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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 30981

FusionGeneSummary for RERE_VAMP3

check button Fusion gene summary
Fusion gene informationFusion gene name: RERE_VAMP3
Fusion gene ID: 30981
HgeneTgene
Gene symbol

RERE

VAMP3

Gene ID

473

9341

Gene namearginine-glutamic acid dipeptide repeatsvesicle associated membrane protein 3
SynonymsARG|ARP|ATN1L|DNB1|NEDBEHCEB
Cytomap

1p36.23

1p36.23

Type of geneprotein-codingprotein-coding
Descriptionarginine-glutamic acid dipeptide repeats proteinarginine-glutamic acid dipeptide (RE) repeatsatrophin 2atrophin-1 like proteinatrophin-1 related proteinvesicle-associated membrane protein 3VAMP-3cellubrevinsynaptobrevin-3
Modification date2018052320180527
UniProtAcc

Q9P2R6

Q15836

Ensembl transtripts involved in fusion geneENST00000337907, ENST00000377464, 
ENST00000400907, ENST00000400908, 
ENST00000476556, ENST00000460659, 
ENST00000054666, ENST00000470357, 
Fusion gene scores* DoF score19 X 16 X 9=27364 X 4 X 3=48
# samples 244
** MAII scorelog2(24/2736*10)=-3.51096191927738
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RERE [Title/Abstract] AND VAMP3 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
TgeneVAMP3

GO:0042147

retrograde transport, endosome to Golgi

18195106

TgeneVAMP3

GO:1903531

negative regulation of secretion by cell

12130530


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLGGTCGA-DU-8166-01AREREchr1

8482787

-VAMP3chr1

7833502

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
Frame-shiftENST00000337907ENST00000054666REREchr1

8482787

-VAMP3chr1

7833502

+
5CDS-5UTRENST00000337907ENST00000470357REREchr1

8482787

-VAMP3chr1

7833502

+
Frame-shiftENST00000377464ENST00000054666REREchr1

8482787

-VAMP3chr1

7833502

+
5CDS-5UTRENST00000377464ENST00000470357REREchr1

8482787

-VAMP3chr1

7833502

+
Frame-shiftENST00000400907ENST00000054666REREchr1

8482787

-VAMP3chr1

7833502

+
5CDS-5UTRENST00000400907ENST00000470357REREchr1

8482787

-VAMP3chr1

7833502

+
Frame-shiftENST00000400908ENST00000054666REREchr1

8482787

-VAMP3chr1

7833502

+
5CDS-5UTRENST00000400908ENST00000470357REREchr1

8482787

-VAMP3chr1

7833502

+
5UTR-3CDSENST00000476556ENST00000054666REREchr1

8482787

-VAMP3chr1

7833502

+
5UTR-5UTRENST00000476556ENST00000470357REREchr1

8482787

-VAMP3chr1

7833502

+
5UTR-3CDSENST00000460659ENST00000054666REREchr1

8482787

-VAMP3chr1

7833502

+
5UTR-5UTRENST00000460659ENST00000470357REREchr1

8482787

-VAMP3chr1

7833502

+

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FusionProtFeatures for RERE_VAMP3


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

Q9P2R6

VAMP3

Q15836

Plays a role as a transcriptional repressor duringdevelopment. May play a role in the control of cell survival.Overexpression of RERE recruits BAX to the nucleus particularly toPOD and triggers caspase-3 activation, leading to cell death.{ECO:0000269|PubMed:11331249}. SNARE involved in vesicular transport from the lateendosomes to the trans-Golgi network.{ECO:0000269|PubMed:18195106}.

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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FusionGeneSequence for RERE_VAMP3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for RERE_VAMP3


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
REREATN1, LZTR1, NR2E1, HDAC1, HDAC2, EHMT2, HIST2H3C, ELAVL1, KRTAP4-12, PLSCR1, TRIM22, CBFA2T2, EFEMP2, ZMYND8, PSMA3, PRRC2A, ALG13, ECM1, EFEMP1, PRRC2B, KAT6A, RBFOX2, WDR5, EP300, AUTS2, FBXW7, CDO1, TRIM25VAMP3STX4, SNAP23, STX2, STX3, NELFE, STX6, VTI1A, STX16, BCAP31, VAMP2, VAMP8, IKBKG, APP, SLC3A2, ATP4A, BCL2L13, CCDC8, STX7, STX8, VTI1B, STX12, STX19, GPR183, MICA, ENPP6, WDFY2, TNFRSF10B, TCTN2, TMEM17, TMEM216, TINF2, RAB11A, RAB8A, PTAR1, CDH1, PPM1H, WDFY1, SYPL1, STX11, SCARB2, TPCN2, RNF11, MANSC1, RINT1, SLCO1B1, KIFAP3, MED21, SNRNP27, USP47, CPLX1, PMS1, TMEM206, CD4, IPPK, EIF2B2, JPH4, DUSP22, LRRIQ1, SYPL2, VAC14, TRIM25, LMNA


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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RelatedDrugs for RERE_VAMP3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for RERE_VAMP3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneREREC3495559Juvenile arthritis1CTD_human
TgeneVAMP3C0005586Bipolar Disorder1PSYGENET
TgeneVAMP3C1839839MAJOR AFFECTIVE DISORDER 21PSYGENET