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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: 30422

FusionGeneSummary for RAPGEF1_MED27

check button Fusion gene summary
Fusion gene informationFusion gene name: RAPGEF1_MED27
Fusion gene ID: 30422
HgeneTgene
Gene symbol

RAPGEF1

MED27

Gene ID

2889

9442

Gene nameRap guanine nucleotide exchange factor 1mediator complex subunit 27
SynonymsC3G|GRF2CRAP34|CRSP34|CRSP8|MED3|TRAP37
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)mediator of RNA polymerase II transcription subunit 27CRSP complex subunit 8cofactor required for Sp1 transcriptional activation, subunit 8, 34kDap37 TRAP/SMCC/PC2 subunittranscriptional coactivator CRSP34
Modification date2018052220180519
UniProtAcc

Q13905

Q6P2C8

Ensembl transtripts involved in fusion geneENST00000372189, ENST00000372195, 
ENST00000372190, ENST00000481260, 
ENST00000357028, ENST00000292035, 
ENST00000474263, 
Fusion gene scores* DoF score17 X 14 X 10=23804 X 6 X 6=144
# samples 218
** MAII scorelog2(21/2380*10)=-3.50250034052918
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/144*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RAPGEF1 [Title/Abstract] AND MED27 [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

TgeneMED27

GO:0006357

regulation of transcription by RNA polymerase II

9989412


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
TCGARVHNSCTCGA-CV-A45W-01ARAPGEF1chr9

134497183

-MED27chr9

134769379

-
TCGALDLGGTCGA-DU-A5TT-01ARAPGEF1chr9

134615157

-MED27chr9

134738527

-
TCGALDLUADTCGA-55-8620-01ARAPGEF1chr9

134615157

-MED27chr9

134769379

-
TCGARVUCSTCGA-NA-A4R1-01ARAPGEF1chr9

134471685

-MED27chr9

134759486

-
* 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
5CDS-intronENST00000372189ENST00000357028RAPGEF1chr9

134497183

-MED27chr9

134769379

-
5CDS-intronENST00000372189ENST00000292035RAPGEF1chr9

134497183

-MED27chr9

134769379

-
5CDS-intronENST00000372189ENST00000474263RAPGEF1chr9

134497183

-MED27chr9

134769379

-
5CDS-intronENST00000372195ENST00000357028RAPGEF1chr9

134497183

-MED27chr9

134769379

-
5CDS-intronENST00000372195ENST00000292035RAPGEF1chr9

134497183

-MED27chr9

134769379

-
5CDS-intronENST00000372195ENST00000474263RAPGEF1chr9

134497183

-MED27chr9

134769379

-
5CDS-intronENST00000372190ENST00000357028RAPGEF1chr9

134497183

-MED27chr9

134769379

-
5CDS-intronENST00000372190ENST00000292035RAPGEF1chr9

134497183

-MED27chr9

134769379

-
5CDS-intronENST00000372190ENST00000474263RAPGEF1chr9

134497183

-MED27chr9

134769379

-
intron-intronENST00000481260ENST00000357028RAPGEF1chr9

134497183

-MED27chr9

134769379

-
intron-intronENST00000481260ENST00000292035RAPGEF1chr9

134497183

-MED27chr9

134769379

-
intron-intronENST00000481260ENST00000474263RAPGEF1chr9

134497183

-MED27chr9

134769379

-
intron-3CDSENST00000372189ENST00000357028RAPGEF1chr9

134615157

-MED27chr9

134738527

-
intron-3CDSENST00000372189ENST00000292035RAPGEF1chr9

134615157

-MED27chr9

134738527

-
intron-intronENST00000372189ENST00000474263RAPGEF1chr9

134615157

-MED27chr9

134738527

-
In-frameENST00000372195ENST00000357028RAPGEF1chr9

134615157

-MED27chr9

134738527

-
In-frameENST00000372195ENST00000292035RAPGEF1chr9

134615157

-MED27chr9

134738527

-
5CDS-intronENST00000372195ENST00000474263RAPGEF1chr9

134615157

-MED27chr9

134738527

-
intron-3CDSENST00000372190ENST00000357028RAPGEF1chr9

134615157

-MED27chr9

134738527

-
intron-3CDSENST00000372190ENST00000292035RAPGEF1chr9

134615157

-MED27chr9

134738527

-
intron-intronENST00000372190ENST00000474263RAPGEF1chr9

134615157

-MED27chr9

134738527

-
intron-3CDSENST00000481260ENST00000357028RAPGEF1chr9

134615157

-MED27chr9

134738527

-
intron-3CDSENST00000481260ENST00000292035RAPGEF1chr9

134615157

-MED27chr9

134738527

-
intron-intronENST00000481260ENST00000474263RAPGEF1chr9

134615157

-MED27chr9

134738527

-
intron-intronENST00000372189ENST00000357028RAPGEF1chr9

134615157

-MED27chr9

134769379

-
intron-intronENST00000372189ENST00000292035RAPGEF1chr9

134615157

-MED27chr9

134769379

-
intron-intronENST00000372189ENST00000474263RAPGEF1chr9

134615157

-MED27chr9

134769379

-
5CDS-intronENST00000372195ENST00000357028RAPGEF1chr9

134615157

-MED27chr9

134769379

-
5CDS-intronENST00000372195ENST00000292035RAPGEF1chr9

134615157

-MED27chr9

134769379

-
5CDS-intronENST00000372195ENST00000474263RAPGEF1chr9

134615157

-MED27chr9

134769379

-
intron-intronENST00000372190ENST00000357028RAPGEF1chr9

134615157

-MED27chr9

134769379

-
intron-intronENST00000372190ENST00000292035RAPGEF1chr9

134615157

-MED27chr9

134769379

-
intron-intronENST00000372190ENST00000474263RAPGEF1chr9

134615157

-MED27chr9

134769379

-
intron-intronENST00000481260ENST00000357028RAPGEF1chr9

134615157

-MED27chr9

134769379

-
intron-intronENST00000481260ENST00000292035RAPGEF1chr9

134615157

-MED27chr9

134769379

-
intron-intronENST00000481260ENST00000474263RAPGEF1chr9

134615157

-MED27chr9

134769379

-
Frame-shitENST00000372189ENST00000357028RAPGEF1chr9

134471685

-MED27chr9

134759486

-
Frame-shitENST00000372189ENST00000292035RAPGEF1chr9

134471685

-MED27chr9

134759486

-
5CDS-intronENST00000372189ENST00000474263RAPGEF1chr9

134471685

-MED27chr9

134759486

-
Frame-shitENST00000372195ENST00000357028RAPGEF1chr9

134471685

-MED27chr9

134759486

-
Frame-shitENST00000372195ENST00000292035RAPGEF1chr9

134471685

-MED27chr9

134759486

-
5CDS-intronENST00000372195ENST00000474263RAPGEF1chr9

134471685

-MED27chr9

134759486

-
Frame-shitENST00000372190ENST00000357028RAPGEF1chr9

134471685

-MED27chr9

134759486

-
Frame-shitENST00000372190ENST00000292035RAPGEF1chr9

134471685

-MED27chr9

134759486

-
5CDS-intronENST00000372190ENST00000474263RAPGEF1chr9

134471685

-MED27chr9

134759486

-
intron-3CDSENST00000481260ENST00000357028RAPGEF1chr9

134471685

-MED27chr9

134759486

-
intron-3CDSENST00000481260ENST00000292035RAPGEF1chr9

134471685

-MED27chr9

134759486

-
intron-intronENST00000481260ENST00000474263RAPGEF1chr9

134471685

-MED27chr9

134759486

-

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FusionProtFeatures for RAPGEF1_MED27


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

Q13905

MED27

Q6P2C8

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}. Component of the Mediator complex, a coactivatorinvolved in the regulated transcription of nearly all RNApolymerase II-dependent genes. Mediator functions as a bridge toconvey information from gene-specific regulatory proteins to thebasal RNA polymerase II transcription machinery. Mediator isrecruited to promoters by direct interactions with regulatoryproteins and serves as a scaffold for the assembly of a functionalpreinitiation complex with RNA polymerase II and the generaltranscription factors. {ECO:0000269|PubMed:10882111,ECO:0000269|PubMed:9989412}.

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_MED27


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.
>In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000357028_chr9_134738527_-_91aa
MSGGLGLRRSPEMSGKIEKAGDRPCHHCPAPLSAAPDAGCRGPILHDLVKKLHKAVPGPVPALREVSAGRPSPDMEGFPNPRSLP_HLPA

>In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000292035_chr9_134738527_-_91aa
MSGGLGLRRSPEMSGKIEKAGDRPCHHCPAPLSAAPDAGCRGPILHDLVKKLHKAVPGPVPALREVSAGRPSPDMEGFPNPRSLP_HLPA


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000357028_chr9_134738527_-_274nt
ATGAGCGGCGGCCTCGGCCTCCGGCGCAGCCCGGAAATGTCCGGCAAGATCGAGAAAGCAGGTGACAGACCATGCCACCACTGCCCTGCT
CCACTATCAGCTGCCCCAGATGCCGGATGTCGTGGTCCGATCCTTCATGACCTGGTTAAGAAGTTACATAAAGCTGTTCCAGGCCCCGTG
CCAGCGCTGCGGGAAGTTTCTGCAGGACGGCCTTCCCCCGACATGGAGGGATTTCCGAACCCTCGAAGCCTTCCATGACACCTGCCGGCA

>In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000292035_chr9_134738527_-_274nt
ATGAGCGGCGGCCTCGGCCTCCGGCGCAGCCCGGAAATGTCCGGCAAGATCGAGAAAGCAGGTGACAGACCATGCCACCACTGCCCTGCT
CCACTATCAGCTGCCCCAGATGCCGGATGTCGTGGTCCGATCCTTCATGACCTGGTTAAGAAGTTACATAAAGCTGTTCCAGGCCCCGTG
CCAGCGCTGCGGGAAGTTTCTGCAGGACGGCCTTCCCCCGACATGGAGGGATTTCCGAACCCTCGAAGCCTTCCATGACACCTGCCGGCA


* Fusion transcript sequences (Full-length transcript).
>In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000357028_chr9_134738527_-_949nt
CGCTGCGCTGCGGCCGGCTCGCGGGCCGGGGGAGCGGCGGCGGGCGCGCGGGAGGCGGAGCGGCGGCGGCGGGCGCGGCGGGAGCGGCTG
GGCCCGGGCGGGCTGGAGCGCGGTCGCCGAGCGCAGGGCCGCGGCCGCGCGGAGCCCGCCATGCCGGCGCGGGTCTGAGGCGTGGCGAGC
CAGGGCCGAGGCGAGCGGCGGGCGCGCCGCCCCTGTCGCCCCGCGGCGGCCCGGCCCGGGCCCGATGAGCGGCGGCCTCGGCCTCCGGCG
CAGCCCGGAAATGTCCGGCAAGATCGAGAAAGCAGGTGACAGACCATGCCACCACTGCCCTGCTCCACTATCAGCTGCCCCAGATGCCGG
ATGTCGTGGTCCGATCCTTCATGACCTGGTTAAGAAGTTACATAAAGCTGTTCCAGGCCCCGTGCCAGCGCTGCGGGAAGTTTCTGCAGG
ACGGCCTTCCCCCGACATGGAGGGATTTCCGAACCCTCGAAGCCTTCCATGACACCTGCCGGCAGTAGCCCCCACGCTGGCCCCAGCCTC
AGACCCCACCCAGCACCTTCCCAGACACGCAGGAAGCCCACAGAAGGCTCAGCTGGTTCCTCACTGCCCAGATGTGTACAGCTGCTCCTC
CCTTTCATAAAGCAGCGCCATGTGTGCAGAGGCCACTCTTGAAGAGCAGACTCCCTCTGTGGCTGATGGGACTAATTATTCCCACTAGCC
AGCGGACTGAAGGCAAAGAAGACCTTTCTAGAACCTGGTAGAAGGAAGCTGTGCAGCATGCTCCTCGTCCATGTGTGTCGGCAGTGCTGG
TGTCTGTCGTCTCCGCGAGCTGTTACTGGAATGAGCCCTTGTGTTCATGGGTATCGTCATGCGGGGTTCTTGTGTTTTGTGGGGCTTGGG

>In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000292035_chr9_134738527_-_949nt
CGCTGCGCTGCGGCCGGCTCGCGGGCCGGGGGAGCGGCGGCGGGCGCGCGGGAGGCGGAGCGGCGGCGGCGGGCGCGGCGGGAGCGGCTG
GGCCCGGGCGGGCTGGAGCGCGGTCGCCGAGCGCAGGGCCGCGGCCGCGCGGAGCCCGCCATGCCGGCGCGGGTCTGAGGCGTGGCGAGC
CAGGGCCGAGGCGAGCGGCGGGCGCGCCGCCCCTGTCGCCCCGCGGCGGCCCGGCCCGGGCCCGATGAGCGGCGGCCTCGGCCTCCGGCG
CAGCCCGGAAATGTCCGGCAAGATCGAGAAAGCAGGTGACAGACCATGCCACCACTGCCCTGCTCCACTATCAGCTGCCCCAGATGCCGG
ATGTCGTGGTCCGATCCTTCATGACCTGGTTAAGAAGTTACATAAAGCTGTTCCAGGCCCCGTGCCAGCGCTGCGGGAAGTTTCTGCAGG
ACGGCCTTCCCCCGACATGGAGGGATTTCCGAACCCTCGAAGCCTTCCATGACACCTGCCGGCAGTAGCCCCCACGCTGGCCCCAGCCTC
AGACCCCACCCAGCACCTTCCCAGACACGCAGGAAGCCCACAGAAGGCTCAGCTGGTTCCTCACTGCCCAGATGTGTACAGCTGCTCCTC
CCTTTCATAAAGCAGCGCCATGTGTGCAGAGGCCACTCTTGAAGAGCAGACTCCCTCTGTGGCTGATGGGACTAATTATTCCCACTAGCC
AGCGGACTGAAGGCAAAGAAGACCTTTCTAGAACCTGGTAGAAGGAAGCTGTGCAGCATGCTCCTCGTCCATGTGTGTCGGCAGTGCTGG
TGTCTGTCGTCTCCGCGAGCTGTTACTGGAATGAGCCCTTGTGTTCATGGGTATCGTCATGCGGGGTTCTTGTGTTTTGTGGGGCTTGGG


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FusionGenePPI for RAPGEF1_MED27


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, RAP2BMED27MED10, MED9, MED29, MED19, MED28, MED26, MED30, MED22, MED1, MED12, MED18, ZC3H13, TRIP4, OBFC1, QKI, TADA2A, MED14, MED4, FBXW7, EPAS1, POLR2C, ARFGAP1, AFP, RBPJ, SOX5, CDK8, CDK19, ESR1, MED7, CCNC, MED16, MED17, MED11, MED13, MED13L, MED15, MED20, MED24, MED6, MED8, MED23, MED21


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_MED27


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_MED27


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