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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:RPAIN-STX8 (FusionGDB2 ID:75224)

Fusion Gene Summary for RPAIN-STX8

check button Fusion gene summary
Fusion gene informationFusion gene name: RPAIN-STX8
Fusion gene ID: 75224
HgeneTgene
Gene symbol

RPAIN

STX8

Gene ID

84268

9482

Gene nameRPA interacting proteinsyntaxin 8
SynonymsHRIP|RIPCARB
Cytomap

17p13.2

17p13.1

Type of geneprotein-codingprotein-coding
DescriptionRPA-interacting proteinRAP interaction proteinnuclear transportersyntaxin-8CIP-1-associated regulator of cyclin B
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000536255, ENST00000381208, 
ENST00000381209, ENST00000327154, 
ENST00000405578, ENST00000574003, 
ENST00000306357, ENST00000574431, 
ENST00000573373, 
Fusion gene scores* DoF score8 X 8 X 4=25624 X 16 X 8=3072
# samples 1029
** MAII scorelog2(10/256*10)=-1.35614381022528
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(29/3072*10)=-3.40505341070622
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RPAIN [Title/Abstract] AND STX8 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRPAIN(5326149)-STX8(9153962), # samples:3
Anticipated loss of major functional domain due to fusion event.RPAIN-STX8 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
HgeneRPAIN

GO:0006606

protein import into nucleus

16135809

TgeneSTX8

GO:0045022

early endosome to late endosome transport

10564279

TgeneSTX8

GO:1903076

regulation of protein localization to plasma membrane

18570918


check buttonFusion gene breakpoints across RPAIN (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 STX8 (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
ChimerDB4SARCTCGA-HB-A2OT-01ARPAINchr17

5326149

+STX8chr17

9153962

-
ChimerDB4SARCTCGA-HB-A2OT-01ARPAINchr17

5326149

+STX8chr17

9153962

-
ChimerDB4SARCTCGA-HB-A2OT-01ARPAINchr17

5331531

+STX8chr17

9153962

-
ChimerDB4SARCTCGA-HB-A2OT-01ARPAINchr17

5326149

-STX8chr17

9153962

-


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Fusion Gene ORF analysis for RPAIN-STX8

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-shiftENST00000536255ENST00000306357RPAINchr17

5326149

+STX8chr17

9153962

-
Frame-shiftENST00000536255ENST00000574431RPAINchr17

5326149

+STX8chr17

9153962

-
5CDS-intronENST00000536255ENST00000573373RPAINchr17

5326149

+STX8chr17

9153962

-
Frame-shiftENST00000381208ENST00000306357RPAINchr17

5326149

+STX8chr17

9153962

-
Frame-shiftENST00000381208ENST00000574431RPAINchr17

5326149

+STX8chr17

9153962

-
5CDS-intronENST00000381208ENST00000573373RPAINchr17

5326149

+STX8chr17

9153962

-
Frame-shiftENST00000381209ENST00000306357RPAINchr17

5326149

+STX8chr17

9153962

-
Frame-shiftENST00000381209ENST00000574431RPAINchr17

5326149

+STX8chr17

9153962

-
5CDS-intronENST00000381209ENST00000573373RPAINchr17

5326149

+STX8chr17

9153962

-
Frame-shiftENST00000327154ENST00000306357RPAINchr17

5326149

+STX8chr17

9153962

-
Frame-shiftENST00000327154ENST00000574431RPAINchr17

5326149

+STX8chr17

9153962

-
5CDS-intronENST00000327154ENST00000573373RPAINchr17

5326149

+STX8chr17

9153962

-
Frame-shiftENST00000405578ENST00000306357RPAINchr17

5326149

+STX8chr17

9153962

-
Frame-shiftENST00000405578ENST00000574431RPAINchr17

5326149

+STX8chr17

9153962

-
5CDS-intronENST00000405578ENST00000573373RPAINchr17

5326149

+STX8chr17

9153962

-
Frame-shiftENST00000574003ENST00000306357RPAINchr17

5326149

+STX8chr17

9153962

-
Frame-shiftENST00000574003ENST00000574431RPAINchr17

5326149

+STX8chr17

9153962

-
5CDS-intronENST00000574003ENST00000573373RPAINchr17

5326149

+STX8chr17

9153962

-
intron-3CDSENST00000536255ENST00000306357RPAINchr17

5331531

+STX8chr17

9153962

-
intron-3CDSENST00000536255ENST00000574431RPAINchr17

5331531

+STX8chr17

9153962

-
intron-intronENST00000536255ENST00000573373RPAINchr17

5331531

+STX8chr17

9153962

-
intron-3CDSENST00000381208ENST00000306357RPAINchr17

5331531

+STX8chr17

9153962

-
intron-3CDSENST00000381208ENST00000574431RPAINchr17

5331531

+STX8chr17

9153962

-
intron-intronENST00000381208ENST00000573373RPAINchr17

5331531

+STX8chr17

9153962

-
In-frameENST00000381209ENST00000306357RPAINchr17

5331531

+STX8chr17

9153962

-
In-frameENST00000381209ENST00000574431RPAINchr17

5331531

+STX8chr17

9153962

-
5CDS-intronENST00000381209ENST00000573373RPAINchr17

5331531

+STX8chr17

9153962

-
intron-3CDSENST00000327154ENST00000306357RPAINchr17

5331531

+STX8chr17

9153962

-
intron-3CDSENST00000327154ENST00000574431RPAINchr17

5331531

+STX8chr17

9153962

-
intron-intronENST00000327154ENST00000573373RPAINchr17

5331531

+STX8chr17

9153962

-
Frame-shiftENST00000405578ENST00000306357RPAINchr17

5331531

+STX8chr17

9153962

-
Frame-shiftENST00000405578ENST00000574431RPAINchr17

5331531

+STX8chr17

9153962

-
5CDS-intronENST00000405578ENST00000573373RPAINchr17

5331531

+STX8chr17

9153962

-
3UTR-3CDSENST00000574003ENST00000306357RPAINchr17

5331531

+STX8chr17

9153962

-
3UTR-3CDSENST00000574003ENST00000574431RPAINchr17

5331531

+STX8chr17

9153962

-
3UTR-intronENST00000574003ENST00000573373RPAINchr17

5331531

+STX8chr17

9153962

-

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)
ENST00000381209RPAINchr175331531+ENST00000306357STX8chr179153962-137512004681205245
ENST00000381209RPAINchr175331531+ENST00000574431STX8chr179153962-135912004681205245

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
ENST00000381209ENST00000306357RPAINchr175331531+STX8chr179153962-0.0159114920.98408854
ENST00000381209ENST00000574431RPAINchr175331531+STX8chr179153962-0.0151230560.984877

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Fusion Genomic Features for RPAIN-STX8


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.

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 RPAIN-STX8


check button Go to

FGviewer for the breakpoints of chr17:5331531-chr17:9153962

.
- 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
TgeneSTX8chr17:5331531chr17:9153962ENST0000030635768233_236214.33333333333334237.0Topological domainVesicular
TgeneSTX8chr17:5331531chr17:9153962ENST0000030635768216_232214.33333333333334237.0TransmembraneHelical%3B Anchor for type IV membrane protein

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRPAINchr17:5331531chr17:9153962ENST00000536255+14164_1800107.0RegionNote=Mediates nuclear export
HgeneRPAINchr17:5331531chr17:9153962ENST00000536255+14137_2120107.0Zinc fingerNote=RIP-type
TgeneSTX8chr17:5331531chr17:9153962ENST000003063576842_65214.33333333333334237.0Coiled coilOntology_term=ECO:0000255
TgeneSTX8chr17:5331531chr17:9153962ENST0000030635768145_207214.33333333333334237.0Domaint-SNARE coiled-coil homology
TgeneSTX8chr17:5331531chr17:9153962ENST00000306357681_215214.33333333333334237.0Topological domainCytoplasmic


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Fusion Gene Sequence for RPAIN-STX8


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.
>In-frame_ENST00000381209_ENST00000306357_TCGA-HB-A2OT-01A_RPAIN_chr17_5331531_+_STX8_chr17_9153962_length(transcript)=1375nt_BP=1200nt
CGGCCGCCATCTTGGCCCAACTGCTCCCCTCACTCCAGTTGCTCAGCCCGCCGCTGAGCACAGCCAATCCGCGGCCGTCCACTCACTGTT
TCGGCCAATCACCGAGCAGACGGCCCGGAAGCTCGAGAGGCTCGTGCCAGGTCGGGGGGCGAAGGCGAGGCCAGCCCACCAAGCAGGGGC
GTCACCAAGGGAAAGCCAATCACCATTATTTCTGAAGCCCAAGGGGGCGGGACGAGAAGTCAACATAATGGTGGTGCTGCTGGAAATCTA
GCACCTGGGGAGAGCCTGAGACTTGTGTATCTAATTGCCTATTGGACACCTCCATCTGGGTAAACCCAGGCATCCAGAACTTTCCCTCAA
GACTTACCTCCCTCAGTGCAGGTCGGGCTGGCCTCACGCATTTCGCTTGGATGCCTAAATCTGTCTCCACGTGGGGCCGGTCGATAAAAC
AACACTTCCCAGAATACGCTGCGATCCATTCGCGGTCTGCACCCGGAAAGTACACCTCCCAGGGGTCTGTGCGCGCCTCCAGGGAACGGG
TCTTGTGGCTTTGTCTCCCGCGAAGAGGAGATGGCGGAGTCGTTGAGGTCTCCGCGCCGCTCCCTGTACAAACTGGTGGGCTCGCCGCCT
TGGAAAGAGGCTTTCCGGCAGAGATGCCTGGAGAGAATGAGAAACAGCCGGGACAGGCTCCTAAACAGGTACCGCCAGGCTGGAAGCAGT
GGGCCAGGGAATTCTCAGAACAGCTTTCTAGTTCAAGAGGTGATGGAAGAAGAGTGGAATGCTTTGCAGTCAGTGGAGAATTGTCCAGAA
GACTTGGCTCAGCTGGAGGAGCTGATAGACATGGCTGTGCTGGAGGAAATTCAACAGGAGCTGATCAACCAAGAGCAGTCCATCATCAGC
GAGTATGAGAAGAGCTTGCAGTTTGATGAAAAGTGTCTCAGCATCATGCTGGCTGAGTGGGAGGCAAACCCACTCATCTGTCCTGTATGT
ACAAAGTACAACCTGAGAATCACAAGCGGTGTGGTGGTGTGTCAGTGTGGCCTGTCCATCCCATCTCATTCTTCTGAGTTGACAGAGCAG
AAGCTTCGTGCCTGTTTAGAGGGTAGTATAAATGAGCACAGTGCACATTGTCCCCACACACCTGAATTTTCAGTCACTGGAGGAACAGAA
GAAAAGTCCAGTCTTCTCATGAGCTGTCTGGGATGATCATGGTGATTTTACTGCTGCTTGTGGCTATCGTGGTTGTTGCAGTCTGGCCGA
CCAACTGATGGCAGTAAAGAGACCACCAGCAGTGACACCTGCCAATGACAGATGCAAGCCCAACACCCTTTTGGTACGCAAAACCTGCTC

>In-frame_ENST00000381209_ENST00000306357_TCGA-HB-A2OT-01A_RPAIN_chr17_5331531_+_STX8_chr17_9153962_length(amino acids)=245AA_start in transcript=468_stop in transcript=1205
MRSIRGLHPESTPPRGLCAPPGNGSCGFVSREEEMAESLRSPRRSLYKLVGSPPWKEAFRQRCLERMRNSRDRLLNRYRQAGSSGPGNSQ
NSFLVQEVMEEEWNALQSVENCPEDLAQLEELIDMAVLEEIQQELINQEQSIISEYEKSLQFDEKCLSIMLAEWEANPLICPVCTKYNLR

--------------------------------------------------------------
>In-frame_ENST00000381209_ENST00000574431_TCGA-HB-A2OT-01A_RPAIN_chr17_5331531_+_STX8_chr17_9153962_length(transcript)=1359nt_BP=1200nt
CGGCCGCCATCTTGGCCCAACTGCTCCCCTCACTCCAGTTGCTCAGCCCGCCGCTGAGCACAGCCAATCCGCGGCCGTCCACTCACTGTT
TCGGCCAATCACCGAGCAGACGGCCCGGAAGCTCGAGAGGCTCGTGCCAGGTCGGGGGGCGAAGGCGAGGCCAGCCCACCAAGCAGGGGC
GTCACCAAGGGAAAGCCAATCACCATTATTTCTGAAGCCCAAGGGGGCGGGACGAGAAGTCAACATAATGGTGGTGCTGCTGGAAATCTA
GCACCTGGGGAGAGCCTGAGACTTGTGTATCTAATTGCCTATTGGACACCTCCATCTGGGTAAACCCAGGCATCCAGAACTTTCCCTCAA
GACTTACCTCCCTCAGTGCAGGTCGGGCTGGCCTCACGCATTTCGCTTGGATGCCTAAATCTGTCTCCACGTGGGGCCGGTCGATAAAAC
AACACTTCCCAGAATACGCTGCGATCCATTCGCGGTCTGCACCCGGAAAGTACACCTCCCAGGGGTCTGTGCGCGCCTCCAGGGAACGGG
TCTTGTGGCTTTGTCTCCCGCGAAGAGGAGATGGCGGAGTCGTTGAGGTCTCCGCGCCGCTCCCTGTACAAACTGGTGGGCTCGCCGCCT
TGGAAAGAGGCTTTCCGGCAGAGATGCCTGGAGAGAATGAGAAACAGCCGGGACAGGCTCCTAAACAGGTACCGCCAGGCTGGAAGCAGT
GGGCCAGGGAATTCTCAGAACAGCTTTCTAGTTCAAGAGGTGATGGAAGAAGAGTGGAATGCTTTGCAGTCAGTGGAGAATTGTCCAGAA
GACTTGGCTCAGCTGGAGGAGCTGATAGACATGGCTGTGCTGGAGGAAATTCAACAGGAGCTGATCAACCAAGAGCAGTCCATCATCAGC
GAGTATGAGAAGAGCTTGCAGTTTGATGAAAAGTGTCTCAGCATCATGCTGGCTGAGTGGGAGGCAAACCCACTCATCTGTCCTGTATGT
ACAAAGTACAACCTGAGAATCACAAGCGGTGTGGTGGTGTGTCAGTGTGGCCTGTCCATCCCATCTCATTCTTCTGAGTTGACAGAGCAG
AAGCTTCGTGCCTGTTTAGAGGGTAGTATAAATGAGCACAGTGCACATTGTCCCCACACACCTGAATTTTCAGTCACTGGAGGAACAGAA
GAAAAGTCCAGTCTTCTCATGAGCTGTCTGGGATGATCATGGTGATTTTACTGCTGCTTGTGGCTATCGTGGTTGTTGCAGTCTGGCCGA
CCAACTGATGGCAGTAAAGAGACCACCAGCAGTGACACCTGCCAATGACAGATGCAAGCCCAACACCCTTTTGGTACGCAAAACCTGCTC

>In-frame_ENST00000381209_ENST00000574431_TCGA-HB-A2OT-01A_RPAIN_chr17_5331531_+_STX8_chr17_9153962_length(amino acids)=245AA_start in transcript=468_stop in transcript=1205
MRSIRGLHPESTPPRGLCAPPGNGSCGFVSREEEMAESLRSPRRSLYKLVGSPPWKEAFRQRCLERMRNSRDRLLNRYRQAGSSGPGNSQ
NSFLVQEVMEEEWNALQSVENCPEDLAQLEELIDMAVLEEIQQELINQEQSIISEYEKSLQFDEKCLSIMLAEWEANPLICPVCTKYNLR

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

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Fusion Gene PPI Analysis for RPAIN-STX8


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 RPAIN-STX8


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 RPAIN-STX8


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