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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:ARAF-VDR (FusionGDB2 ID:HG369TG7421)

Fusion Gene Summary for ARAF-VDR

check button Fusion gene summary
Fusion gene informationFusion gene name: ARAF-VDR
Fusion gene ID: hg369tg7421
HgeneTgene
Gene symbol

ARAF

VDR

Gene ID

369

7421

Gene nameA-Raf proto-oncogene, serine/threonine kinasevitamin D receptor
SynonymsA-RAF|ARAF1|PKS2|RAFA1NR1I1|PPP1R163
Cytomap('ARAF')('VDR')

Xp11.3

12q13.11

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase A-RafA-Raf proto-oncogene serine/threonine-protein kinaseOncogene ARAF1Ras-binding protein DA-Rafproto-oncogene A-Raf-1proto-oncogene Pksv-raf murine sarcoma 3611 viral oncogene homolog 1v-raf murine sarcoma 3611 virvitamin D3 receptor1,25-dihydroxyvitamin D3 receptornuclear receptor subfamily 1 group I member 1protein phosphatase 1, regulatory subunit 163vitamin D (1,25- dihydroxyvitamin D3) receptorvitamin D nuclear receptor variant 1
Modification date2020032720200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000290277, ENST00000377039, 
ENST00000377045, ENST00000470206, 
Fusion gene scores* DoF score3 X 3 X 2=185 X 7 X 5=175
# samples 38
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(8/175*10)=-1.12928301694497
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARAF [Title/Abstract] AND VDR [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARAF(47424718)-VDR(48328907), # samples:2
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
HgeneARAF

GO:0033138

positive regulation of peptidyl-serine phosphorylation

19667065

HgeneARAF

GO:0043066

negative regulation of apoptotic process

19667065

TgeneVDR

GO:0000122

negative regulation of transcription by RNA polymerase II

17426122

TgeneVDR

GO:0008285

negative regulation of cell proliferation

16549446

TgeneVDR

GO:0010980

positive regulation of vitamin D 24-hydroxylase activity

16549446

TgeneVDR

GO:0038183

bile acid signaling pathway

12016314

TgeneVDR

GO:0045892

negative regulation of transcription, DNA-templated

11891224

TgeneVDR

GO:0070561

vitamin D receptor signaling pathway

16549446



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
ChiTaRS5.0N/ADD229674ARAFchrX

47424718

+VDRchr12

48328907

-
ChiTaRS5.0N/ADI094652ARAFchrX

47424718

+VDRchr12

48328907

-


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Fusion Gene ORF analysis for ARAF-VDR

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-intronENST00000290277ENST00000229022ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000290277ENST00000395324ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000290277ENST00000535672ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000290277ENST00000549336ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000290277ENST00000550325ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000377039ENST00000229022ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000377039ENST00000395324ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000377039ENST00000535672ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000377039ENST00000549336ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000377039ENST00000550325ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000377045ENST00000229022ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000377045ENST00000395324ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000377045ENST00000535672ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000377045ENST00000549336ARAFchrX

47424718

+VDRchr12

48328907

-
5CDS-intronENST00000377045ENST00000550325ARAFchrX

47424718

+VDRchr12

48328907

-
intron-intronENST00000470206ENST00000229022ARAFchrX

47424718

+VDRchr12

48328907

-
intron-intronENST00000470206ENST00000395324ARAFchrX

47424718

+VDRchr12

48328907

-
intron-intronENST00000470206ENST00000535672ARAFchrX

47424718

+VDRchr12

48328907

-
intron-intronENST00000470206ENST00000549336ARAFchrX

47424718

+VDRchr12

48328907

-
intron-intronENST00000470206ENST00000550325ARAFchrX

47424718

+VDRchr12

48328907

-

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 ARAF-VDR


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 ARAF-VDR


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/:47424718/:48328907)
- 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


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Fusion Gene Sequence for ARAF-VDR


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 ARAF-VDR


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 ARAF-VDR


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 ARAF-VDR


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneARAFC0006142Malignant neoplasm of breast1CTD_human
HgeneARAFC0678222Breast Carcinoma1CTD_human
HgeneARAFC1257931Mammary Neoplasms, Human1CTD_human
HgeneARAFC1458155Mammary Neoplasms1CTD_human
HgeneARAFC4704874Mammary Carcinoma, Human1CTD_human
TgeneC0342646Vitamin D-Dependent Rickets, Type 2A13CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0035579Rickets3CTD_human
TgeneC0002170Alopecia2CTD_human
TgeneC0006142Malignant neoplasm of breast2CTD_human
TgeneC0023176Lead Poisoning2CTD_human
TgeneC0086873Pseudopelade2CTD_human
TgeneC0162311Androgenetic Alopecia2CTD_human
TgeneC0263477Female pattern alopecia (disorder)2CTD_human
TgeneC0678222Breast Carcinoma2CTD_human
TgeneC1257931Mammary Neoplasms, Human2CTD_human
TgeneC1458155Mammary Neoplasms2CTD_human
TgeneC4083212Alopecia, Male Pattern2CTD_human
TgeneC4704874Mammary Carcinoma, Human2CTD_human
TgeneC0005586Bipolar Disorder1PSYGENET
TgeneC0006826Malignant Neoplasms1CTD_human
TgeneC0007138Carcinoma, Transitional Cell1CTD_human
TgeneC0007785Cerebral Infarction1CTD_human
TgeneC0014556Epilepsy, Temporal Lobe1CTD_human
TgeneC0014558Uncinate Epilepsy1CTD_human
TgeneC0020538Hypertensive disease1CTD_human
TgeneC0023434Chronic Lymphocytic Leukemia1CTD_human
TgeneC0026769Multiple Sclerosis1CTD_human
TgeneC0027651Neoplasms1CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0041948Uremia1CTD_human
TgeneC0042870Vitamin D Deficiency1CTD_human
TgeneC0086132Depressive Symptoms1PSYGENET
TgeneC0086692Benign Neoplasm1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC0393672Epilepsy, Benign Psychomotor, Childhood1CTD_human
TgeneC0393682Epilepsy, Lateral Temporal1CTD_human
TgeneC0751010Cerebral Infarction, Left Hemisphere1CTD_human
TgeneC0751011Cerebral Infarction, Right Hemisphere1CTD_human
TgeneC0751012Anterior Choroidal Artery Infarction1CTD_human
TgeneC0751014Subcortical Infarction1CTD_human
TgeneC0751324Multiple Sclerosis, Acute Fulminating1CTD_human
TgeneC0887799Posterior Choroidal Artery Infarction1CTD_human
TgeneC3536983Familial Hypophosphatemic Rickets1ORPHANET