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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: 41450

FusionGeneSummary for VGLL4_UPF2

check button Fusion gene summary
Fusion gene informationFusion gene name: VGLL4_UPF2
Fusion gene ID: 41450
HgeneTgene
Gene symbol

VGLL4

UPF2

Gene ID

9686

26019

Gene namevestigial like family member 4UPF2, regulator of nonsense mediated mRNA decay
SynonymsVGL-4HUPF2|RENT2|smg-3
Cytomap

3p25.3-p25.2

10p14

Type of geneprotein-codingprotein-coding
Descriptiontranscription cofactor vestigial-like protein 4Vestigial-like 4vestigial like 4regulator of nonsense transcripts 2FRS2/UPF2/LEMD3 fusionLEMD3/UPF2 fusionUPF2 regulator of nonsense transcripts homolognonsense mRNA reducing factor 2smg-3 homolog, nonsense mediated mRNA decay factorup-frameshift suppressor 2 homologyeast Upf2p h
Modification date2018051920180523
UniProtAcc

Q14135

Q9HAU5

Ensembl transtripts involved in fusion geneENST00000273038, ENST00000430365, 
ENST00000404339, ENST00000480288, 
ENST00000413604, ENST00000451674, 
ENST00000424529, 
ENST00000356352, 
ENST00000357604, ENST00000397053, 
ENST00000460569, 
Fusion gene scores* DoF score13 X 10 X 6=7805 X 7 X 3=105
# samples 1710
** MAII scorelog2(17/780*10)=-2.19793937761191
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/105*10)=-0.070389327891398
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: VGLL4 [Title/Abstract] AND UPF2 [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

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
TCGARVBLCATCGA-XF-A8HD-01AVGLL4chr3

11744445

-UPF2chr10

12021164

-
* 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-shitENST00000273038ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
Frame-shitENST00000273038ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
Frame-shitENST00000273038ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
5CDS-intronENST00000273038ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000430365ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000430365ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000430365ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-intronENST00000430365ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
5UTR-3CDSENST00000404339ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
5UTR-3CDSENST00000404339ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
5UTR-3CDSENST00000404339ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
5UTR-intronENST00000404339ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000480288ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000480288ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000480288ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-intronENST00000480288ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000413604ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000413604ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000413604ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-intronENST00000413604ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000451674ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000451674ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000451674ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-intronENST00000451674ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000424529ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000424529ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000424529ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-intronENST00000424529ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-

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FusionProtFeatures for VGLL4_UPF2


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
VGLL4

Q14135

UPF2

Q9HAU5

May act as a specific coactivator for the mammalianTEFs. {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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FusionGeneSequence for VGLL4_UPF2


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 VGLL4_UPF2


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
VGLL4TEAD1, MEF2A, ELAVL1, TERF2IP, IRF2BP2, CDK6, IRF2BP1, IRF2BPL, TEAD4, TEAD3, USP11, TRIM25UPF2RPS25, UPF3B, EIF4A1, XRN2, UPF1, UPF2, DCP2, XRN1, EXOSC10, EXOSC2, EXOSC4, PARN, UPF3A, SMG1, POLD1, ELAVL1, RNPS1, PAIP1, PRPF31, MMS22L, RBM8A, HBB, TP63, RPS15, RPL5, RPS7, PHB2, MAP1LC3B, NOB1, RPL13, SERBP1, BLM, KRT18, TUBB2A, ENO1, ATP1B3, ITGB1, MRPL40, TOP3B, CALR, E4F1, HBZ, ZBTB48, HS3ST3A1, HSF2BP, CIZ1, NOMO1, RRP7A, WNK1, ZGPAT, SUMO3, TYMS, MIF, RPS6, COMTD1, NDUFA7, LDHA, RPL8, CYBA, TK1, SERF2, CENPU, GADD45GIP1, HMGA1, AGPAT1, GLTSCR2, MTERF3, ZNF44, RSRC2, TNNI2, ABCF2, PITX1, DPF2, EXOSC8, EXOSC6, ZNF408, ZFP36, DCP1B, EXOSC1, LSM1, SKIV2L2, MYB, MAP1A, ART4, LGR4, PUF60, FUS, SMARCD1, SMARCD2, SMARCD3, TRIP10, NTRK1, XPO1, KIF15


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 VGLL4_UPF2


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 VGLL4_UPF2


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