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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: 30420

FusionGeneSummary for RAPGEF1_MALAT1

check button Fusion gene summary
Fusion gene informationFusion gene name: RAPGEF1_MALAT1
Fusion gene ID: 30420
HgeneTgene
Gene symbol

RAPGEF1

MALAT1

Gene ID

2889

378938

Gene nameRap guanine nucleotide exchange factor 1metastasis associated lung adenocarcinoma transcript 1
SynonymsC3G|GRF2HCN|LINC00047|NCRNA00047|NEAT2|PRO2853
Cytomap

9q34.13

11q13.1

Type of geneprotein-codingncRNA
Descriptionrap guanine nucleotide exchange factor 1CRK SH3-binding GNRPRap guanine nucleotide exchange factor (GEF) 1guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)hepcarcinlong intergenic non-protein coding RNA 47metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)nuclear enriched abundant transcript 2nuclear paraspeckle assembly transcript 2 (non-protein coding)
Modification date2018052220180527
UniProtAcc

Q13905

Ensembl transtripts involved in fusion geneENST00000372189, ENST00000372195, 
ENST00000372190, ENST00000481260, 
ENST00000534336, 
Fusion gene scores* DoF score17 X 14 X 10=238071 X 110 X 1=7810
# samples 21126
** MAII scorelog2(21/2380*10)=-3.50250034052918
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(126/7810*10)=-2.63189881464206
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RAPGEF1 [Title/Abstract] AND MALAT1 [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
ChiTaRS3.1BF935964RAPGEF1chr9

134573581

+MALAT1chr11

65270084

-
ChiTaRS3.1BF935963RAPGEF1chr9

134573581

+MALAT1chr11

65270084

-
* 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-3UTRENST00000372189ENST00000534336RAPGEF1chr9

134573581

+MALAT1chr11

65270084

-
intron-3UTRENST00000372195ENST00000534336RAPGEF1chr9

134573581

+MALAT1chr11

65270084

-
intron-3UTRENST00000372190ENST00000534336RAPGEF1chr9

134573581

+MALAT1chr11

65270084

-
intron-3UTRENST00000481260ENST00000534336RAPGEF1chr9

134573581

+MALAT1chr11

65270084

-

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FusionProtFeatures for RAPGEF1_MALAT1


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

Q13905

MALAT1

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}. 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


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FusionGeneSequence for RAPGEF1_MALAT1


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_MALAT1


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


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RelatedDrugs for RAPGEF1_MALAT1


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_MALAT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneMALAT1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneMALAT1C0023903Liver neoplasms1CTD_human
TgeneMALAT1C0027626Neoplasm Invasiveness1CTD_human
TgeneMALAT1C0027627Neoplasm Metastasis1CTD_human
TgeneMALAT1C0032460Polycystic Ovary Syndrome1CTD_human
TgeneMALAT1C0236663Alcohol withdrawal syndrome1PSYGENET
TgeneMALAT1C0279626Squamous cell carcinoma of esophagus1CTD_human