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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:CD63-PUM1 (FusionGDB2 ID:14634)

Fusion Gene Summary for CD63-PUM1

check button Fusion gene summary
Fusion gene informationFusion gene name: CD63-PUM1
Fusion gene ID: 14634
HgeneTgene
Gene symbol

CD63

PUM1

Gene ID

967

9698

Gene nameCD63 moleculepumilio RNA binding family member 1
SynonymsLAMP-3|ME491|MLA1|OMA81H|TSPAN30HSPUM|PUMH|PUMH1|PUML1|SCA47
Cytomap

12q13.2

1p35.2

Type of geneprotein-codingprotein-coding
DescriptionCD63 antigenCD63 antigen (melanoma 1 antigen)granulophysinlysosomal-associated membrane protein 3lysosome-associated membrane glycoprotein 3melanoma-associated antigen ME491melanoma-associated antigen MLA1ocular melanoma-associated antigentetraspapumilio homolog 1pumilio-1
Modification date2020032720200313
UniProtAcc

P08962

.
Ensembl transtripts involved in fusion geneENST00000548898, ENST00000552067, 
ENST00000420846, ENST00000548160, 
ENST00000546939, ENST00000552692, 
ENST00000549117, ENST00000257857, 
ENST00000552754, ENST00000550776, 
ENST00000424085, ENST00000257075, 
ENST00000373747, ENST00000426105, 
ENST00000440538, ENST00000373741, 
ENST00000423018, ENST00000373742, 
ENST00000490546, 
Fusion gene scores* DoF score23 X 19 X 9=393312 X 12 X 5=720
# samples 2313
** MAII scorelog2(23/3933*10)=-4.09592441999854
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/720*10)=-2.46948528330122
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CD63 [Title/Abstract] AND PUM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCD63(56120031)-PUM1(31439038), # 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
HgeneCD63

GO:0034613

cellular protein localization

15647390

HgeneCD63

GO:1901379

regulation of potassium ion transmembrane transport

15647390

TgenePUM1

GO:0010608

posttranscriptional regulation of gene expression

25100735

TgenePUM1

GO:0043488

regulation of mRNA stability

26724866

TgenePUM1

GO:0051726

regulation of cell cycle

20818387

TgenePUM1

GO:0051983

regulation of chromosome segregation

26724866

TgenePUM1

GO:1900246

positive regulation of RIG-I signaling pathway

25340845

TgenePUM1

GO:2000637

positive regulation of gene silencing by miRNA

20818387|22345517


check buttonFusion gene breakpoints across CD63 (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 PUM1 (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
ChiTaRS5.0N/ABF814933CD63chr12

56120031

+PUM1chr1

31439038

-
ChiTaRS5.0N/ABF814941CD63chr12

56120031

+PUM1chr1

31439038

-


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Fusion Gene ORF analysis for CD63-PUM1

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
intron-3CDSENST00000548898ENST00000424085CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548898ENST00000257075CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548898ENST00000373747CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548898ENST00000426105CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548898ENST00000440538CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548898ENST00000373741CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548898ENST00000423018CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548898ENST00000373742CD63chr12

56120031

+PUM1chr1

31439038

-
intron-5UTRENST00000548898ENST00000490546CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552067ENST00000424085CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552067ENST00000257075CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552067ENST00000373747CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552067ENST00000426105CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552067ENST00000440538CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552067ENST00000373741CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552067ENST00000423018CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552067ENST00000373742CD63chr12

56120031

+PUM1chr1

31439038

-
intron-5UTRENST00000552067ENST00000490546CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000420846ENST00000424085CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000420846ENST00000257075CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000420846ENST00000373747CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000420846ENST00000426105CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000420846ENST00000440538CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000420846ENST00000373741CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000420846ENST00000423018CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000420846ENST00000373742CD63chr12

56120031

+PUM1chr1

31439038

-
intron-5UTRENST00000420846ENST00000490546CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548160ENST00000424085CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548160ENST00000257075CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548160ENST00000373747CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548160ENST00000426105CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548160ENST00000440538CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548160ENST00000373741CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548160ENST00000423018CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000548160ENST00000373742CD63chr12

56120031

+PUM1chr1

31439038

-
intron-5UTRENST00000548160ENST00000490546CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000546939ENST00000424085CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000546939ENST00000257075CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000546939ENST00000373747CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000546939ENST00000426105CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000546939ENST00000440538CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000546939ENST00000373741CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000546939ENST00000423018CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000546939ENST00000373742CD63chr12

56120031

+PUM1chr1

31439038

-
intron-5UTRENST00000546939ENST00000490546CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552692ENST00000424085CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552692ENST00000257075CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552692ENST00000373747CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552692ENST00000426105CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552692ENST00000440538CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552692ENST00000373741CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552692ENST00000423018CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552692ENST00000373742CD63chr12

56120031

+PUM1chr1

31439038

-
intron-5UTRENST00000552692ENST00000490546CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000549117ENST00000424085CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000549117ENST00000257075CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000549117ENST00000373747CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000549117ENST00000426105CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000549117ENST00000440538CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000549117ENST00000373741CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000549117ENST00000423018CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000549117ENST00000373742CD63chr12

56120031

+PUM1chr1

31439038

-
intron-5UTRENST00000549117ENST00000490546CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000257857ENST00000424085CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000257857ENST00000257075CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000257857ENST00000373747CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000257857ENST00000426105CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000257857ENST00000440538CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000257857ENST00000373741CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000257857ENST00000423018CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000257857ENST00000373742CD63chr12

56120031

+PUM1chr1

31439038

-
intron-5UTRENST00000257857ENST00000490546CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552754ENST00000424085CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552754ENST00000257075CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552754ENST00000373747CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552754ENST00000426105CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552754ENST00000440538CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552754ENST00000373741CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552754ENST00000423018CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000552754ENST00000373742CD63chr12

56120031

+PUM1chr1

31439038

-
intron-5UTRENST00000552754ENST00000490546CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000550776ENST00000424085CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000550776ENST00000257075CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000550776ENST00000373747CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000550776ENST00000426105CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000550776ENST00000440538CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000550776ENST00000373741CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000550776ENST00000423018CD63chr12

56120031

+PUM1chr1

31439038

-
intron-3CDSENST00000550776ENST00000373742CD63chr12

56120031

+PUM1chr1

31439038

-
intron-5UTRENST00000550776ENST00000490546CD63chr12

56120031

+PUM1chr1

31439038

-

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 CD63-PUM1


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 CD63-PUM1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CD63

P08962

.
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}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 CD63-PUM1


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 CD63-PUM1


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 CD63-PUM1


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 CD63-PUM1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCD63C0019207Hepatoma, Morris1CTD_human
HgeneCD63C0019208Hepatoma, Novikoff1CTD_human
HgeneCD63C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneCD63C0023904Liver Neoplasms, Experimental1CTD_human
HgeneCD63C0086404Experimental Hepatoma1CTD_human
TgenePUM1C0004134Ataxia1GENOMICS_ENGLAND
TgenePUM1C0010417Cryptorchidism1GENOMICS_ENGLAND
TgenePUM1C0019193Hepatitis, Toxic1CTD_human
TgenePUM1C0036572Seizures1GENOMICS_ENGLAND
TgenePUM1C0557874Global developmental delay1GENOMICS_ENGLAND
TgenePUM1C0860207Drug-Induced Liver Disease1CTD_human
TgenePUM1C1262760Hepatitis, Drug-Induced1CTD_human
TgenePUM1C3658290Drug-Induced Acute Liver Injury1CTD_human
TgenePUM1C3714756Intellectual Disability1GENOMICS_ENGLAND
TgenePUM1C4025871Abnormality of the face1GENOMICS_ENGLAND
TgenePUM1C4277682Chemical and Drug Induced Liver Injury1CTD_human
TgenePUM1C4279912Chemically-Induced Liver Toxicity1CTD_human
TgenePUM1C4693672SPINOCEREBELLAR ATAXIA 471GENOMICS_ENGLAND;UNIPROT