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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:ARF1-HSPA9 (FusionGDB2 ID:HG375TG3313)

Fusion Gene Summary for ARF1-HSPA9

check button Fusion gene summary
Fusion gene informationFusion gene name: ARF1-HSPA9
Fusion gene ID: hg375tg3313
HgeneTgene
Gene symbol

ARF1

HSPA9

Gene ID

375

3313

Gene nameADP ribosylation factor 1heat shock protein family A (Hsp70) member 9
SynonymsPVNH8CRP40|CSA|EVPLS|GRP-75|GRP75|HEL-S-124m|HSPA9B|MOT|MOT2|MTHSP75|PBP74|SAAN|SIDBA4
Cytomap('ARF1')('HSPA9')

1q42.13

5q31.2

Type of geneprotein-codingprotein-coding
DescriptionADP-ribosylation factor 1stress-70 protein, mitochondrial75 kDa glucose-regulated proteincatecholamine-regulated protein 40epididymis secretory sperm binding protein Li 124mheat shock 70kD protein 9Bheat shock 70kDa protein 9 (mortalin)mortalin, perinuclearmortalin-2morta
Modification date2020032220200327
UniProtAcc

P84077

.
Ensembl transtripts involved in fusion geneENST00000478424, ENST00000272102, 
ENST00000540651, ENST00000541182, 
Fusion gene scores* DoF score18 X 9 X 7=113410 X 9 X 4=360
# samples 1810
** MAII scorelog2(18/1134*10)=-2.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/360*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARF1 [Title/Abstract] AND HSPA9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARF1(228270466)-HSPA9(137904738), # samples:5
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 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
ChimerDB4PRADTCGA-KK-A6E1-01AARF1chr1

228270466

-HSPA9chr5

137904738

-
ChimerDB4PRADTCGA-KK-A6E1-01AARF1chr1

228270466

+HSPA9chr5

137904738

-
ChimerDB4PRADTCGA-KK-A6E1ARF1chr1

228270466

+HSPA9chr5

137904738

-
ChimerDB4PRADTCGA-KK-A6E1ARF1chr1

228271053

+HSPA9chr5

137904738

-


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Fusion Gene ORF analysis for ARF1-HSPA9

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
3UTR-3CDSENST00000478424ENST00000297185ARF1chr1

228270466

+HSPA9chr5

137904738

-
3UTR-intronENST00000478424ENST00000501917ARF1chr1

228270466

+HSPA9chr5

137904738

-
5UTR-3CDSENST00000272102ENST00000297185ARF1chr1

228270466

+HSPA9chr5

137904738

-
5UTR-3CDSENST00000540651ENST00000297185ARF1chr1

228270466

+HSPA9chr5

137904738

-
5UTR-3CDSENST00000541182ENST00000297185ARF1chr1

228271053

+HSPA9chr5

137904738

-
5UTR-intronENST00000272102ENST00000501917ARF1chr1

228270466

+HSPA9chr5

137904738

-
5UTR-intronENST00000540651ENST00000501917ARF1chr1

228270466

+HSPA9chr5

137904738

-
5UTR-intronENST00000541182ENST00000501917ARF1chr1

228271053

+HSPA9chr5

137904738

-
intron-3CDSENST00000272102ENST00000297185ARF1chr1

228271053

+HSPA9chr5

137904738

-
intron-3CDSENST00000478424ENST00000297185ARF1chr1

228271053

+HSPA9chr5

137904738

-
intron-3CDSENST00000540651ENST00000297185ARF1chr1

228271053

+HSPA9chr5

137904738

-
intron-3CDSENST00000541182ENST00000297185ARF1chr1

228270466

+HSPA9chr5

137904738

-
intron-intronENST00000272102ENST00000501917ARF1chr1

228271053

+HSPA9chr5

137904738

-
intron-intronENST00000478424ENST00000501917ARF1chr1

228271053

+HSPA9chr5

137904738

-
intron-intronENST00000540651ENST00000501917ARF1chr1

228271053

+HSPA9chr5

137904738

-
intron-intronENST00000541182ENST00000501917ARF1chr1

228270466

+HSPA9chr5

137904738

-

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 ARF1-HSPA9


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)


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Fusion Protein Features for ARF1-HSPA9


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/:228270466/:137904738)
- 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
ARF1

P84077

.
FUNCTION: GTP-binding protein involved in protein trafficking among different compartments. Modulates vesicle budding and uncoating within the Golgi complex. Deactivation induces the redistribution of the entire Golgi complex to the endoplasmic reticulum, suggesting a crucial role in protein trafficking. In its GTP-bound form, its triggers the association with coat proteins with the Golgi membrane. The hydrolysis of ARF1-bound GTP, which is mediated by ARFGAPs proteins, is required for dissociation of coat proteins from Golgi membranes and vesicles. The GTP-bound form interacts with PICK1 to limit PICK1-mediated inhibition of Arp2/3 complex activity; the function is linked to AMPA receptor (AMPAR) trafficking, regulation of synaptic plasicity of excitatory synapses and spine shrinkage during long-term depression (LTD).; FUNCTION: (Microbial infection) Functions as an allosteric activator of the cholera toxin catalytic subunit, an ADP-ribosyltransferase. {ECO:0000305}.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


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Fusion Gene Sequence for ARF1-HSPA9


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 ARF1-HSPA9


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 ARF1-HSPA9


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneARF1P84077DB09462GlycerinSmall moleculeApproved|Investigational

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Related Diseases for ARF1-HSPA9


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneARF1C0006142Malignant neoplasm of breast1CTD_human
HgeneARF1C0027626Neoplasm Invasiveness1CTD_human
HgeneARF1C0678222Breast Carcinoma1CTD_human
HgeneARF1C1257931Mammary Neoplasms, Human1CTD_human
HgeneARF1C1458155Mammary Neoplasms1CTD_human
HgeneARF1C1868720Periventricular Nodular Heterotopia1ORPHANET
HgeneARF1C4704874Mammary Carcinoma, Human1CTD_human
HgeneARF1C4748602PERIVENTRICULAR NODULAR HETEROTOPIA 81UNIPROT
TgeneC4225180EVEN-PLUS SYNDROME2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0002896Sideroblastic anemia1CTD_human;GENOMICS_ENGLAND
TgeneC0004364Autoimmune Diseases1CTD_human
TgeneC0007134Renal Cell Carcinoma1CTD_human
TgeneC0019693HIV Infections1CTD_human
TgeneC0030567Parkinson Disease1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0042164Uveitis1CTD_human
TgeneC0151744Myocardial Ischemia1CTD_human
TgeneC0221765Chronic schizophrenia1PSYGENET
TgeneC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
TgeneC0376618Endotoxemia1CTD_human
TgeneC0520459Necrotizing Enterocolitis1CTD_human
TgeneC1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneC1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneC2239176Liver carcinoma1CTD_human
TgeneC4225428ANEMIA, SIDEROBLASTIC, 41GENOMICS_ENGLAND;UNIPROT
TgeneC4274077Autosomal recessive sideroblastic anemia1ORPHANET
TgeneC4505456HIV Coinfection1CTD_human