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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: 30427

FusionGeneSummary for RAPGEF1_TTF1

check button Fusion gene summary
Fusion gene informationFusion gene name: RAPGEF1_TTF1
Fusion gene ID: 30427
HgeneTgene
Gene symbol

RAPGEF1

TTF1

Gene ID

2889

7270

Gene nameRap guanine nucleotide exchange factor 1transcription termination factor 1
SynonymsC3G|GRF2TTF-1|TTF-I
Cytomap

9q34.13

9q34.13

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)transcription termination factor 1transcription termination factor, RNA polymerase I
Modification date2018052220180519
UniProtAcc

Q13905

Q15361

Ensembl transtripts involved in fusion geneENST00000372189, ENST00000372195, 
ENST00000372190, ENST00000481260, 
ENST00000334270, ENST00000461970, 
Fusion gene scores* DoF score17 X 14 X 10=23803 X 3 X 3=27
# samples 213
** MAII scorelog2(21/2380*10)=-3.50250034052918
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: RAPGEF1 [Title/Abstract] AND TTF1 [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


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
TCGARVLUADTCGA-4B-A93V-01ARAPGEF1chr9

134514022

-TTF1chr9

135251555

-
* 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-shitENST00000372189ENST00000334270RAPGEF1chr9

134514022

-TTF1chr9

135251555

-
5CDS-5UTRENST00000372189ENST00000461970RAPGEF1chr9

134514022

-TTF1chr9

135251555

-
Frame-shitENST00000372195ENST00000334270RAPGEF1chr9

134514022

-TTF1chr9

135251555

-
5CDS-5UTRENST00000372195ENST00000461970RAPGEF1chr9

134514022

-TTF1chr9

135251555

-
Frame-shitENST00000372190ENST00000334270RAPGEF1chr9

134514022

-TTF1chr9

135251555

-
5CDS-5UTRENST00000372190ENST00000461970RAPGEF1chr9

134514022

-TTF1chr9

135251555

-
5UTR-3CDSENST00000481260ENST00000334270RAPGEF1chr9

134514022

-TTF1chr9

135251555

-
5UTR-5UTRENST00000481260ENST00000461970RAPGEF1chr9

134514022

-TTF1chr9

135251555

-

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FusionProtFeatures for RAPGEF1_TTF1


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

Q13905

TTF1

Q15361

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}. Multifunctional nucleolar protein that terminatesribosomal gene transcription, mediates replication fork arrest andregulates RNA polymerase I transcription on chromatin. Plays adual role in rDNA regulation, being involved in both activationand silencing of rDNA transcription. Interaction with BAZ2A/TIP5recovers DNA-binding activity. {ECO:0000269|PubMed:7597036}.

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 RAPGEF1_TTF1


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 RAPGEF1_TTF1


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
RAPGEF1BCAR1, HCK, CRKL, NEDD9, GRB2, CRK, SHC1, CBL, ATXN1, MBIP, RPS15, SLC20A1, MOV10, NXF1, ABL1, EGFR, SPATS2L, RAP1A, RAP2BTTF1PTRF, KAT2B, BAZ2A, MDM2, CDKN2A, SIRT7, SMAD7, SMAD1, RPL14, NIFK, PRR11, RNASEH2A, GPSM2, NLRP2, VPS26B, FOXL2, GPATCH4, WDR46, DGCR8, RPL18A, CNBP, RBM34, HIST1H1T, RPL30, RPS14, RPL37A


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 RAPGEF1_TTF1


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 RAPGEF1_TTF1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneTTF1C0152013Adenocarcinoma of lung (disorder)1CTD_human