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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:REV3L-ARHGEF25 (FusionGDB2 ID:73582)

Fusion Gene Summary for REV3L-ARHGEF25

check button Fusion gene summary
Fusion gene informationFusion gene name: REV3L-ARHGEF25
Fusion gene ID: 73582
HgeneTgene
Gene symbol

REV3L

ARHGEF25

Gene ID

5980

115557

Gene nameREV3 like, DNA directed polymerase zeta catalytic subunitRho guanine nucleotide exchange factor 25
SynonymsPOLZ|REV3GEFT|p63RhoGEF
Cytomap

6q21

12q13.3

Type of geneprotein-codingprotein-coding
DescriptionDNA polymerase zeta catalytic subunitREV3-like, polymerase (DNA directed), zeta, catalytic subunitRev-3, yeast, homolog-like (polymerase, DNA, zeta)rho guanine nucleotide exchange factor 25RAC/CDC42 exchange factorRho guanine nucleotide exchange factor (GEF) 25RhoA/RAC/CDC42 exchange factorguanine nucleotide exchange factor GEFTrac/Cdc42/Rho exchange factor GEFTrhoA/Rac/Cdc42 guanine nucleotide
Modification date2020031320200313
UniProtAcc.

Q86VW2

Ensembl transtripts involved in fusion geneENST00000358835, ENST00000368802, 
ENST00000368805, ENST00000435970, 
ENST00000462119, 		ENST00000477314, 
ENST00000286494, ENST00000333972, 
Fusion gene scores* DoF score17 X 20 X 10=34005 X 6 X 3=90
# samples 265
** MAII scorelog2(26/3400*10)=-3.70895121799661
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/90*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: REV3L [Title/Abstract] AND ARHGEF25 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointREV3L(111803953)-ARHGEF25(58008472), # samples:2
Anticipated loss of major functional domain due to fusion event.REV3L-ARHGEF25 seems lost the major protein functional domain in Tgene 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 buttonFusion gene breakpoints across REV3L (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 ARHGEF25 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4BRCATCGA-EW-A6SD-01AREV3Lchr6

111803953

-ARHGEF25chr12

58008472

+


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Fusion Gene ORF analysis for REV3L-ARHGEF25

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-intronENST00000358835ENST00000477314REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
5CDS-intronENST00000368802ENST00000477314REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
5CDS-intronENST00000368805ENST00000477314REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
5UTR-3CDSENST00000435970ENST00000286494REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
5UTR-3CDSENST00000435970ENST00000333972REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
5UTR-intronENST00000435970ENST00000477314REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
Frame-shiftENST00000358835ENST00000286494REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
Frame-shiftENST00000358835ENST00000333972REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
Frame-shiftENST00000368805ENST00000286494REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
Frame-shiftENST00000368805ENST00000333972REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
In-frameENST00000368802ENST00000286494REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
In-frameENST00000368802ENST00000333972REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
intron-3CDSENST00000462119ENST00000286494REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
intron-3CDSENST00000462119ENST00000333972REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+
intron-intronENST00000462119ENST00000477314REV3Lchr6

111803953

-ARHGEF25chr12

58008472

+

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)
ENST00000368802REV3Lchr6111803953-ENST00000333972ARHGEF25chr1258008472+17384623451388347
ENST00000368802REV3Lchr6111803953-ENST00000286494ARHGEF25chr1258008472+17384623451388347

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
ENST00000368802ENST00000333972REV3Lchr6111803953-ARHGEF25chr1258008472+0.037738070.962262
ENST00000368802ENST00000286494REV3Lchr6111803953-ARHGEF25chr1258008472+0.037738070.962262

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Fusion Genomic Features for REV3L-ARHGEF25


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)
REV3Lchr6111803952-ARHGEF25chr1258008471+7.58E-111
REV3Lchr6111803952-ARHGEF25chr1258008471+7.58E-111

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.
genomic feature

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for REV3L-ARHGEF25


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/chr6:111803953/chr12:58008472)
- 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
.ARHGEF25

Q86VW2

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: May play a role in actin cytoskeleton reorganization in different tissues since its activation induces formation of actin stress fibers. It works as a guanine nucleotide exchange factor for Rho family of small GTPases. Links specifically G alpha q/11-coupled receptors to RHOA activation. May be an important regulator of processes involved in axon and dendrite formation. In neurons seems to be an exchange factor primarily for RAC1. Involved in skeletal myogenesis (By similarity). {ECO:0000250, ECO:0000269|PubMed:11861769, ECO:0000269|PubMed:12547822, ECO:0000269|PubMed:15069594, ECO:0000269|PubMed:15632174, ECO:0000269|PubMed:16314529, ECO:0000269|PubMed:17606614}.

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
TgeneARHGEF25chr6:111803953chr12:58008472ENST00000286494715348_466272581.0DomainPH
TgeneARHGEF25chr6:111803953chr12:58008472ENST00000333972816348_466311620.0DomainPH
TgeneARHGEF25chr6:111803953chr12:58008472ENST00000286494715278_299272581.0RegionNote=Important for binding to Rho GTPases
TgeneARHGEF25chr6:111803953chr12:58008472ENST00000286494715467_493272581.0RegionNote=Sufficient to bind activated GNAQ
TgeneARHGEF25chr6:111803953chr12:58008472ENST00000333972816467_493311620.0RegionNote=Sufficient to bind activated GNAQ

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneREV3Lchr6:111803953chr12:58008472ENST00000358835-2333086_3104463131.0MotifNote=CysB motif
HgeneREV3Lchr6:111803953chr12:58008472ENST00000368802-1323086_3104463131.0MotifNote=CysB motif
HgeneREV3Lchr6:111803953chr12:58008472ENST00000368805-2333086_3104463131.0MotifNote=CysB motif
HgeneREV3Lchr6:111803953chr12:58008472ENST00000435970-2343086_310403053.0MotifNote=CysB motif
HgeneREV3Lchr6:111803953chr12:58008472ENST00000358835-2333042_3057463131.0Zinc fingerNote=CysA-type
HgeneREV3Lchr6:111803953chr12:58008472ENST00000368802-1323042_3057463131.0Zinc fingerNote=CysA-type
HgeneREV3Lchr6:111803953chr12:58008472ENST00000368805-2333042_3057463131.0Zinc fingerNote=CysA-type
HgeneREV3Lchr6:111803953chr12:58008472ENST00000435970-2343042_305703053.0Zinc fingerNote=CysA-type
TgeneARHGEF25chr6:111803953chr12:58008472ENST00000286494715160_336272581.0DomainDH
TgeneARHGEF25chr6:111803953chr12:58008472ENST00000333972816160_336311620.0DomainDH
TgeneARHGEF25chr6:111803953chr12:58008472ENST00000333972816278_299311620.0RegionNote=Important for binding to Rho GTPases


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Fusion Gene Sequence for REV3L-ARHGEF25


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.
>73582_73582_1_REV3L-ARHGEF25_REV3L_chr6_111803953_ENST00000368802_ARHGEF25_chr12_58008472_ENST00000286494_length(transcript)=1738nt_BP=462nt
CATCATCATGGCAACAAGAGCTGCAGCCTGGGACCGAGGAGCCCGTGTGATTCCCGGCGGTGGCGGCAGTGGCGGCAGCACCAGCACCGA
CGAAAGCTCGAGGGCTTCTCTCCTGCGGCCCCTTGCCGGGTGCTCCTGAGGAGGCGGCGGCAGCAGCGCCTACACCGCCCCGCCCGCCGC
TCCTCGAGGTGCCTCTGTGTGAGGGGAGGGGGCCGTGCCGAGAAGGGGAGGGGGCGCCGCCGCCGCTGCGGAGGGAGCCGCCGCCGCTGC
TGCTGCCGCTGCCGGGTCGCCAGTGAAGGGAGGCAGTGGCGGCGGCGGCGAACATGTTTTCAGTAAGGATAGTGACTGCAGACTACTACA
TGGCCAGCCCGCTGCAGGGGCTGGATACCTGCCAATCCCCCCTCACCCAGGCCCCTGTCAAGAAGGTGCCGGTGGTGCGAGTCTTCGGAG
CGACCCCGGCAGGAGCTCCGGCAGCAGCTGGGGCACCGCCTGCAGCTGAACGACCTCCTCATCAAACCTGTGCAGCGGATCATGAAATAC
CAGCTGCTGCTCAAGGATTTTCTCAAGTATTACAATAGAGCTGGGATGGATACTGCAGACCTAGAGCAAGCTGTGGAGGTCATGTGCTTT
GTGCCCAAGCGCTGCAACGATATGATGACGCTGGGGAGATTGCGGGGATTTGAGGGCAAACTGACTGCTCAGGGGAAGCTCTTGGGCCAG
GACACTTTCTGGGTCACCGAGCCTGAGGCTGGAGGGCTGCTGTCTTCCCGAGGTCGAGAGAGGCGCGTCTTCCTCTTTGAGCAAATCATC
ATCTTCAGTGAAGCCCTGGGAGGAGGAGTGAGAGGTGGAACACAGCCTGGATATGTATACAAGAACAGCATTAAGGTGAGCTGCCTGGGA
CTGGAGGGGAACCTCCAAGGTGACCCTTGCCGCTTTGCACTGACCTCCAGAGGGCCAGAGGGTGGGATCCAGCGCTATGTCCTGCAGGCT
GCAGACCCTGCTATCAGTCAGGCCTGGATCAAGCATGTGGCTCAGATCTTGGAGAGCCAACGGGACTTCCTCAACGCATTGCAGTCACCC
ATTGAGTACCAGAGACGGGAGAGCCAGACCAACAGCCTGGGGCGGCCAAGAGGGCCTGGAGTGGGGAGCCCTGGAAGAATTCAGCTTGGA
GATCAGGCCCAGGGCAGCACACACACACCCATCAATGGCTCTCTCCCCTCTCTGCTGCTGTCACCCAAAGGGGAGGTGGCCAGAGCCCTC
TTGCCACTGGATAAACAGGCCCTTGGTGACATCCCCCAGGCTCCCCATGACTCTCCTCCAGTCTCTCCAACTCCAAAAACCCCTCCCTGC
CAAGCCAGACTTGCCAAGCTGGATGAAGATGAGCTGTAACTGGTGAAAACCATGGGGGTGGTGCTGACTCAGCCGCCTATTCCCCAAGGA
GCTTCAGGGCAGTCCTTCTGGCACTGCTCCAGAATTCCTCCTTCTTGGTGTGTCTGGAGGGTGGGCAAGGCTGGGAGGGATATCAACTTG
GAGGAGAACACCTAGACCCAAGGACTTTTTTCTGCCCAAGGAACACAGTTTCCTTCAGCTCCCATCCCTATGCATGCATCATGGTCCCCC
CAAAAGGAGGATATGTGGGTGGGTGGGAGGGCTGGGGCAGGGGCCAGATAGAAATTATTGGTTTTGTTTTTTAATTTTGTTTTTCCTGTT

>73582_73582_1_REV3L-ARHGEF25_REV3L_chr6_111803953_ENST00000368802_ARHGEF25_chr12_58008472_ENST00000286494_length(amino acids)=347AA_BP=38
MQTTTWPARCRGWIPANPPSPRPLSRRCRWCESSERPRQELRQQLGHRLQLNDLLIKPVQRIMKYQLLLKDFLKYYNRAGMDTADLEQAV
EVMCFVPKRCNDMMTLGRLRGFEGKLTAQGKLLGQDTFWVTEPEAGGLLSSRGRERRVFLFEQIIIFSEALGGGVRGGTQPGYVYKNSIK
VSCLGLEGNLQGDPCRFALTSRGPEGGIQRYVLQAADPAISQAWIKHVAQILESQRDFLNALQSPIEYQRRESQTNSLGRPRGPGVGSPG

--------------------------------------------------------------
>73582_73582_2_REV3L-ARHGEF25_REV3L_chr6_111803953_ENST00000368802_ARHGEF25_chr12_58008472_ENST00000333972_length(transcript)=1738nt_BP=462nt
CATCATCATGGCAACAAGAGCTGCAGCCTGGGACCGAGGAGCCCGTGTGATTCCCGGCGGTGGCGGCAGTGGCGGCAGCACCAGCACCGA
CGAAAGCTCGAGGGCTTCTCTCCTGCGGCCCCTTGCCGGGTGCTCCTGAGGAGGCGGCGGCAGCAGCGCCTACACCGCCCCGCCCGCCGC
TCCTCGAGGTGCCTCTGTGTGAGGGGAGGGGGCCGTGCCGAGAAGGGGAGGGGGCGCCGCCGCCGCTGCGGAGGGAGCCGCCGCCGCTGC
TGCTGCCGCTGCCGGGTCGCCAGTGAAGGGAGGCAGTGGCGGCGGCGGCGAACATGTTTTCAGTAAGGATAGTGACTGCAGACTACTACA
TGGCCAGCCCGCTGCAGGGGCTGGATACCTGCCAATCCCCCCTCACCCAGGCCCCTGTCAAGAAGGTGCCGGTGGTGCGAGTCTTCGGAG
CGACCCCGGCAGGAGCTCCGGCAGCAGCTGGGGCACCGCCTGCAGCTGAACGACCTCCTCATCAAACCTGTGCAGCGGATCATGAAATAC
CAGCTGCTGCTCAAGGATTTTCTCAAGTATTACAATAGAGCTGGGATGGATACTGCAGACCTAGAGCAAGCTGTGGAGGTCATGTGCTTT
GTGCCCAAGCGCTGCAACGATATGATGACGCTGGGGAGATTGCGGGGATTTGAGGGCAAACTGACTGCTCAGGGGAAGCTCTTGGGCCAG
GACACTTTCTGGGTCACCGAGCCTGAGGCTGGAGGGCTGCTGTCTTCCCGAGGTCGAGAGAGGCGCGTCTTCCTCTTTGAGCAAATCATC
ATCTTCAGTGAAGCCCTGGGAGGAGGAGTGAGAGGTGGAACACAGCCTGGATATGTATACAAGAACAGCATTAAGGTGAGCTGCCTGGGA
CTGGAGGGGAACCTCCAAGGTGACCCTTGCCGCTTTGCACTGACCTCCAGAGGGCCAGAGGGTGGGATCCAGCGCTATGTCCTGCAGGCT
GCAGACCCTGCTATCAGTCAGGCCTGGATCAAGCATGTGGCTCAGATCTTGGAGAGCCAACGGGACTTCCTCAACGCATTGCAGTCACCC
ATTGAGTACCAGAGACGGGAGAGCCAGACCAACAGCCTGGGGCGGCCAAGAGGGCCTGGAGTGGGGAGCCCTGGAAGAATTCAGCTTGGA
GATCAGGCCCAGGGCAGCACACACACACCCATCAATGGCTCTCTCCCCTCTCTGCTGCTGTCACCCAAAGGGGAGGTGGCCAGAGCCCTC
TTGCCACTGGATAAACAGGCCCTTGGTGACATCCCCCAGGCTCCCCATGACTCTCCTCCAGTCTCTCCAACTCCAAAAACCCCTCCCTGC
CAAGCCAGACTTGCCAAGCTGGATGAAGATGAGCTGTAACTGGTGAAAACCATGGGGGTGGTGCTGACTCAGCCGCCTATTCCCCAAGGA
GCTTCAGGGCAGTCCTTCTGGCACTGCTCCAGAATTCCTCCTTCTTGGTGTGTCTGGAGGGTGGGCAAGGCTGGGAGGGATATCAACTTG
GAGGAGAACACCTAGACCCAAGGACTTTTTTCTGCCCAAGGAACACAGTTTCCTTCAGCTCCCATCCCTATGCATGCATCATGGTCCCCC
CAAAAGGAGGATATGTGGGTGGGTGGGAGGGCTGGGGCAGGGGCCAGATAGAAATTATTGGTTTTGTTTTTTAATTTTGTTTTTCCTGTT

>73582_73582_2_REV3L-ARHGEF25_REV3L_chr6_111803953_ENST00000368802_ARHGEF25_chr12_58008472_ENST00000333972_length(amino acids)=347AA_BP=38
MQTTTWPARCRGWIPANPPSPRPLSRRCRWCESSERPRQELRQQLGHRLQLNDLLIKPVQRIMKYQLLLKDFLKYYNRAGMDTADLEQAV
EVMCFVPKRCNDMMTLGRLRGFEGKLTAQGKLLGQDTFWVTEPEAGGLLSSRGRERRVFLFEQIIIFSEALGGGVRGGTQPGYVYKNSIK
VSCLGLEGNLQGDPCRFALTSRGPEGGIQRYVLQAADPAISQAWIKHVAQILESQRDFLNALQSPIEYQRRESQTNSLGRPRGPGVGSPG

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Fusion Gene PPI Analysis for REV3L-ARHGEF25


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 REV3L-ARHGEF25


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 REV3L-ARHGEF25


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