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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:SPAG9-PCMT1 (FusionGDB2 ID:84873)

Fusion Gene Summary for SPAG9-PCMT1

check button Fusion gene summary
Fusion gene informationFusion gene name: SPAG9-PCMT1
Fusion gene ID: 84873
HgeneTgene
Gene symbol

SPAG9

PCMT1

Gene ID

9043

5110

Gene namesperm associated antigen 9protein-L-isoaspartate (D-aspartate) O-methyltransferase
SynonymsCT89|HLC-6|HLC4|HLC6|JIP-4|JIP4|JLP|PHET|PIG6PIMT
Cytomap

17q21.33

6q25.1

Type of geneprotein-codingprotein-coding
DescriptionC-Jun-amino-terminal kinase-interacting protein 4JNK interacting proteinJNK/SAPK-associated proteinMax-binding proteinc-Jun NH2-terminal kinase-associated leucine zipper proteincancer/testis antigen 89human lung cancer oncogene 6 proteinlung cancerprotein-L-isoaspartate(D-aspartate) O-methyltransferaseL-isoaspartyl protein carboxyl methyltransferaseepididymis secretory sperm binding proteinprotein L-isoaspartyl/D-aspartyl methyltransferaseprotein-beta-aspartate methyltransferase
Modification date2020031520200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000262013, ENST00000505279, 
ENST00000357122, ENST00000509724, 
ENST00000510283, 		ENST00000367384, 
ENST00000367378, ENST00000464889, 
ENST00000367380, ENST00000544496, 
ENST00000480010, 
Fusion gene scores* DoF score20 X 21 X 10=42004 X 3 X 4=48
# samples 254
** MAII scorelog2(25/4200*10)=-4.0703893278914
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

PubMed: SPAG9 [Title/Abstract] AND PCMT1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSPAG9(49124736)-PCMT1(150092298), # samples:4
Anticipated loss of major functional domain due to fusion event.SPAG9-PCMT1 seems lost the major protein functional domain in Hgene partner, which is a essential gene 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
HgeneSPAG9

GO:0042147

retrograde transport, endosome to Golgi

19056739


check buttonFusion gene breakpoints across SPAG9 (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 PCMT1 (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
ChimerDB4BLCATCGA-BL-A0C8-01ASPAG9chr17

49124736

-PCMT1chr6

150092298

+
ChimerDB4BLCATCGA-BL-A0C8-01ASPAG9chr17

49124736

-PCMT1chr6

150092298

+
ChimerDB4BLCATCGA-BL-A0C8-01BSPAG9chr17

49124736

-PCMT1chr6

150092298

+
ChimerDB4BLCATCGA-BL-A0C8-01ASPAG9chr17

49124736

-PCMT1chr6

150092298

+


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Fusion Gene ORF analysis for SPAG9-PCMT1

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
Frame-shiftENST00000262013ENST00000367384SPAG9chr17

49124736

-PCMT1chr6

150092298

+
Frame-shiftENST00000262013ENST00000367378SPAG9chr17

49124736

-PCMT1chr6

150092298

+
Frame-shiftENST00000262013ENST00000464889SPAG9chr17

49124736

-PCMT1chr6

150092298

+
Frame-shiftENST00000262013ENST00000367380SPAG9chr17

49124736

-PCMT1chr6

150092298

+
5CDS-intronENST00000262013ENST00000544496SPAG9chr17

49124736

-PCMT1chr6

150092298

+
5CDS-intronENST00000262013ENST00000480010SPAG9chr17

49124736

-PCMT1chr6

150092298

+
Frame-shiftENST00000505279ENST00000367384SPAG9chr17

49124736

-PCMT1chr6

150092298

+
Frame-shiftENST00000505279ENST00000367378SPAG9chr17

49124736

-PCMT1chr6

150092298

+
Frame-shiftENST00000505279ENST00000464889SPAG9chr17

49124736

-PCMT1chr6

150092298

+
Frame-shiftENST00000505279ENST00000367380SPAG9chr17

49124736

-PCMT1chr6

150092298

+
5CDS-intronENST00000505279ENST00000544496SPAG9chr17

49124736

-PCMT1chr6

150092298

+
5CDS-intronENST00000505279ENST00000480010SPAG9chr17

49124736

-PCMT1chr6

150092298

+
Frame-shiftENST00000357122ENST00000367384SPAG9chr17

49124736

-PCMT1chr6

150092298

+
Frame-shiftENST00000357122ENST00000367378SPAG9chr17

49124736

-PCMT1chr6

150092298

+
Frame-shiftENST00000357122ENST00000464889SPAG9chr17

49124736

-PCMT1chr6

150092298

+
Frame-shiftENST00000357122ENST00000367380SPAG9chr17

49124736

-PCMT1chr6

150092298

+
5CDS-intronENST00000357122ENST00000544496SPAG9chr17

49124736

-PCMT1chr6

150092298

+
5CDS-intronENST00000357122ENST00000480010SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-3CDSENST00000509724ENST00000367384SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-3CDSENST00000509724ENST00000367378SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-3CDSENST00000509724ENST00000464889SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-3CDSENST00000509724ENST00000367380SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-intronENST00000509724ENST00000544496SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-intronENST00000509724ENST00000480010SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-3CDSENST00000510283ENST00000367384SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-3CDSENST00000510283ENST00000367378SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-3CDSENST00000510283ENST00000464889SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-3CDSENST00000510283ENST00000367380SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-intronENST00000510283ENST00000544496SPAG9chr17

49124736

-PCMT1chr6

150092298

+
intron-intronENST00000510283ENST00000480010SPAG9chr17

49124736

-PCMT1chr6

150092298

+

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 SPAG9-PCMT1


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)
SPAG9chr1749124735-PCMT1chr6150092297+5.57E-101
SPAG9chr1749124735-PCMT1chr6150092297+5.57E-101
SPAG9chr1749124735-PCMT1chr6150092297+5.57E-101
SPAG9chr1749124735-PCMT1chr6150092297+5.57E-101

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 SPAG9-PCMT1


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
..
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.
- 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 SPAG9-PCMT1


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 SPAG9-PCMT1


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 SPAG9-PCMT1


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 SPAG9-PCMT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgenePCMT1C0038219Status Dysraphicus1CTD_human
TgenePCMT1C0080178Spina Bifida1CTD_human
TgenePCMT1C0266508Rachischisis1CTD_human