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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:ASAP1-TRAPPC9 (FusionGDB2 ID:HG50807TG83696)

Fusion Gene Summary for ASAP1-TRAPPC9

check button Fusion gene summary
Fusion gene informationFusion gene name: ASAP1-TRAPPC9
Fusion gene ID: hg50807tg83696
HgeneTgene
Gene symbol

ASAP1

TRAPPC9

Gene ID

50807

83696

Gene nameArfGAP with SH3 domain, ankyrin repeat and PH domain 1trafficking protein particle complex 9
SynonymsAMAP1|CENTB4|DDEF1|PAG2|PAP|ZG14PIBP|IKBKBBP|MRT13|NIBP|T1|TRS120
Cytomap('ASAP1')('TRAPPC9')

8q24.21-q24.22

8q24.3

Type of geneprotein-codingprotein-coding
Descriptionarf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1130 kDa phosphatidylinositol 4,5-biphosphate-dependent ARF1 GTPase-activating protein130 kDa phosphatidylinositol 4,5-bisphosphate-dependent ARF1 GTPase-activating proteinADP-ribosyltrafficking protein particle complex subunit 9IKK2 binding proteinNIK and IKK-beta binding proteinNIK- and IKBKB-binding proteinTRAPP 120 kDa subunittularik gene 1 protein
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000357668, ENST00000518721, 
ENST00000520625, 
Fusion gene scores* DoF score25 X 17 X 13=552520 X 19 X 14=5320
# samples 2840
** MAII scorelog2(28/5525*10)=-4.30247573222119
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(40/5320*10)=-3.73335434061383
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ASAP1 [Title/Abstract] AND TRAPPC9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointASAP1(131226802)-TRAPPC9(140743471), # samples:1
Anticipated loss of major functional domain due to fusion event.ASAP1-TRAPPC9 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.
ASAP1-TRAPPC9 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.
ASAP1-TRAPPC9 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ASAP1-TRAPPC9 seems lost the major protein functional domain in Tgene 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

check buttonFusion gene breakpoints across ASAP1 (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 TRAPPC9 (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
* 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-DX-A6YX-01AASAP1chr8

131226802

-TRAPPC9chr8

140743471

-


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Fusion Gene ORF analysis for ASAP1-TRAPPC9

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-5UTRENST00000357668ENST00000522504ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-
5CDS-5UTRENST00000518721ENST00000522504ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-
Frame-shiftENST00000357668ENST00000389327ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-
Frame-shiftENST00000357668ENST00000389328ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-
Frame-shiftENST00000357668ENST00000438773ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-
Frame-shiftENST00000518721ENST00000389327ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-
Frame-shiftENST00000518721ENST00000438773ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-
In-frameENST00000518721ENST00000389328ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-
intron-3CDSENST00000520625ENST00000389327ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-
intron-3CDSENST00000520625ENST00000389328ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-
intron-3CDSENST00000520625ENST00000438773ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-
intron-5UTRENST00000520625ENST00000522504ASAP1chr8

131226802

-TRAPPC9chr8

140743471

-

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)
ENST00000518721ASAP1chr8131226802-ENST00000389328TRAPPC9chr8140743471-15196338491517223

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
ENST00000518721ENST00000389328ASAP1chr8131226802-TRAPPC9chr8140743471-0.0153130980.9846869

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Fusion Genomic Features for ASAP1-TRAPPC9


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

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Fusion Protein Features for ASAP1-TRAPPC9


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/chr8:131226802/chr8:140743471)
- 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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneASAP1chr8:131226802chr8:140743471ENST00000357668-429783_9931351130.0Compositional biasNote=Pro-rich
HgeneASAP1chr8:131226802chr8:140743471ENST00000518721-530783_9931351130.0Compositional biasNote=Pro-rich
HgeneASAP1chr8:131226802chr8:140743471ENST00000357668-4291067_11291351130.0DomainSH3
HgeneASAP1chr8:131226802chr8:140743471ENST00000357668-429324_4161351130.0DomainPH
HgeneASAP1chr8:131226802chr8:140743471ENST00000357668-429439_5601351130.0DomainArf-GAP
HgeneASAP1chr8:131226802chr8:140743471ENST00000518721-5301067_11291351130.0DomainSH3
HgeneASAP1chr8:131226802chr8:140743471ENST00000518721-530324_4161351130.0DomainPH
HgeneASAP1chr8:131226802chr8:140743471ENST00000518721-530439_5601351130.0DomainArf-GAP
HgeneASAP1chr8:131226802chr8:140743471ENST00000357668-429600_6321351130.0RepeatNote=ANK 1
HgeneASAP1chr8:131226802chr8:140743471ENST00000357668-429636_6651351130.0RepeatNote=ANK 2
HgeneASAP1chr8:131226802chr8:140743471ENST00000518721-530600_6321351130.0RepeatNote=ANK 1
HgeneASAP1chr8:131226802chr8:140743471ENST00000518721-530636_6651351130.0RepeatNote=ANK 2
HgeneASAP1chr8:131226802chr8:140743471ENST00000357668-429454_4771351130.0Zinc fingerC4-type
HgeneASAP1chr8:131226802chr8:140743471ENST00000518721-530454_4771351130.0Zinc fingerC4-type


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Fusion Gene Sequence for ASAP1-TRAPPC9


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.
>6974_6974_1_ASAP1-TRAPPC9_ASAP1_chr8_131226802_ENST00000518721_TRAPPC9_chr8_140743471_ENST00000389328_length(transcript)=1519nt_BP=633nt
CCCTTCCTGCGCCGCGCTCGGCTCCCGCGCCTCGCCTGGCCTGGCCGCTGCCGCGGGCGAGCACTGTGCGCTGGGCAGCCCCGGGCCCGC
GCCTCCCGCCCAGCCGGCGCTTCCCGGTCGCAGTTCGCTTTCCCACCCGAGAGCCGCGAGCGCCCGGCCGAACCCGCGATGGAATAATGC
CCAGCGGCCCGCCAGGTCCCGGTCGTTTTCTGATGTGACGGCTGAGACATGAGATCTTCAGCCTCCAGGCTCTCCAGTTTTTCGTCGAGA
GATTCACTATGGAATCGGATGCCGGACCAGATCTCTGTCTCGGAGTTCATCGCCGAGACCACCGAGGACTACAACTCGCCCACCACGTCC
AGCTTCACCACGCGGCTGCACAACTGCAGGAACACCGTCACGCTGCTGGAGGAGGCTCTAGACCAAGATAGAACAGCCCTTCAGAAAGTG
AAGAAGTCTGTAAAAGCAATATATAATTCTGGTCAAGATCATGTACAAAATGAAGAAAACTATGCACAAGTTCTTGATAAGTTTGGGAGT
AATTTTTTAAGTCGAGACAACCCCGACCTTGGCACCGCGTTTGTCAAGTTTTCTACTCTTACAAAGGAACTGTCCACACTGCTGAAAAAT
CTGGTGCAGCCGTCCGGCCAGTCGGCCTGCCTCGGGGCCCTCCTCTTCCTCTACACGGGAGACTTCTTCCTCCACATCCGGTTCCACGAG
GACAGCACCAGCAAGGAGCTGCCACCCTCTTGGTTCTGCCTGCCCAGTGTGCACGTGTGTGCCCTGGAGGCGCAGGCCTGAGCCCGCCTA
CTTCCGTCCCTCTTTCTGCAGGGCCAGAGGTGACCCTGCCTGGCCTCCCACACCCCCTGCAATGAGCAAGGCCTTCACTGCAGCCCCATC
TCCTCCTCCTCCCCCAGACCCCTCCCAGCCCTCTCCTCCTGTTCCTCCTGTAGCATCTTTGCTGGGCTACGCAGAAGCCCCGGACATGGC
AGCCCCACCCCATGCCACGCCCCTTCCTACACTGTTCCCTGGACCATACACAGGCTGAAGCAGAGGAAATCCCAAAGCGGGTGCCCATCC
AGCCCAGGTCCCAGGATCCCTGCACCCATTTCTGTGACCTGGGGCCCCAGCCGTGCTGTGCTGCTCATCCCAGCAGAGGGACCTCCCTCG
TCCAGCGACTTCCCTTTGGCCATAGAAAGAAATGGTGAGCATGAGACTGGGCACAGCCTGAGGGCGTGGGCAGCTTCCCACCCTCCCTGG
GCCTTGGAATCCCCCAAGGCTGGTTTTCTTCCTGGAGACCCCCATGGGCAACTTGGCAGGAGAGATGGTGCCGTAGGAGGTCGTGGATGG
TTGATGCCAAGAGAGGCCCTCCACCCGTGGTGGGCAAATGTCCAGGCCTGGGCTGGCAGCCCAGGGCTGTTTCTGGGTGCTCCCTGGCCC

>6974_6974_1_ASAP1-TRAPPC9_ASAP1_chr8_131226802_ENST00000518721_TRAPPC9_chr8_140743471_ENST00000389328_length(amino acids)=223AA_BP=
MASHTPCNEQGLHCSPISSSSPRPLPALSSCSSCSIFAGLRRSPGHGSPTPCHAPSYTVPWTIHRLKQRKSQSGCPSSPGPRIPAPISVT
WGPSRAVLLIPAEGPPSSSDFPLAIERNGEHETGHSLRAWAASHPPWALESPKAGFLPGDPHGQLGRRDGAVGGRGWLMPREALHPWWAN

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

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Fusion Gene PPI Analysis for ASAP1-TRAPPC9


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 ASAP1-TRAPPC9


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 ASAP1-TRAPPC9


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneASAP1C0005684Malignant neoplasm of urinary bladder1CTD_human
HgeneASAP1C0005695Bladder Neoplasm1CTD_human
HgeneASAP1C0041327Tuberculosis, Pulmonary1CTD_human
HgeneASAP1C0087031Juvenile-Onset Still Disease1CTD_human
HgeneASAP1C3495559Juvenile arthritis1CTD_human
HgeneASAP1C3714758Juvenile psoriatic arthritis1CTD_human
HgeneASAP1C4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneASAP1C4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human
TgeneC2750791MENTAL RETARDATION, AUTOSOMAL RECESSIVE 131CTD_human;GENOMICS_ENGLAND