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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:SMYD3-ZNF695 (FusionGDB2 ID:84390)

Fusion Gene Summary for SMYD3-ZNF695

check button Fusion gene summary
Fusion gene informationFusion gene name: SMYD3-ZNF695
Fusion gene ID: 84390
HgeneTgene
Gene symbol

SMYD3

ZNF695

Gene ID

64754

57116

Gene nameSET and MYND domain containing 3zinc finger protein 695
SynonymsKMT3E|ZMYND1|ZNFN3A1|bA74P14.1SBZF3
Cytomap

1q44

1q44

Type of geneprotein-codingprotein-coding
Descriptionhistone-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 1zinc finger protein 695zinc finger protein SBZF3
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000388985, ENST00000403792, 
ENST00000490107, ENST00000366517, 
ENST00000541742, 		ENST00000498046, 
ENST00000339986, ENST00000487338, 
Fusion gene scores* DoF score22 X 13 X 10=28603 X 2 X 4=24
# samples 244
** MAII scorelog2(24/2860*10)=-3.57490883605723
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SMYD3 [Title/Abstract] AND ZNF695 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMYD3(246670356)-ZNF695(247131094), # samples:3
ZNF695(247171208)-SMYD3(246093239), # samples:1
Anticipated loss of major functional domain due to fusion event.SMYD3-ZNF695 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
SMYD3-ZNF695 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
SMYD3-ZNF695 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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

check buttonFusion gene breakpoints across SMYD3 (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 ZNF695 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4BLCATCGA-DK-AA6W-01ASMYD3chr1

246670356

-ZNF695chr1

247109129

-
ChimerDB4BLCATCGA-DK-AA6WSMYD3chr1

246670356

-ZNF695chr1

247109129

-
ChimerDB4ESCATCGA-LN-A4A1-01ASMYD3chr1

246670356

-ZNF695chr1

247131094

-
ChimerDB4ESCATCGA-LN-A4A1SMYD3chr1

246670356

-ZNF695chr1

247131094

-
ChimerDB4HNSCTCGA-CN-6018-01ASMYD3chr1

246670356

-ZNF695chr1

247131094

-


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Fusion Gene ORF analysis for SMYD3-ZNF695

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-5UTRENST00000388985ENST00000498046SMYD3chr1

246670356

-ZNF695chr1

247109129

-
5CDS-5UTRENST00000388985ENST00000498046SMYD3chr1

246670356

-ZNF695chr1

247131094

-
5CDS-5UTRENST00000403792ENST00000498046SMYD3chr1

246670356

-ZNF695chr1

247109129

-
5CDS-5UTRENST00000403792ENST00000498046SMYD3chr1

246670356

-ZNF695chr1

247131094

-
5CDS-intronENST00000388985ENST00000339986SMYD3chr1

246670356

-ZNF695chr1

247109129

-
5CDS-intronENST00000388985ENST00000339986SMYD3chr1

246670356

-ZNF695chr1

247131094

-
5CDS-intronENST00000403792ENST00000339986SMYD3chr1

246670356

-ZNF695chr1

247109129

-
5CDS-intronENST00000403792ENST00000339986SMYD3chr1

246670356

-ZNF695chr1

247131094

-
5UTR-3CDSENST00000490107ENST00000487338SMYD3chr1

246670356

-ZNF695chr1

247109129

-
5UTR-3CDSENST00000490107ENST00000487338SMYD3chr1

246670356

-ZNF695chr1

247131094

-
5UTR-5UTRENST00000490107ENST00000498046SMYD3chr1

246670356

-ZNF695chr1

247109129

-
5UTR-5UTRENST00000490107ENST00000498046SMYD3chr1

246670356

-ZNF695chr1

247131094

-
5UTR-intronENST00000490107ENST00000339986SMYD3chr1

246670356

-ZNF695chr1

247109129

-
5UTR-intronENST00000490107ENST00000339986SMYD3chr1

246670356

-ZNF695chr1

247131094

-
Frame-shiftENST00000388985ENST00000487338SMYD3chr1

246670356

-ZNF695chr1

247109129

-
Frame-shiftENST00000403792ENST00000487338SMYD3chr1

246670356

-ZNF695chr1

247109129

-
In-frameENST00000388985ENST00000487338SMYD3chr1

246670356

-ZNF695chr1

247131094

-
In-frameENST00000403792ENST00000487338SMYD3chr1

246670356

-ZNF695chr1

247131094

-
intron-3CDSENST00000366517ENST00000487338SMYD3chr1

246670356

-ZNF695chr1

247109129

-
intron-3CDSENST00000366517ENST00000487338SMYD3chr1

246670356

-ZNF695chr1

247131094

-
intron-3CDSENST00000541742ENST00000487338SMYD3chr1

246670356

-ZNF695chr1

247109129

-
intron-3CDSENST00000541742ENST00000487338SMYD3chr1

246670356

-ZNF695chr1

247131094

-
intron-5UTRENST00000366517ENST00000498046SMYD3chr1

246670356

-ZNF695chr1

247109129

-
intron-5UTRENST00000366517ENST00000498046SMYD3chr1

246670356

-ZNF695chr1

247131094

-
intron-5UTRENST00000541742ENST00000498046SMYD3chr1

246670356

-ZNF695chr1

247109129

-
intron-5UTRENST00000541742ENST00000498046SMYD3chr1

246670356

-ZNF695chr1

247131094

-
intron-intronENST00000366517ENST00000339986SMYD3chr1

246670356

-ZNF695chr1

247109129

-
intron-intronENST00000366517ENST00000339986SMYD3chr1

246670356

-ZNF695chr1

247131094

-
intron-intronENST00000541742ENST00000339986SMYD3chr1

246670356

-ZNF695chr1

247109129

-
intron-intronENST00000541742ENST00000339986SMYD3chr1

246670356

-ZNF695chr1

247131094

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000388985SMYD3chr1246670356-ENST00000487338ZNF695chr1247131094-415164279193
ENST00000403792SMYD3chr1246670356-ENST00000487338ZNF695chr1247131094-5102593740125

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
ENST00000388985ENST00000487338SMYD3chr1246670356-ZNF695chr1247131094-0.80940960.1905904
ENST00000403792ENST00000487338SMYD3chr1246670356-ZNF695chr1247131094-0.76161950.23838052

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Fusion Genomic Features for SMYD3-ZNF695


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.
genomic feature

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for SMYD3-ZNF695


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/chr1:246670356/chr1:247131094)
- 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: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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
HgeneSMYD3chr1:246670356chr1:247131094ENST00000388985-11214_1654429.0RegionS-adenosyl-L-methionine binding
TgeneZNF695chr1:246670356chr1:247131094ENST00000339986044_870516.0DomainKRAB
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604156_1780516.0Zinc fingerC2H2-type 1%3B atypical
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604184_2060516.0Zinc fingerC2H2-type 2%3B degenerate
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604212_2340516.0Zinc fingerC2H2-type 3%3B atypical
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604240_2620516.0Zinc fingerC2H2-type 4%3B degenerate
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604268_2900516.0Zinc fingerC2H2-type 5
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604296_3180516.0Zinc fingerC2H2-type 6
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604324_3460516.0Zinc fingerC2H2-type 7
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604352_3740516.0Zinc fingerC2H2-type 8
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604380_4020516.0Zinc fingerC2H2-type 9
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604408_4300516.0Zinc fingerC2H2-type 10
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604436_4580516.0Zinc fingerC2H2-type 11
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604464_4860516.0Zinc fingerC2H2-type 12
TgeneZNF695chr1:246670356chr1:247131094ENST0000033998604492_5140516.0Zinc fingerC2H2-type 13
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836156_178130173.0Zinc fingerC2H2-type 1%3B atypical
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836184_206130173.0Zinc fingerC2H2-type 2%3B degenerate
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836212_234130173.0Zinc fingerC2H2-type 3%3B atypical
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836240_262130173.0Zinc fingerC2H2-type 4%3B degenerate
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836268_290130173.0Zinc fingerC2H2-type 5
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836296_318130173.0Zinc fingerC2H2-type 6
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836324_346130173.0Zinc fingerC2H2-type 7
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836352_374130173.0Zinc fingerC2H2-type 8
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836380_402130173.0Zinc fingerC2H2-type 9
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836408_430130173.0Zinc fingerC2H2-type 10
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836436_458130173.0Zinc fingerC2H2-type 11
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836464_486130173.0Zinc fingerC2H2-type 12
TgeneZNF695chr1:246670356chr1:247131094ENST0000048733836492_514130173.0Zinc fingerC2H2-type 13

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSMYD3chr1:246670356chr1:247131094ENST00000388985-1124_24054429.0DomainSET
HgeneSMYD3chr1:246670356chr1:247131094ENST00000490107-1124_2400370.0DomainSET
HgeneSMYD3chr1:246670356chr1:247131094ENST00000541742-1124_2400370.0DomainSET
HgeneSMYD3chr1:246670356chr1:247131094ENST00000388985-112205_20654429.0RegionS-adenosyl-L-methionine binding
HgeneSMYD3chr1:246670356chr1:247131094ENST00000490107-11214_160370.0RegionS-adenosyl-L-methionine binding
HgeneSMYD3chr1:246670356chr1:247131094ENST00000490107-112205_2060370.0RegionS-adenosyl-L-methionine binding
HgeneSMYD3chr1:246670356chr1:247131094ENST00000541742-11214_160370.0RegionS-adenosyl-L-methionine binding
HgeneSMYD3chr1:246670356chr1:247131094ENST00000541742-112205_2060370.0RegionS-adenosyl-L-methionine binding
HgeneSMYD3chr1:246670356chr1:247131094ENST00000388985-11249_8754429.0Zinc fingerMYND-type
HgeneSMYD3chr1:246670356chr1:247131094ENST00000490107-11249_870370.0Zinc fingerMYND-type
HgeneSMYD3chr1:246670356chr1:247131094ENST00000541742-11249_870370.0Zinc fingerMYND-type
TgeneZNF695chr1:246670356chr1:247131094ENST00000487338364_87130173.0DomainKRAB


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Fusion Gene Sequence for SMYD3-ZNF695


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>84390_84390_1_SMYD3-ZNF695_SMYD3_chr1_246670356_ENST00000388985_ZNF695_chr1_247131094_ENST00000487338_length(transcript)=415nt_BP=164nt
ATGGAGCCGCTGAAGGTGGAAAAGTTCGCAACCGCCAAGAGGGGAAACGGGCTGCGCGCCGTGACCCCGCTGCGCCCCGGAGAGCTACTC
TTCCGCTCGGATCCCTTGGCGTACACGGTGTGCAAGGGGAGTCGTGGCGTCGTCTGCGACCGCTGCCTTCTCGGCCATGTGAAGATGTGC
TTGCTTCCCCTTTGCCTTCTGCCATGATTCTAAGTTTCCTGAGGCCTCCCCAGAAGCAGAAGCATGTAAAGCCCACAGAACCGGTCCAGT
CGTCGACCATCGAGCTGCTTTGAAGACCCTGCGGAGGTTCCGTCGCTGCTTGAACACAGTGCCTGGACTCCCTGCTCCGTGAGGCGAATT

>84390_84390_1_SMYD3-ZNF695_SMYD3_chr1_246670356_ENST00000388985_ZNF695_chr1_247131094_ENST00000487338_length(amino acids)=93AA_BP=6
MVDDWTGSVGFTCFCFWGGLRKLRIMAEGKGEASTSSHGREGSGRRRRHDSPCTPCTPRDPSGRVALRGAAGSRRAARFPSWRLRTFPPS

--------------------------------------------------------------
>84390_84390_2_SMYD3-ZNF695_SMYD3_chr1_246670356_ENST00000403792_ZNF695_chr1_247131094_ENST00000487338_length(transcript)=510nt_BP=259nt
GTGCGCGCAGGGCGCAGGCGCGCGGGTCCCGGCAGCCCGTGAGACGCCCGCTGCTGGACGCGGGTAGCCGTCTGAGGTGCCGGAGCTGCG
GGAGGATGGAGCCGCTGAAGGTGGAAAAGTTCGCAACCGCCAAGAGGGGAAACGGGCTGCGCGCCGTGACCCCGCTGCGCCCCGGAGAGC
TACTCTTCCGCTCGGATCCCTTGGCGTACACGGTGTGCAAGGGGAGTCGTGGCGTCGTCTGCGACCGCTGCCTTCTCGGCCATGTGAAGA
TGTGCTTGCTTCCCCTTTGCCTTCTGCCATGATTCTAAGTTTCCTGAGGCCTCCCCAGAAGCAGAAGCATGTAAAGCCCACAGAACCGGT
CCAGTCGTCGACCATCGAGCTGCTTTGAAGACCCTGCGGAGGTTCCGTCGCTGCTTGAACACAGTGCCTGGACTCCCTGCTCCGTGAGGC

>84390_84390_2_SMYD3-ZNF695_SMYD3_chr1_246670356_ENST00000403792_ZNF695_chr1_247131094_ENST00000487338_length(amino acids)=125AA_BP=6
MVDDWTGSVGFTCFCFWGGLRKLRIMAEGKGEASTSSHGREGSGRRRRHDSPCTPCTPRDPSGRVALRGAAGSRRAARFPSWRLRTFPPS

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

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Fusion Gene PPI Analysis for SMYD3-ZNF695


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


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Related Drugs for SMYD3-ZNF695


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for SMYD3-ZNF695


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