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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:ARHGEF38-COL25A1 (FusionGDB2 ID:HG54848TG84570)

Fusion Gene Summary for ARHGEF38-COL25A1

check button Fusion gene summary
Fusion gene informationFusion gene name: ARHGEF38-COL25A1
Fusion gene ID: hg54848tg84570
HgeneTgene
Gene symbol

ARHGEF38

COL25A1

Gene ID

54848

84570

Gene nameRho guanine nucleotide exchange factor 38collagen type XXV alpha 1 chain
Synonyms-AMY|CFEOM5|CLAC|CLAC-P|CLACP
Cytomap('ARHGEF38')('COL25A1')

4q24

4q25

Type of geneprotein-codingprotein-coding
Descriptionrho guanine nucleotide exchange factor 38Rho guanine nucleotide exchange factor (GEF) 38collagen alpha-1(XXV) chainalzheimer disease amyloid-associated proteincollagen-like Alzheimer amyloid plaque componentcollagenous Alzheimer amyloid plaque component
Modification date2020031320200313
UniProtAcc

Q9NXL2

Q9BXS0

Ensembl transtripts involved in fusion geneENST00000265154, ENST00000420470, 
ENST00000508036, 
Fusion gene scores* DoF score6 X 5 X 3=905 X 5 X 4=100
# samples 65
** MAII scorelog2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARHGEF38 [Title/Abstract] AND COL25A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARHGEF38(106534664)-COL25A1(109767375), # samples:2
Anticipated loss of major functional domain due to fusion event.ARHGEF38-COL25A1 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


check button Fusion gene information
* 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
ChimerDB4PRADTCGA-VP-A87K-01AARHGEF38chr4

106534664

+COL25A1chr4

109767375

-
ChimerDB4PRADTCGA-VP-A87KARHGEF38chr4

106534664

+COL25A1chr4

109767375

-


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Fusion Gene ORF analysis for ARHGEF38-COL25A1

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-shiftENST00000265154ENST00000399126ARHGEF38chr4

106534664

+COL25A1chr4

109767375

-
Frame-shiftENST00000265154ENST00000399127ARHGEF38chr4

106534664

+COL25A1chr4

109767375

-
Frame-shiftENST00000265154ENST00000399132ARHGEF38chr4

106534664

+COL25A1chr4

109767375

-
Frame-shiftENST00000420470ENST00000399126ARHGEF38chr4

106534664

+COL25A1chr4

109767375

-
Frame-shiftENST00000420470ENST00000399127ARHGEF38chr4

106534664

+COL25A1chr4

109767375

-
Frame-shiftENST00000420470ENST00000399132ARHGEF38chr4

106534664

+COL25A1chr4

109767375

-
intron-3CDSENST00000508036ENST00000399126ARHGEF38chr4

106534664

+COL25A1chr4

109767375

-
intron-3CDSENST00000508036ENST00000399127ARHGEF38chr4

106534664

+COL25A1chr4

109767375

-
intron-3CDSENST00000508036ENST00000399132ARHGEF38chr4

106534664

+COL25A1chr4

109767375

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

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

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Fusion Genomic Features for ARHGEF38-COL25A1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for ARHGEF38-COL25A1


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/:106534664/:109767375)
- 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
ARHGEF38

Q9NXL2

COL25A1

Q9BXS0

FUNCTION: May act as a guanine-nucleotide releasing factor. {ECO:0000250}.FUNCTION: Inhibits fibrillization of amyloid-beta peptide during the elongation phase. Has also been shown to assemble amyloid fibrils into protease-resistant aggregates. Binds heparin. {ECO:0000269|PubMed:15522881, ECO:0000269|PubMed:15615705, ECO:0000269|PubMed:15853808, ECO:0000269|PubMed:16300410}.

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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Fusion Gene Sequence for ARHGEF38-COL25A1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for ARHGEF38-COL25A1


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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Related Drugs for ARHGEF38-COL25A1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for ARHGEF38-COL25A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0013261Duane Retraction Syndrome2ORPHANET
TgeneC0266573Congenital ptosis2ORPHANET
TgeneC4015552FIBROSIS OF EXTRAOCULAR MUSCLES, CONGENITAL, 51CTD_human;GENOMICS_ENGLAND;UNIPROT