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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:RNF38-PAX5 (FusionGDB2 ID:75080)

Fusion Gene Summary for RNF38-PAX5

check button Fusion gene summary
Fusion gene informationFusion gene name: RNF38-PAX5
Fusion gene ID: 75080
HgeneTgene
Gene symbol

RNF38

PAX5

Gene ID

152006

5079

Gene namering finger protein 38paired box 5
Synonyms-ALL3|BSAP
Cytomap

9p13.2

9p13.2

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase RNF38RING-type E3 ubiquitin transferase RNF38paired box protein Pax-5B-cell lineage specific activatorpaired box homeotic gene 5paired domain gene 5transcription factor PAX 5
Modification date2020031320200313
UniProtAcc.

Q02548

Ensembl transtripts involved in fusion geneENST00000259605, ENST00000350199, 
ENST00000353739, ENST00000357058, 
ENST00000377877, ENST00000377885, 
ENST00000491349, 
ENST00000358127, 
ENST00000377847, ENST00000377852, 
ENST00000377853, ENST00000414447, 
ENST00000446742, ENST00000520154, 
ENST00000520281, ENST00000522003, 
ENST00000523145, ENST00000523241, 
Fusion gene scores* DoF score12 X 6 X 9=6488 X 7 X 6=336
# samples 139
** MAII scorelog2(13/648*10)=-2.31748218985617
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/336*10)=-1.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RNF38 [Title/Abstract] AND PAX5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRNF38(36424610)-PAX5(36923481), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneRNF38

GO:0016567

protein ubiquitination

23973461


check buttonFusion gene breakpoints across RNF38 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across PAX5 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4BLCATCGA-GV-A3QI-01ARNF38chr9

36424610

-PAX5chr9

36923481

-


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Fusion Gene ORF analysis for RNF38-PAX5

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-3CDSENST00000259605ENST00000358127RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-3CDSENST00000350199ENST00000358127RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-3CDSENST00000353739ENST00000358127RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-3CDSENST00000357058ENST00000358127RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-3CDSENST00000377877ENST00000358127RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-3CDSENST00000377885ENST00000358127RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-3CDSENST00000491349ENST00000358127RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000259605ENST00000377847RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000259605ENST00000377852RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000259605ENST00000377853RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000259605ENST00000414447RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000259605ENST00000446742RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000259605ENST00000520154RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000259605ENST00000520281RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000259605ENST00000522003RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000259605ENST00000523145RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000259605ENST00000523241RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000350199ENST00000377847RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000350199ENST00000377852RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000350199ENST00000377853RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000350199ENST00000414447RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000350199ENST00000446742RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000350199ENST00000520154RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000350199ENST00000520281RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000350199ENST00000522003RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000350199ENST00000523145RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000350199ENST00000523241RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000353739ENST00000377847RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000353739ENST00000377852RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000353739ENST00000377853RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000353739ENST00000414447RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000353739ENST00000446742RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000353739ENST00000520154RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000353739ENST00000520281RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000353739ENST00000522003RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000353739ENST00000523145RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000353739ENST00000523241RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000357058ENST00000377847RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000357058ENST00000377852RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000357058ENST00000377853RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000357058ENST00000414447RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000357058ENST00000446742RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000357058ENST00000520154RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000357058ENST00000520281RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000357058ENST00000522003RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000357058ENST00000523145RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000357058ENST00000523241RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377877ENST00000377847RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377877ENST00000377852RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377877ENST00000377853RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377877ENST00000414447RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377877ENST00000446742RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377877ENST00000520154RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377877ENST00000520281RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377877ENST00000522003RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377877ENST00000523145RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377877ENST00000523241RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377885ENST00000377847RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377885ENST00000377852RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377885ENST00000377853RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377885ENST00000414447RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377885ENST00000446742RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377885ENST00000520154RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377885ENST00000520281RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377885ENST00000522003RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377885ENST00000523145RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000377885ENST00000523241RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000491349ENST00000377847RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000491349ENST00000377852RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000491349ENST00000377853RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000491349ENST00000414447RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000491349ENST00000446742RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000491349ENST00000520154RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000491349ENST00000520281RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000491349ENST00000522003RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000491349ENST00000523145RNF38chr9

36424610

-PAX5chr9

36923481

-
intron-intronENST00000491349ENST00000523241RNF38chr9

36424610

-PAX5chr9

36923481

-

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 RNF38-PAX5


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)

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.

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.

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Fusion Protein Features for RNF38-PAX5


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/:36424610/:36923481)
- 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
.PAX5

Q02548

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: Transcription factor that plays an essential role in commitment of lymphoid progenitors to the B-lymphocyte lineage (PubMed:10811620, PubMed:27181361). Fulfills a dual role by repressing B-lineage inappropriate genes and simultaneously activating B-lineage-specific genes (PubMed:10811620, PubMed:27181361). In turn, regulates cell adhesion and migration, induces V(H)-to-D(H)J(H) recombination, facilitates pre-B-cell receptor signaling and promotes development to the mature B-cell stage (PubMed:32612238). Repression of the cohesin-release factor WAPL causes global changes of the chromosomal architecture in pro-B cells to facilitate the generation of a diverse antibody repertoire (PubMed:32612238). {ECO:0000269|PubMed:10811620, ECO:0000269|PubMed:27181361, ECO:0000269|PubMed:32612238}.; FUNCTION: (Microbial infection) Plays an essential role in the maintenance of Epstein-Barr virus genome copy number within the host cell by promoting EBNA1/oriP-dependent binding and transcription (PubMed:31941781). Participates also in the inhibition of lytic EBV reactivation by modulating viral BZLF1 activity (PubMed:23678172). {ECO:0000269|PubMed:23678172, ECO:0000269|PubMed:31941781}.

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 RNF38-PAX5


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 RNF38-PAX5


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 RNF38-PAX5


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 RNF38-PAX5


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