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: 30423

FusionGeneSummary for RAPGEF1_PPP1CB

check button Fusion gene summary
Fusion gene informationFusion gene name: RAPGEF1_PPP1CB
Fusion gene ID: 30423
HgeneTgene
Gene symbol

RAPGEF1

PPP1CB

Gene ID

2889

5500

Gene nameRap guanine nucleotide exchange factor 1protein phosphatase 1 catalytic subunit beta
SynonymsC3G|GRF2HEL-S-80p|NSLH2|PP-1B|PP1B|PP1beta|PPP1CD
Cytomap

9q34.13

2p23.2

Type of geneprotein-codingprotein-coding
Descriptionrap guanine nucleotide exchange factor 1CRK SH3-binding GNRPRap guanine nucleotide exchange factor (GEF) 1guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)serine/threonine-protein phosphatase PP1-beta catalytic subunitepididymis secretory sperm binding protein Li 80pprotein phosphatase 1, catalytic subunit, beta isoformprotein phosphatase 1, catalytic subunit, beta isozymeprotein phosphatase 1, catalyti
Modification date2018052220180522
UniProtAcc

Q13905

P62140

Ensembl transtripts involved in fusion geneENST00000372189, ENST00000372195, 
ENST00000372190, ENST00000481260, 
ENST00000358506, ENST00000296122, 
ENST00000395366, 
Fusion gene scores* DoF score17 X 14 X 10=23806 X 7 X 2=84
# samples 217
** MAII scorelog2(21/2380*10)=-3.50250034052918
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/84*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RAPGEF1 [Title/Abstract] AND PPP1CB [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
HgeneRAPGEF1

GO:0038180

nerve growth factor signaling pathway

17724123

HgeneRAPGEF1

GO:0043547

positive regulation of GTPase activity

10548487

HgeneRAPGEF1

GO:0071320

cellular response to cAMP

21840392

HgeneRAPGEF1

GO:1990090

cellular response to nerve growth factor stimulus

17724123

TgenePPP1CB

GO:0030155

regulation of cell adhesion

20354225


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
ChiTaRS3.1T06907RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
* 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-5UTRENST00000372189ENST00000358506RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
intron-5UTRENST00000372189ENST00000296122RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
intron-5UTRENST00000372189ENST00000395366RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
intron-5UTRENST00000372195ENST00000358506RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
intron-5UTRENST00000372195ENST00000296122RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
intron-5UTRENST00000372195ENST00000395366RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
intron-5UTRENST00000372190ENST00000358506RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
intron-5UTRENST00000372190ENST00000296122RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
intron-5UTRENST00000372190ENST00000395366RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
intron-5UTRENST00000481260ENST00000358506RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
intron-5UTRENST00000481260ENST00000296122RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+
intron-5UTRENST00000481260ENST00000395366RAPGEF1chr9

134453266

-PPP1CBchr2

28974976

+

Top

FusionProtFeatures for RAPGEF1_PPP1CB


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RAPGEF1

Q13905

PPP1CB

P62140

Guanine nucleotide-releasing protein that binds to SH3domain of CRK and GRB2/ASH. Transduces signals from CRK toactivate RAS. Plays a role in the establishment of basalendothelial barrier function. Plays a role in nerve growth factor(NGF)-induced sustained activation of Rap1 and neurite outgrowth.{ECO:0000269|PubMed:17724123, ECO:0000269|PubMed:21840392,ECO:0000269|PubMed:7806500}. Protein phosphatase that associates with over 200regulatory proteins to form highly specific holoenzymes whichdephosphorylate hundreds of biological targets. Proteinphosphatase (PP1) is essential for cell division, it participatesin the regulation of glycogen metabolism, muscle contractility andprotein synthesis. Involved in regulation of ionic conductancesand long-term synaptic plasticity. Component of the PTW/PP1phosphatase complex, which plays a role in the control ofchromatin structure and cell cycle progression during thetransition from mitosis into interphase. In balance with CSNK1Dand CSNK1E, determines the circadian period length, through theregulation of the speed and rhythmicity of PER1 and PER2phosphorylation. May dephosphorylate CSNK1D and CSNK1E.Dephosphorylates the 'Ser-418' residue of FOXP3 in regulatory T-cells (Treg) from patients with rheumatoid arthritis, therebyinactivating FOXP3 and rendering Treg cells functionally defective(PubMed:23396208). {ECO:0000269|PubMed:20516061,ECO:0000269|PubMed:21712997, ECO:0000269|PubMed:23396208}.

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 RAPGEF1_PPP1CB


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 RAPGEF1_PPP1CB


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


Top

RelatedDrugs for RAPGEF1_PPP1CB


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 RAPGEF1_PPP1CB


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