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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: 30442

FusionGeneSummary for RAPGEF5_LUC7L2

check button Fusion gene summary
Fusion gene informationFusion gene name: RAPGEF5_LUC7L2
Fusion gene ID: 30442
HgeneTgene
Gene symbol

RAPGEF5

LUC7L2

Gene ID

9771

51631

Gene nameRap guanine nucleotide exchange factor 5LUC7 like 2, pre-mRNA splicing factor
SynonymsGFR|MR-GEF|REPACCGI-59|CGI-74|LUC7B2
Cytomap

7p15.3

7q34

Type of geneprotein-codingprotein-coding
Descriptionrap guanine nucleotide exchange factor 5M-Ras-regulated GEFM-Ras-regulated Rap GEFRap guanine nucleotide exchange factor (GEF) 5guanine nucleotide exchange factor for Rap1related to Epacputative RNA-binding protein Luc7-like 2LUC7-like 2
Modification date2018051920180523
UniProtAcc

Q92565

Ensembl transtripts involved in fusion geneENST00000344041, ENST00000475788, 
ENST00000405243, ENST00000401957, 
ENST00000541515, 
Fusion gene scores* DoF score11 X 11 X 6=7268 X 9 X 4=288
# samples 1111
** MAII scorelog2(11/726*10)=-2.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(11/288*10)=-1.38856528791765
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RAPGEF5 [Title/Abstract] AND LUC7L2 [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
ChiTaRS3.1DA302213RAPGEF5chr7

22232984

-LUC7L2chr7

139060804

+
* 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
In-frameENST00000344041ENST00000541515RAPGEF5chr7

22232984

-LUC7L2chr7

139060804

+
5UTR-3CDSENST00000475788ENST00000541515RAPGEF5chr7

22232984

-LUC7L2chr7

139060804

+
intron-3CDSENST00000405243ENST00000541515RAPGEF5chr7

22232984

-LUC7L2chr7

139060804

+
Frame-shitENST00000401957ENST00000541515RAPGEF5chr7

22232984

-LUC7L2chr7

139060804

+

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FusionProtFeatures for RAPGEF5_LUC7L2


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RAPGEF5

Q92565

LUC7L2

Guanine nucleotide exchange factor (GEF) for RAP1A,RAP2A and MRAS/M-Ras-GTP. Its association with MRAS inhibits Rap1activation. {ECO:0000269|PubMed:10777494,ECO:0000269|PubMed:10934204}. 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}.

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
HgeneRAPGEF5chr7:22232984chr7:139060804ENST00000401957-116345_57998581DomainRas-GEF
HgeneRAPGEF5chr7:22232984chr7:139060804ENST00000401957-11668_20198581DomainN-terminal Ras-GEF


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FusionGeneSequence for RAPGEF5_LUC7L2


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).
>In-frame_RAPGEF5_ENST00000344041_chr7_22232984_-_LUC7L2_ENST00000541515_chr7_139060804_+_2435nt
GCTGCGGCCGCGGCTGAGGGACCTGCCCGCGCTGCTGCGGAGCGGGCTCACGCTGCGGAGGAAGCGGAGCGCCGCTGGGGGCCGGACTCT
ATCAAGAAGAATATCTAATCCGTACCTTGAACATACGCCTTCCCAGATTTATGGAGAGAATTCTTCTTGTGCAGGAAGAGCATTGAGGAA
TATTATTATCGTTCAAGCAGCTGACCTGATAAAGGACAGAGTGAACCTCAAGGGGTTTTACAGGAGGAGCTGCGTTGGGTCAGAGCTGGT
AGACTGGCTTCTAGAACACTGTCCTTTCGTCCAGTGCAGATCTATGGCCATAGGAGTCTGGCAACTCCTACTGGACATGGGAATTATGTT
ATCAGTGGACCAGCATCTATACTTTCAAGATACTTATGTTTTCTACCAGTTTTCCTCTGATGAATGTAGCTACTTGTACTGTGAATTTGA
AAGAGAAGAAGAATGGCAAAATGGTGTCAAGCTTTTACTGCAACTTGTGCCTCTCATTCCTGCCAGAGGTGGCATCTGTGAACTGTCTCA
TCAGAAAATTGAAGACTCCGAAGAAAGCAGTGATGAAATTCTTGTGCGTCTAACATCTGCGGTGCAGAGAGAGCTAGCAGCTGTTATTGC
TTTGAAAGCAAGGAAGTCTGCAATTGAACAAGATGAAGAAAACAACGACAAACATGTAGCTGTAACAGAAGCCGAAAGTGTTCCAGATTC
TCAGGCAGGGGTGATGTGCAAGCTCCAGGAAAGAGATGAAATCGGACGAATTGAACTAGTCCAGAAGCTGGCAAAAGAAAACTATCAGTT
TTTGCAGACGGACAAAAAAGAACAGGAGAAGTCTGAACACCAAGATGATGAAGTGACGACTGTTCAGGTTAAAGAGCAAGACCAGAGCGT
CCTGGTGCTGAAGAAAGTGCAGTGCTGTGGCCCAGCCCCCACAGCTGGGAGTGCGGAGAGCCATTGGAGATATGTGGTGGTGTCCGGGAC
CCCGGAGAAGATTTTGGAGCACCTTTTGAATGACTTGCACCTGGAAGAAGTCCAGGACAAAGAAACAGGAGATACAACTCGTCAACGAAT
CAAATTCAGTGATGACAGAGTATGCAAGAGTCACCTTCTCAACTGTTGTCCTCATGATGTCCTTTCTGGAACTAGAATGGATCTTGGAGA
ATGTCTGAAAGTCCATGACCTGGCTTTAAGAGCGGATTATGAAATTGCATCCAAAGAACAAGATTTTTTCTTTGAACTTGATGCCATGGA
TCATCTGCAGTCATTCATTGCAGATTGTGATCGTAGAACAGAAGTGGCCAAGAAAAGATTAGCAGAAACTCAAGAAGAGATTAGTGCTGA
AGTAGCAGCAAAGGCAGAACGTGTTCATGAGTTAAATGAAGAAATTGGTAAATTGTTAGCCAAGGTGGAACAACTAGGAGCTGAAGGGAA
TGTGGAGGAATCCCAGAAAGTAATGGATGAAGTAGAGAAAGCACGGGCAAAGAAAAGAGAAGCAGAGGAAGTTTATCGGAATTCTATGCC
AGCTTCCAGTTTTCAGCAGCAGAAACTTCGAGTCTGTGAAGTCTGCTCTGCCTATTTAGGACTTCATGATAATGACAGACGACTGGCTGA
TCATTTTGGGGGTAAACTGCACCTGGGATTTATTGAAATAAGAGAGAAGCTTGAAGAATTAAAGAGAGTCGTAGCTGAGAAGCAGGAGAA
AAGAAACCAGGAACGGCTGAAACGAAGAGAAGAGAGAGAGAGAGAAGAAAGGGAGAAGCTGAGGAGGTCCCGATCACACAGCAAGAATCC
AAAAAGATCCAGGTCCAGAGAGCATCGCAGACATCGATCTCGCTCCATGTCACGTGAACGCAAGAGGAGAACTCGATCCAAATCTCGGGA
GAAACGCCATCGCCACAGGTCCCGCTCCAGCAGCCGTAGCCGCAGCCGTAGCCACCAGAGAAGTCGGCACAGTTCTAGAGATAGGAGCAG
AGAACGATCCAAGAGGAGATCCTCAAAAGAAAGATTCAGAGACCAAGACTTAGCATCATGTGACAGAGACAGGAGTTCAAGAGACAGATC
ACCTCGTGACAGAGATCGGAAAGATAAGAAGCGGTCCTATGAGAGTGCTAATGGCAGATCAGAAGACAGGAGGAGCTCTGAAGAGCGCGA
AGCAGGGGAGATCTAACTAGCTGTGTACATTTCTTCAGTCCTTAAGCTTCCTACGGAGTTACGTACTATTGTTTAGTTCACAGCTGTTCA
GGGTGACAGTGAGCAGATCCAGACACCAGATCCAGCTAGGCTAGATGTACAGTATCTAACTTGATCTGAACTGAACCTGTTTTCCTTGAT
GATGCCTAAAACTACATCCATAGTTTCTGGTGAACCTGTAATACAGTTCTGAAAGTACAGTTTTATATAATAAGATGCTGATCTCTTTAT


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FusionGenePPI for RAPGEF5_LUC7L2


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
RAPGEF5RAP2A, RAP1A, MRAS, KCND3, PLAC9, VANGL1, TMEM253, ANK3, ANK1, MAPK8IP2, ANK2, DDHD2, TUBB1, HSP90AA4P, CCDC88A, UBB, HERC1, PPFIBP1, RICTOR, PLEC, ZNHIT2, WNK1, PRKAR1B, PPP2R5D, PRKACB, PIK3CB, FLNC, ATP2B2LUC7L2RNPS1, YWHAG, YWHAQ, PTCD3, LUC7L2, PEA15, NKAP, SSFA2, SVIL, KLHL20, ALB, ATRX, LINC00341, NAT9, NDUFA4L2, LPL, UNC119, MAN2A2, MAP1LC3B, FAM173A, NAP1L5, NASP, NUTF2, OFD1, SAT1, ZCCHC10, CDK5RAP2, CCDC53, FXR1, CHD3, KIAA1377, PTN, NSF, ULK2, RRP1B, MEPCE, IKBKG, NEDD4, RBM39, NOP56, NDEL1, EXOC1, GSK3B, GADD45G, AIMP2, PDPK1, CDC37, CDK4, SETDB1, PIK3R3, JMJD6, ELAVL1, CUL3, COPS5, CAND1, HAP1, APP, RPL19, RPL15, RPL18A, RPL7A, RPS4X, SNRPD2, RPLP0P6, BARD1, PAXIP1, CD81, SRPK2, SRPK1, TARDBP, CARS, HSPA4L, ARFIP1, ATP6V1C1, PBDC1, IVNS1ABP, MAN2B1, STAT3, SHMT2, STAU1, HUWE1, NFYA, SRSF6, SRSF7, APPBP2, EZH2, SUZ12, RNF2, EAF1, TRA2A, ZRANB2, LUC7L, CSNK2A2, LARP7, ZC3H18, BCLAF1, THRAP3, PRPF4B, CCDC9, ACIN1, C17orf85, C1QBP, PABPC4, GPATCH8, U2AF2, PAIP1, UBE2O, RBM22, PNN, LARP1, LARP1B, SRSF1, SNW1, CLASRP, PAIP2B, SRRT, CSNK2A1, CCDC12, LUC7L3, MOV10, CDC40, DDX46, SF3A1, ZC3H14, CPSF6, SNRNP27, CLK3, IK, CASC3, FAM98A, FTL, SNRNP70, MKRN2, SCAF11, MKRN1, TRA2B, SRSF8, SRSF12, SRSF10, SREK1, CLK2, HNRNPR, DDX5, PABPC1, PRPF6, PRPF8, RBM8A, RPL22, SNRPD3, SRSF11, TIA1, SF3B3, SNRNP200, SNRPD1, SNRPE, SYNCRIP, U2AF1, SFN, NTRK1, CNTRL, OTUB1, RC3H1, CRBN, FTH1, PPIL4, ISY1, SRRM2, INO80B, RPAP3, FOXA1, TRIM25, UHRF2


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 RAPGEF5_LUC7L2


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 RAPGEF5_LUC7L2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRAPGEF5C0005586Bipolar Disorder1PSYGENET
HgeneRAPGEF5C0033975Psychotic Disorders1PSYGENET
HgeneRAPGEF5C0036341Schizophrenia1PSYGENET
HgeneRAPGEF5C0041696Unipolar Depression1PSYGENET
HgeneRAPGEF5C0236733Amphetamine-Related Disorders1CTD_human
HgeneRAPGEF5C0349204Nonorganic psychosis1PSYGENET
HgeneRAPGEF5C1269683Major Depressive Disorder1PSYGENET