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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:SETD5-SPATS2 (FusionGDB2 ID:80361)

Fusion Gene Summary for SETD5-SPATS2

check button Fusion gene summary
Fusion gene informationFusion gene name: SETD5-SPATS2
Fusion gene ID: 80361
HgeneTgene
Gene symbol

SETD5

SPATS2

Gene ID

55209

65244

Gene nameSET domain containing 5spermatogenesis associated serine rich 2
Synonyms-Nbla00526|P59SCR|SCR59|SPATA10
Cytomap

3p25.3

12q13.12

Type of geneprotein-codingprotein-coding
Descriptionhistone-lysine N-methyltransferase SETD5SET domain-containing protein 5spermatogenesis-associated serine-rich protein 2putative protein product of Nbla00526serine-rich spermatocytes and round spermatid 59 kDa proteinserine-rich spermatocytes and round spermatid protein
Modification date2020031320200315
UniProtAcc.

SPATS2L

Ensembl transtripts involved in fusion geneENST00000402198, ENST00000402466, 
ENST00000406341, ENST00000407969, 
ENST00000302463, ENST00000488236, 
ENST00000553127, ENST00000321898, 
ENST00000552918, ENST00000547865, 
ENST00000552557, 
Fusion gene scores* DoF score19 X 16 X 7=212812 X 14 X 7=1176
# samples 2315
** MAII scorelog2(23/2128*10)=-3.20979238455681
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/1176*10)=-2.97085365434048
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SETD5 [Title/Abstract] AND SPATS2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSETD5(9439661)-SPATS2(49908337), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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 SETD5 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across SPATS2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4STADTCGA-D7-8573SETD5chr3

9439661

+SPATS2chr12

49908337

+


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Fusion Gene ORF analysis for SETD5-SPATS2

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-3CDSENST00000402198ENST00000553127SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-3CDSENST00000402198ENST00000321898SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-3CDSENST00000402198ENST00000552918SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-intronENST00000402198ENST00000547865SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-3UTRENST00000402198ENST00000552557SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-3CDSENST00000402466ENST00000553127SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-3CDSENST00000402466ENST00000321898SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-3CDSENST00000402466ENST00000552918SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-intronENST00000402466ENST00000547865SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-3UTRENST00000402466ENST00000552557SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-3CDSENST00000406341ENST00000553127SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-3CDSENST00000406341ENST00000321898SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-3CDSENST00000406341ENST00000552918SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-intronENST00000406341ENST00000547865SETD5chr3

9439661

+SPATS2chr12

49908337

+
5UTR-3UTRENST00000406341ENST00000552557SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3CDSENST00000407969ENST00000553127SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3CDSENST00000407969ENST00000321898SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3CDSENST00000407969ENST00000552918SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-intronENST00000407969ENST00000547865SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3UTRENST00000407969ENST00000552557SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3CDSENST00000302463ENST00000553127SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3CDSENST00000302463ENST00000321898SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3CDSENST00000302463ENST00000552918SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-intronENST00000302463ENST00000547865SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3UTRENST00000302463ENST00000552557SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3CDSENST00000488236ENST00000553127SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3CDSENST00000488236ENST00000321898SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3CDSENST00000488236ENST00000552918SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-intronENST00000488236ENST00000547865SETD5chr3

9439661

+SPATS2chr12

49908337

+
intron-3UTRENST00000488236ENST00000552557SETD5chr3

9439661

+SPATS2chr12

49908337

+

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)

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

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Fusion Genomic Features for SETD5-SPATS2


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)
SETD5chr39439661+SPATS2chr1249908337+6.39E-050.9999361
SETD5chr39439661+SPATS2chr1249908337+6.39E-050.9999361

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.

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 SETD5-SPATS2


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.SPATS2

SPATS2L

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.558

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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Fusion Gene Sequence for SETD5-SPATS2


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.

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Fusion Gene PPI Analysis for SETD5-SPATS2


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 SETD5-SPATS2


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 SETD5-SPATS2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSETD5C3810406MENTAL RETARDATION, AUTOSOMAL DOMINANT 235CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneSETD5C0270972Cornelia De Lange Syndrome1ORPHANET
HgeneSETD5C1535926Neurodevelopmental Disorders1CTD_human