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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:RAB3IP-CD63 (FusionGDB2 ID:71386)

Fusion Gene Summary for RAB3IP-CD63

check button Fusion gene summary
Fusion gene informationFusion gene name: RAB3IP-CD63
Fusion gene ID: 71386
HgeneTgene
Gene symbol

RAB3IP

CD63

Gene ID

117177

967

Gene nameRAB3A interacting proteinCD63 molecule
SynonymsRABIN3|RABIN8LAMP-3|ME491|MLA1|OMA81H|TSPAN30
Cytomap

12q15

12q13.2

Type of geneprotein-codingprotein-coding
Descriptionrab-3A-interacting proteinSSX2 interacting proteinrab3A-interacting proteinrabin-3CD63 antigenCD63 antigen (melanoma 1 antigen)granulophysinlysosomal-associated membrane protein 3lysosome-associated membrane glycoprotein 3melanoma-associated antigen ME491melanoma-associated antigen MLA1ocular melanoma-associated antigentetraspa
Modification date2020032720200327
UniProtAcc.

P08962

Ensembl transtripts involved in fusion geneENST00000247833, ENST00000325555, 
ENST00000378815, ENST00000483530, 
ENST00000362025, ENST00000550536, 
ENST00000550847, ENST00000551641, 
ENST00000553099, 		ENST00000257857, 
ENST00000420846, ENST00000546939, 
ENST00000548160, ENST00000548898, 
ENST00000549117, ENST00000550776, 
ENST00000552067, ENST00000552692, 
ENST00000552754, 
Fusion gene scores* DoF score21 X 9 X 12=22689 X 8 X 6=432
# samples 279
** MAII scorelog2(27/2268*10)=-3.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/432*10)=-2.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RAB3IP [Title/Abstract] AND CD63 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRAB3IP(70132811)-CD63(56120045), # samples:3
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
HgeneRAB3IP

GO:0006612

protein targeting to membrane

23382462

TgeneCD63

GO:0034613

cellular protein localization

15647390

TgeneCD63

GO:1901379

regulation of potassium ion transmembrane transport

15647390


check buttonFusion gene breakpoints across RAB3IP (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 CD63 (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
ChimerDB4BLCATCGA-4Z-AA7S-01ARAB3IPchr12

70132811

-CD63chr12

56120045

-
ChimerDB4BLCATCGA-4Z-AA7S-01ARAB3IPchr12

70132811

+CD63chr12

56120045

-
ChimerDB4BLCATCGA-4Z-AA7SRAB3IPchr12

70132811

+CD63chr12

56120045

-


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Fusion Gene ORF analysis for RAB3IP-CD63

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
5UTR-3CDSENST00000247833ENST00000257857RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000247833ENST00000420846RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000247833ENST00000546939RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000247833ENST00000548160RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000247833ENST00000548898RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000247833ENST00000549117RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000247833ENST00000550776RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000247833ENST00000552067RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000247833ENST00000552692RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000247833ENST00000552754RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000325555ENST00000257857RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000325555ENST00000420846RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000325555ENST00000546939RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000325555ENST00000548160RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000325555ENST00000548898RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000325555ENST00000549117RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000325555ENST00000550776RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000325555ENST00000552067RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000325555ENST00000552692RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000325555ENST00000552754RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000378815ENST00000257857RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000378815ENST00000420846RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000378815ENST00000546939RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000378815ENST00000548160RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000378815ENST00000548898RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000378815ENST00000549117RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000378815ENST00000550776RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000378815ENST00000552067RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000378815ENST00000552692RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000378815ENST00000552754RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000483530ENST00000257857RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000483530ENST00000420846RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000483530ENST00000546939RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000483530ENST00000548160RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000483530ENST00000548898RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000483530ENST00000549117RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000483530ENST00000550776RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000483530ENST00000552067RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000483530ENST00000552692RAB3IPchr12

70132811

+CD63chr12

56120045

-
5UTR-3CDSENST00000483530ENST00000552754RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000362025ENST00000257857RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000362025ENST00000420846RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000362025ENST00000546939RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000362025ENST00000548160RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000362025ENST00000548898RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000362025ENST00000549117RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000362025ENST00000550776RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000362025ENST00000552067RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000362025ENST00000552692RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000362025ENST00000552754RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550536ENST00000257857RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550536ENST00000420846RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550536ENST00000546939RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550536ENST00000548160RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550536ENST00000548898RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550536ENST00000549117RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550536ENST00000550776RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550536ENST00000552067RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550536ENST00000552692RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550536ENST00000552754RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550847ENST00000257857RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550847ENST00000420846RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550847ENST00000546939RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550847ENST00000548160RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550847ENST00000548898RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550847ENST00000549117RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550847ENST00000550776RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550847ENST00000552067RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550847ENST00000552692RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000550847ENST00000552754RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000551641ENST00000257857RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000551641ENST00000420846RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000551641ENST00000546939RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000551641ENST00000548160RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000551641ENST00000548898RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000551641ENST00000549117RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000551641ENST00000550776RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000551641ENST00000552067RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000551641ENST00000552692RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000551641ENST00000552754RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000553099ENST00000257857RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000553099ENST00000420846RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000553099ENST00000546939RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000553099ENST00000548160RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000553099ENST00000548898RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000553099ENST00000549117RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000553099ENST00000550776RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000553099ENST00000552067RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000553099ENST00000552692RAB3IPchr12

70132811

+CD63chr12

56120045

-
intron-3CDSENST00000553099ENST00000552754RAB3IPchr12

70132811

+CD63chr12

56120045

-

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 RAB3IP-CD63


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 RAB3IP-CD63


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/:70132811/:56120045)
- 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
.CD63

P08962

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: Functions as cell surface receptor for TIMP1 and plays a role in the activation of cellular signaling cascades. Plays a role in the activation of ITGB1 and integrin signaling, leading to the activation of AKT, FAK/PTK2 and MAP kinases. Promotes cell survival, reorganization of the actin cytoskeleton, cell adhesion, spreading and migration, via its role in the activation of AKT and FAK/PTK2. Plays a role in VEGFA signaling via its role in regulating the internalization of KDR/VEGFR2. Plays a role in intracellular vesicular transport processes, and is required for normal trafficking of the PMEL luminal domain that is essential for the development and maturation of melanocytes. Plays a role in the adhesion of leukocytes onto endothelial cells via its role in the regulation of SELP trafficking. May play a role in mast cell degranulation in response to Ms4a2/FceRI stimulation, but not in mast cell degranulation in response to other stimuli. {ECO:0000269|PubMed:16917503, ECO:0000269|PubMed:21803846, ECO:0000269|PubMed:21962903, ECO:0000269|PubMed:23632027, ECO:0000269|PubMed:24635319}.

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 RAB3IP-CD63


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 RAB3IP-CD63


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 RAB3IP-CD63


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 RAB3IP-CD63


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