYND14-
Cytomap

1q32.3

1q32.3

Type of geneprotein-codingprotein-coding
DescriptionN-lysine methyltransferase SMYD2SET and MYND domain-containing protein 2histone methyltransferase SMYD2lysine N-methyltransferase 3Czinc finger, MYND domain containing 14prospero homeobox protein 1homeobox prospero-like protein PROX1prospero-related homeobox 1
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000491455, ENST00000366957, 
ENST00000415093, 
ENST00000261454, 
ENST00000366958, ENST00000435016, 
ENST00000498508, ENST00000607726, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 7 X 7=4904 X 4 X 3=48
# samples 114
** MAII scorelog2(11/490*10)=-2.15527822547791
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SMYD2 [Title/Abstract] AND PROX1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SMYD2(214501067)-PROX1(214208992), # samples:3
PROX1(214178615)-SMYD2(214488105), # samples:1
Anticipated loss of major functional domain due to fusion event.SMYD2-PROX1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
SMYD2-PROX1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
SMYD2-PROX1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
SMYD2-PROX1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
SMYD2-PROX1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
SMYD2-PROX1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
SMYD2-PROX1 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
SMYD2-PROX1 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
* 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
HgeneSMYD2

GO:0018026

peptidyl-lysine monomethylation

17108971|20870719

TgenePROX1

GO:0000122

negative regulation of transcription by RNA polymerase II

15205472

TgenePROX1

GO:0001938

positive regulation of endothelial cell proliferation

19210544

TgenePROX1

GO:0001946

lymphangiogenesis

12412020

TgenePROX1

GO:0008284

positive regulation of cell proliferation

12198161

TgenePROX1

GO:0010468

regulation of gene expression

12198161

TgenePROX1

GO:0010595

positive regulation of endothelial cell migration

19210544

TgenePROX1

GO:0043433

negative regulation of DNA-binding transcription factor activity

15205472|16488887

TgenePROX1

GO:0045071

negative regulation of viral genome replication

19264593

TgenePROX1

GO:0045737

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

19210544

TgenePROX1

GO:0045892

negative regulation of transcription, DNA-templated

15143342|15205472

TgenePROX1

GO:0060836

lymphatic endothelial cell differentiation

12198161


check buttonFusion gene breakpoints across SMYD2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across PROX1 (3'-gene)
* 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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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4LIHCTCGA-ED-A7PX-01ASMYD2chr1

214501067

-PROX1chr1

214208992

+
ChimerDB4LIHCTCGA-ED-A7PX-01ASMYD2chr1

214501067

+PROX1chr1

214208992

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000415093SMYD2chr1214501067+ENST00000366958PROX1chr1214208992+633172722912296
ENST00000366957SMYD2chr1214501067+ENST00000366958PROX1chr1214208992+633172722912296

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000415093ENST00000366958SMYD2chr1214501067+PROX1chr1214208992+0.0002391270.9997609
ENST00000366957ENST00000366958SMYD2chr1214501067+PROX1chr1214208992+0.0002391270.9997609

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>84362_84362_1_SMYD2-PROX1_SMYD2_chr1_214501067_ENST00000366957_PROX1_chr1_214208992_ENST00000366958_length(amino acids)=296AA_BP=235
MRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLEC
SPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVN
CNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVPERFLEVAQITLREFFNAIIAGKDVDPSWKKAIY

--------------------------------------------------------------

>84362_84362_2_SMYD2-PROX1_SMYD2_chr1_214501067_ENST00000415093_PROX1_chr1_214208992_ENST00000366958_length(amino acids)=296AA_BP=235
MRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLEC
SPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVN
CNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVPERFLEVAQITLREFFNAIIAGKDVDPSWKKAIY

--------------------------------------------------------------

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:214501067/chr1:214208992)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSMYD2chr1:214501067chr1:214208992ENST00000366957+71217_19235.0434.0RegionNote=S-adenosyl-L-methionine binding
HgeneSMYD2chr1:214501067chr1:214208992ENST00000366957+712183_185235.0434.0RegionNote=Peptide substrate binding
HgeneSMYD2chr1:214501067chr1:214208992ENST00000366957+712206_207235.0434.0RegionNote=S-adenosyl-L-methionine binding
HgeneSMYD2chr1:214501067chr1:214208992ENST00000366957+71252_90235.0434.0Zinc fingerMYND-type

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSMYD2chr1:214501067chr1:214208992ENST00000366957+7127_241235.0434.0DomainSET
HgeneSMYD2chr1:214501067chr1:214208992ENST00000366957+712258_260235.0434.0RegionNote=S-adenosyl-L-methionine binding
TgenePROX1chr1:214501067chr1:214208992ENST0000026145424215_219676.0738.0Compositional biasNote=Poly-Gln
TgenePROX1chr1:214501067chr1:214208992ENST0000036695835215_219676.0738.0Compositional biasNote=Poly-Gln
TgenePROX1chr1:214501067chr1:214208992ENST0000043501635215_219676.0738.0Compositional biasNote=Poly-Gln
TgenePROX1chr1:214501067chr1:214208992ENST0000049850835215_219676.0738.0Compositional biasNote=Poly-Gln
TgenePROX1chr1:214501067chr1:214208992ENST0000026145424577_635676.0738.0DomainProspero-type homeo
TgenePROX1chr1:214501067chr1:214208992ENST0000026145424636_735676.0738.0DomainProspero
TgenePROX1chr1:214501067chr1:214208992ENST0000036695835577_635676.0738.0DomainProspero-type homeo
TgenePROX1chr1:214501067chr1:214208992ENST0000036695835636_735676.0738.0DomainProspero
TgenePROX1chr1:214501067chr1:214208992ENST0000043501635577_635676.0738.0DomainProspero-type homeo
TgenePROX1chr1:214501067chr1:214208992ENST0000043501635636_735676.0738.0DomainProspero
TgenePROX1chr1:214501067chr1:214208992ENST0000049850835577_635676.0738.0DomainProspero-type homeo
TgenePROX1chr1:214501067chr1:214208992ENST0000049850835636_735676.0738.0DomainProspero
TgenePROX1chr1:214501067chr1:214208992ENST0000026145424577_735676.0738.0RegionHomeo-Prospero
TgenePROX1chr1:214501067chr1:214208992ENST0000036695835577_735676.0738.0RegionHomeo-Prospero
TgenePROX1chr1:214501067chr1:214208992ENST0000043501635577_735676.0738.0RegionHomeo-Prospero
TgenePROX1chr1:214501067chr1:214208992ENST0000049850835577_735676.0738.0RegionHomeo-Prospero


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
SMYD2
PROX1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
TgenePROX1chr1:214501067chr1:214208992ENST00000261454241_28676.0738.0RORG
TgenePROX1chr1:214501067chr1:214208992ENST00000366958351_28676.0738.0RORG
TgenePROX1chr1:214501067chr1:214208992ENST00000435016351_28676.0738.0RORG
TgenePROX1chr1:214501067chr1:214208992ENST00000498508351_28676.0738.0RORG


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Related Drugs to SMYD2-PROX1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to SMYD2-PROX1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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