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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:DHX9-VIM

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: DHX9-VIM
FusionPDB ID: 22734
FusionGDB2.0 ID: 22734
HgeneTgene
Gene symbol

DHX9

VIM

Gene ID

1660

7431

Gene nameDExH-box helicase 9vimentin
SynonymsDDX9|LKP|NDH2|NDHII|RHA-
Cytomap

1q25.3

10p13

Type of geneprotein-codingprotein-coding
DescriptionATP-dependent RNA helicase ADEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9DEAH (Asp-Glu-Ala-His) box helicase 9DEAH (Asp-Glu-Ala-His) box polypeptide 9DEAH box protein 9DEAH-box helicase 9RNA helicase Aleukophysinnuclear DNA helicase IIvimentinepididymis secretory sperm binding protein
Modification date2020032220200327
UniProtAcc

Q08211

VMAC

Ensembl transtripts involved in fusion geneENST idsENST00000367549, ENST00000485081, 
ENST00000485947, ENST00000224237, 
ENST00000544301, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 10 X 7=98042 X 25 X 11=11550
# samples 1541
** MAII scorelog2(15/980*10)=-2.70781924850669
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(41/11550*10)=-4.81612513168534
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: DHX9 [Title/Abstract] AND VIM [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)DHX9(182821479)-VIM(17278292), # samples:1
Anticipated loss of major functional domain due to fusion event.DHX9-VIM 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.
DHX9-VIM 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.
DHX9-VIM 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.
DHX9-VIM 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.
* 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
HgeneDHX9

GO:0010501

RNA secondary structure unwinding

1537828|9111062

HgeneDHX9

GO:0032508

DNA duplex unwinding

9111062|21561811

HgeneDHX9

GO:0034622

cellular protein-containing complex assembly

23361462

HgeneDHX9

GO:0039695

DNA-templated viral transcription

11096080

HgeneDHX9

GO:0044806

G-quadruplex DNA unwinding

21561811

HgeneDHX9

GO:0046833

positive regulation of RNA export from nucleus

11402034

HgeneDHX9

GO:0050434

positive regulation of viral transcription

11096080

HgeneDHX9

GO:0050684

regulation of mRNA processing

28355180

HgeneDHX9

GO:2000765

regulation of cytoplasmic translation

28355180


check buttonFusion gene breakpoints across DHX9 (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 VIM (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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-HU-A4GQDHX9chr1

182821479

+VIMchr10

17278292

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000367549DHX9chr1182821479+ENST00000544301VIMchr1017278292+916474110601163
ENST00000367549DHX9chr1182821479+ENST00000224237VIMchr1017278292+924474110601163

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
ENST00000367549ENST00000544301DHX9chr1182821479+VIMchr1017278292+0.0024586110.9975414
ENST00000367549ENST00000224237DHX9chr1182821479+VIMchr1017278292+0.0027821230.9972179

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>22734_22734_1_DHX9-VIM_DHX9_chr1_182821479_ENST00000367549_VIM_chr10_17278292_ENST00000224237_length(amino acids)=163AA_BP=121
MGDVKNFLYAWCGKRKMTPSYEIRAVGNKNRQKFMCEVQVEGYNYTGMGNSTNKKDAQSNAARDFVNYLVRINEIKSEEVPAFGVASPPP

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

>22734_22734_2_DHX9-VIM_DHX9_chr1_182821479_ENST00000367549_VIM_chr10_17278292_ENST00000544301_length(amino acids)=163AA_BP=121
MGDVKNFLYAWCGKRKMTPSYEIRAVGNKNRQKFMCEVQVEGYNYTGMGNSTNKKDAQSNAARDFVNYLVRINEIKSEEVPAFGVASPPP

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

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Fusion Protein Functional Features


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/chr1:182821479/chr10:17278292)
- 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
DHX9

Q08211

VIM

VMAC

FUNCTION: Multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and that plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation and RNA-mediated gene silencing (PubMed:9111062, PubMed:11416126, PubMed:12711669, PubMed:15355351, PubMed:16680162, PubMed:17531811, PubMed:20669935, PubMed:21561811, PubMed:24049074, PubMed:25062910, PubMed:24990949, PubMed:28221134). Requires a 3'-single-stranded tail as entry site for acid nuclei unwinding activities as well as the binding and hydrolyzing of any of the four ribo- or deoxyribo-nucleotide triphosphates (NTPs) (PubMed:1537828). Unwinds numerous nucleic acid substrates such as double-stranded (ds) DNA and RNA, DNA:RNA hybrids, DNA and RNA forks composed of either partially complementary DNA duplexes or DNA:RNA hybrids, respectively, and also DNA and RNA displacement loops (D- and R-loops), triplex-helical DNA (H-DNA) structure and DNA and RNA-based G-quadruplexes (PubMed:20669935, PubMed:21561811, PubMed:24049074). Binds dsDNA, single-stranded DNA (ssDNA), dsRNA, ssRNA and poly(A)-containing RNA (PubMed:9111062, PubMed:10198287). Binds also to circular dsDNA or dsRNA of either linear and/or circular forms and stimulates the relaxation of supercoiled DNAs catalyzed by topoisomerase TOP2A (PubMed:12711669). Plays a role in DNA replication at origins of replication and cell cycle progression (PubMed:24990949). Plays a role as a transcriptional coactivator acting as a bridging factor between polymerase II holoenzyme and transcription factors or cofactors, such as BRCA1, CREBBP, RELA and SMN1 (PubMed:11149922, PubMed:9323138, PubMed:9662397, PubMed:11038348, PubMed:11416126, PubMed:15355351, PubMed:28221134). Binds to the CDKN2A promoter (PubMed:11038348). Plays several roles in post-transcriptional regulation of gene expression (PubMed:28221134, PubMed:28355180). In cooperation with NUP98, promotes pre-mRNA alternative splicing activities of a subset of genes (PubMed:11402034, PubMed:16680162, PubMed:28221134, PubMed:28355180). As component of a large PER complex, is involved in the negative regulation of 3' transcriptional termination of circadian target genes such as PER1 and NR1D1 and the control of the circadian rhythms (By similarity). Acts also as a nuclear resolvase that is able to bind and neutralize harmful massive secondary double-stranded RNA structures formed by inverted-repeat Alu retrotransposon elements that are inserted and transcribed as parts of genes during the process of gene transposition (PubMed:28355180). Involved in the positive regulation of nuclear export of constitutive transport element (CTE)-containing unspliced mRNA (PubMed:9162007, PubMed:10924507, PubMed:11402034). Component of the coding region determinant (CRD)-mediated complex that promotes cytoplasmic MYC mRNA stability (PubMed:19029303). Plays a role in mRNA translation (PubMed:28355180). Positively regulates translation of selected mRNAs through its binding to post-transcriptional control element (PCE) in the 5'-untranslated region (UTR) (PubMed:16680162). Involved with LARP6 in the translation stimulation of type I collagen mRNAs for CO1A1 and CO1A2 through binding of a specific stem-loop structure in their 5'-UTRs (PubMed:22190748). Stimulates LIN28A-dependent mRNA translation probably by facilitating ribonucleoprotein remodeling during the process of translation (PubMed:21247876). Plays also a role as a small interfering (siRNA)-loading factor involved in the RNA-induced silencing complex (RISC) loading complex (RLC) assembly, and hence functions in the RISC-mediated gene silencing process (PubMed:17531811). Binds preferentially to short double-stranded RNA, such as those produced during rotavirus intestinal infection (PubMed:28636595). This interaction may mediate NLRP9 inflammasome activation and trigger inflammatory response, including IL18 release and pyroptosis (PubMed:28636595). Finally, mediates the attachment of heterogeneous nuclear ribonucleoproteins (hnRNPs) to actin filaments in the nucleus (PubMed:11687588). {ECO:0000250|UniProtKB:O70133, ECO:0000269|PubMed:10198287, ECO:0000269|PubMed:10924507, ECO:0000269|PubMed:11038348, ECO:0000269|PubMed:11149922, ECO:0000269|PubMed:11402034, ECO:0000269|PubMed:11416126, ECO:0000269|PubMed:11687588, ECO:0000269|PubMed:12711669, ECO:0000269|PubMed:15355351, ECO:0000269|PubMed:1537828, ECO:0000269|PubMed:16680162, ECO:0000269|PubMed:17531811, ECO:0000269|PubMed:19029303, ECO:0000269|PubMed:20669935, ECO:0000269|PubMed:21247876, ECO:0000269|PubMed:21561811, ECO:0000269|PubMed:22190748, ECO:0000269|PubMed:24049074, ECO:0000269|PubMed:24990949, ECO:0000269|PubMed:25062910, ECO:0000269|PubMed:28221134, ECO:0000269|PubMed:28355180, ECO:0000269|PubMed:28636595, ECO:0000269|PubMed:9111062, ECO:0000269|PubMed:9162007, ECO:0000269|PubMed:9323138, ECO:0000269|PubMed:9662397}.; FUNCTION: (Microbial infection) Plays a role in HIV-1 replication and virion infectivity (PubMed:11096080, PubMed:19229320, PubMed:25149208, PubMed:27107641). Enhances HIV-1 transcription by facilitating the binding of RNA polymerase II holoenzyme to the proviral DNA (PubMed:11096080, PubMed:25149208). Binds (via DRBM domain 2) to the HIV-1 TAR RNA and stimulates HIV-1 transcription of transactivation response element (TAR)-containing mRNAs (PubMed:9892698, PubMed:11096080). Involved also in HIV-1 mRNA splicing and transport (PubMed:25149208). Positively regulates HIV-1 gag mRNA translation, through its binding to post-transcriptional control element (PCE) in the 5'-untranslated region (UTR) (PubMed:16680162). Binds (via DRBM domains) to a HIV-1 double-stranded RNA region of the primer binding site (PBS)-segment of the 5'-UTR, and hence stimulates DHX9 incorporation into virions and virion infectivity (PubMed:27107641). Plays also a role as a cytosolic viral MyD88-dependent DNA and RNA sensors in plasmacytoid dendritic cells (pDCs), and hence induce antiviral innate immune responses (PubMed:20696886, PubMed:21957149). Binds (via the OB-fold region) to viral single-stranded DNA unmethylated C-phosphate-G (CpG) oligonucleotide (PubMed:20696886). {ECO:0000269|PubMed:11096080, ECO:0000269|PubMed:16680162, ECO:0000269|PubMed:19229320, ECO:0000269|PubMed:20696886, ECO:0000269|PubMed:21957149, ECO:0000269|PubMed:25149208, ECO:0000269|PubMed:27107641, ECO:0000269|PubMed:9892698}.169

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+4283_71121.333333333333331271.0DomainDRBM 1
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+42853_55121.333333333333331271.0RegionsiRNA-binding
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+4285_9121.333333333333331271.0RegionsiRNA-binding

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428180_252121.333333333333331271.0DomainDRBM 2
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428398_564121.333333333333331271.0DomainHelicase ATP-binding
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428636_809121.333333333333331271.0DomainHelicase C-terminal
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+4281155_1173121.333333333333331271.0MotifNuclear localization signal (NLS2)
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428511_514121.333333333333331271.0MotifNote=DEIH box
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428586_595121.333333333333331271.0MotifNuclear localization signal (NLS1)
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428411_419121.333333333333331271.0Nucleotide bindingATP
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+4281150_1270121.333333333333331271.0RegionRGG
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428182_186121.333333333333331271.0RegionsiRNA-binding
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428234_236121.333333333333331271.0RegionsiRNA-binding
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428331_380121.333333333333331271.0RegionMTAD
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428398_809121.333333333333331271.0RegionCore helicase
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428831_919121.333333333333331271.0RegionHA2
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428958_1074121.333333333333331271.0RegionOB-fold
TgeneVIMchr1:182821479chr10:17278292ENST0000022423769154_245424.3333333333333467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr1:182821479chr10:17278292ENST0000022423769303_407424.3333333333333467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr1:182821479chr10:17278292ENST000002242376996_131424.3333333333333467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr1:182821479chr10:17278292ENST00000544301710154_245424.3333333333333467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr1:182821479chr10:17278292ENST00000544301710303_407424.3333333333333467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr1:182821479chr10:17278292ENST0000054430171096_131424.3333333333333467.0Coiled coilOntology_term=ECO:0000269
TgeneVIMchr1:182821479chr10:17278292ENST0000022423769103_411424.3333333333333467.0DomainIF rod
TgeneVIMchr1:182821479chr10:17278292ENST00000544301710103_411424.3333333333333467.0DomainIF rod
TgeneVIMchr1:182821479chr10:17278292ENST0000022423769326_329424.3333333333333467.0Motif[IL]-x-C-x-x-[DE] motif
TgeneVIMchr1:182821479chr10:17278292ENST00000544301710326_329424.3333333333333467.0Motif[IL]-x-C-x-x-[DE] motif
TgeneVIMchr1:182821479chr10:17278292ENST0000022423769132_153424.3333333333333467.0RegionNote=Linker 1
TgeneVIMchr1:182821479chr10:17278292ENST0000022423769246_268424.3333333333333467.0RegionNote=Linker 12
TgeneVIMchr1:182821479chr10:17278292ENST0000022423769269_407424.3333333333333467.0RegionNote=Coil 2
TgeneVIMchr1:182821479chr10:17278292ENST00000224237692_95424.3333333333333467.0RegionNote=Head
TgeneVIMchr1:182821479chr10:17278292ENST0000022423769408_466424.3333333333333467.0RegionNote=Tail
TgeneVIMchr1:182821479chr10:17278292ENST00000544301710132_153424.3333333333333467.0RegionNote=Linker 1
TgeneVIMchr1:182821479chr10:17278292ENST00000544301710246_268424.3333333333333467.0RegionNote=Linker 12
TgeneVIMchr1:182821479chr10:17278292ENST00000544301710269_407424.3333333333333467.0RegionNote=Coil 2
TgeneVIMchr1:182821479chr10:17278292ENST000005443017102_95424.3333333333333467.0RegionNote=Head
TgeneVIMchr1:182821479chr10:17278292ENST00000544301710408_466424.3333333333333467.0RegionNote=Tail


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
DHX9
VIM


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+428230_325121.333333333333331271.0BRCA1
HgeneDHX9chr1:182821479chr10:17278292ENST00000367549+4281_250121.333333333333331271.0CREBBP


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Related Drugs to DHX9-VIM


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to DHX9-VIM


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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