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Center for Computational Systems Medicine level2
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:ARHGEF11-CD48

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ARHGEF11-CD48
FusionPDB ID: 6193
FusionGDB2.0 ID: 6193
HgeneTgene
Gene symbol

ARHGEF11

CD48

Gene ID

9826

962

Gene nameRho guanine nucleotide exchange factor 11CD48 molecule
SynonymsGTRAP48|PDZ-RHOGEFBCM1|BLAST|BLAST1|MEM-102|SLAMF2|hCD48|mCD48
Cytomap

1q23.1

1q23.3

Type of geneprotein-codingprotein-coding
Descriptionrho guanine nucleotide exchange factor 11Rho guanine exchange factor (GEF) 11Rho guanine nucleotide exchange factor (GEF) 11RhoA-specific guanine nucleotide exchange factorRhoGEF glutamate transport modulatorglutamate transporter EAAT4-associated proCD48 antigenB-lymphocyte activation marker BLAST-1BCM1 surface antigenCD48 antigen (B-cell membrane protein)SLAM family member 2TCT.1leukocyte antigen MEM-102signaling lymphocytic activation molecule 2
Modification date2020031320200313
UniProtAcc

O15085

P09326

Ensembl transtripts involved in fusion geneENST idsENST00000361409, ENST00000368194, 
ENST00000315174, ENST00000487682, 
ENST00000368046, ENST00000368045, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score11 X 5 X 7=3854 X 2 X 3=24
# samples 144
** MAII scorelog2(14/385*10)=-1.4594316186373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: ARHGEF11 [Title/Abstract] AND CD48 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ARHGEF11(157014091)-CD48(160654979), # samples:3
Anticipated loss of major functional domain due to fusion event.ARHGEF11-CD48 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ARHGEF11-CD48 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ARHGEF11-CD48 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
ARHGEF11-CD48 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
ARHGEF11-CD48 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
* 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
HgeneARHGEF11

GO:0007186

G protein-coupled receptor signaling pathway

15755723

HgeneARHGEF11

GO:0007266

Rho protein signal transduction

10026210

HgeneARHGEF11

GO:0045893

positive regulation of transcription, DNA-templated

10026210


check buttonFusion gene breakpoints across ARHGEF11 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across CD48 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4SARCTCGA-DX-A1L2-01AARHGEF11chr1

157014091

-CD48chr1

160654979

-
ChimerDB4SARCTCGA-DX-A8BJ-01AARHGEF11chr1

157014091

-CD48chr1

160654979

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000368194ARHGEF11chr1157014091-ENST00000368045CD48chr1160654979-2743107210771499140
ENST00000361409ARHGEF11chr1157014091-ENST00000368045CD48chr1160654979-24467757801202140

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000368194ENST00000368045ARHGEF11chr1157014091-CD48chr1160654979-0.0279324460.9720676
ENST00000361409ENST00000368045ARHGEF11chr1157014091-CD48chr1160654979-0.085581760.9144183

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>6193_6193_1_ARHGEF11-CD48_ARHGEF11_chr1_157014091_ENST00000361409_CD48_chr1_160654979_ENST00000368045_length(amino acids)=140AA_BP=
MVHMTVVSGSNVTLNISESLPENYKQLTWFYTFDQKIVEWDSRKSKYFESKFKGRVRLDPQSGALYISKVQKEDNSTYIMRVLKKTGNEQ

--------------------------------------------------------------

>6193_6193_2_ARHGEF11-CD48_ARHGEF11_chr1_157014091_ENST00000368194_CD48_chr1_160654979_ENST00000368045_length(amino acids)=140AA_BP=
MVHMTVVSGSNVTLNISESLPENYKQLTWFYTFDQKIVEWDSRKSKYFESKFKGRVRLDPQSGALYISKVQKEDNSTYIMRVLKKTGNEQ

--------------------------------------------------------------

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:157014091/chr1:160654979)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
ARHGEF11

O15085

CD48

P09326

FUNCTION: May play a role in the regulation of RhoA GTPase by guanine nucleotide-binding alpha-12 (GNA12) and alpha-13 (GNA13). Acts as guanine nucleotide exchange factor (GEF) for RhoA GTPase and may act as GTPase-activating protein (GAP) for GNA12 and GNA13. Involved in neurotrophin-induced neurite outgrowth. {ECO:0000269|PubMed:21670212}.FUNCTION: Ligand for CD2. Might facilitate interaction between activated lymphocytes. Probably involved in regulating T-cell activation.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneCD48chr1:157014091chr1:160654979ENST0000036804604132_21227.333333333333332244.0DomainNote=Ig-like C2-type 2
TgeneCD48chr1:157014091chr1:160654979ENST000003680460429_12727.333333333333332244.0DomainNote=Ig-like C2-type 1

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000361409-140444_47010.6666666666666661523.0Coiled coilOntology_term=ECO:0000255
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000368194-141444_47010.6666666666666661563.0Coiled coilOntology_term=ECO:0000255
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000361409-1401094_109910.6666666666666661523.0Compositional biasNote=Poly-Pro
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000368194-1411094_109910.6666666666666661563.0Compositional biasNote=Poly-Pro
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000361409-140306_48610.6666666666666661523.0DomainRGSL
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000361409-14047_12610.6666666666666661523.0DomainPDZ
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000361409-140734_92310.6666666666666661523.0DomainDH
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000361409-140965_107910.6666666666666661523.0DomainPH
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000368194-141306_48610.6666666666666661563.0DomainRGSL
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000368194-14147_12610.6666666666666661563.0DomainPDZ
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000368194-141734_92310.6666666666666661563.0DomainDH
HgeneARHGEF11chr1:157014091chr1:160654979ENST00000368194-141965_107910.6666666666666661563.0DomainPH


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>100_ARHGEF11_157014091_CD48_160654979_ranked_0.pdbARHGEF11157014091157014091ENST00000368045CD48chr1160654979-
MVHMTVVSGSNVTLNISESLPENYKQLTWFYTFDQKIVEWDSRKSKYFESKFKGRVRLDPQSGALYISKVQKEDNSTYIMRVLKKTGNEQ
140


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
ARHGEF11_pLDDT.png
all structure
all structure
CD48_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
ARHGEF11
CD48


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to ARHGEF11-CD48


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to ARHGEF11-CD48


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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