FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

FusionGeneSummary

leaf

FusionProtFeature

leaf

FusionGeneSequence

leaf

FusionGenePPI

leaf

RelatedDrugs

leaf

RelatedDiseases

Fusion gene ID: 29723

FusionGeneSummary for PVT1_FARP1

check button Fusion gene summary
Fusion gene informationFusion gene name: PVT1_FARP1
Fusion gene ID: 29723
HgeneTgene
Gene symbol

PVT1

FARP1

Gene ID

5820

10160

Gene namePvt1 oncogeneFERM, ARH/RhoGEF and pleckstrin domain protein 1
SynonymsLINC00079|MIR1204HG|MYC|NCRNA00079|onco-lncRNA-100CDEP|FARP1-IT1|PLEKHC2|PPP1R75
Cytomap

8q24.21

13q32.2

Type of genencRNAprotein-coding
DescriptionCXCR4/PVT1 fusionHIST1H2BD/PVT1 fusionMIR1204, MIR1205, MIR1206 and MIR1207 hostOncogene PVT-1 (MYC activator)PVT1/CASC8 fusionPVT1/CCDC26 fusionPVT1/IFRD1 fusionPVT1/IRF2BP2 fusionPVT1/LINC00824 fusionPVT1/MYC fusionPVT1/NFIL3 fusionPVT1/NSMCEFERM, ARHGEF and pleckstrin domain-containing protein 1FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)FERM, RhoGEF and pleckstrin domain-containing protein 1PH domain-containing family C member 2chondrocyte-derived ezrin-li
Modification date2018052020180519
UniProtAcc

Q9Y4F1

Ensembl transtripts involved in fusion geneENST00000408388, ENST00000595437, 
ENST00000376586, ENST00000319562, 
ENST00000376581, ENST00000593990, 
Fusion gene scores* DoF score37 X 12 X 15=66609 X 10 X 5=450
# samples 3910
** MAII scorelog2(39/6660*10)=-4.09397614820901
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/450*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PVT1 [Title/Abstract] AND FARP1 [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
TgeneFARP1

GO:0010923

negative regulation of phosphatase activity

19389623


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
TCGALDESCATCGA-R6-A6L6-01BPVT1chr8

128806980

+FARP1chr13

99076826

+
* 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
intron-3CDSENST00000408388ENST00000595437PVT1chr8

128806980

+FARP1chr13

99076826

+
intron-3CDSENST00000408388ENST00000376586PVT1chr8

128806980

+FARP1chr13

99076826

+
intron-3CDSENST00000408388ENST00000319562PVT1chr8

128806980

+FARP1chr13

99076826

+
intron-intronENST00000408388ENST00000376581PVT1chr8

128806980

+FARP1chr13

99076826

+
intron-intronENST00000408388ENST00000593990PVT1chr8

128806980

+FARP1chr13

99076826

+

Top

FusionProtFeatures for PVT1_FARP1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PVT1

FARP1

Q9Y4F1

Lectin that binds to various sugars: galactose > mannose= fucose > N-acetylglucosamine > N-acetylgalactosamine(PubMed:10224141). Acts as a chemoattractant, probably involved inthe regulation of cell migration (PubMed:28301481).{ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}. Functions as guanine nucleotide exchange factor forRAC1. May play a role in semaphorin signaling. Plays a role in theassembly and disassembly of dendritic filopodia, the formation ofdendritic spines, regulation of dendrite length and ultimately theformation of synapses (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


Top

FusionGeneSequence for PVT1_FARP1


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).

Top

FusionGenePPI for PVT1_FARP1


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
PVT1TRIM25FARP1ELAVL1, NTRK1, CAPZA2, MYO1C, PDGFRA, AKAP1, SYNPO, GAR1, GEMIN7, BRD2, PTPRG, SNRPN, SDC1, SDC2, DCAF8, TRIM25


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


Top

RelatedDrugs for PVT1_FARP1


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

Top

RelatedDiseases for PVT1_FARP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePVT1C0019829Hodgkin Disease1CTD_human
HgenePVT1C0162538Immunoglobulin A deficiency (disorder)1CTD_human
TgeneFARP1C0236969Substance-Related Disorders1CTD_human