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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:DENND1B-RGL1 (FusionGDB2 ID:22223)

Fusion Gene Summary for DENND1B-RGL1

check button Fusion gene summary
Fusion gene informationFusion gene name: DENND1B-RGL1
Fusion gene ID: 22223
HgeneTgene
Gene symbol

DENND1B

RGL1

Gene ID

163486

64333

Gene nameDENN domain containing 1BRho GTPase activating protein 9
SynonymsC1ORF18|C1orf218|FAM31B10C|RGL1
Cytomap

1q31.3

12q13.3

Type of geneprotein-codingprotein-coding
DescriptionDENN domain-containing protein 1BDENN/MADD domain containing 1Bconnecdenn 2family with sequence similarity 31, member Brho GTPase-activating protein 9rho-type GTPase-activating protein 9
Modification date2020032020200320
UniProtAcc

Q6P3S1

.
Ensembl transtripts involved in fusion geneENST00000367396, ENST00000235453, 
ENST00000477581, ENST00000400967, 
ENST00000536277, ENST00000304685, 
ENST00000360851, ENST00000539189, 
Fusion gene scores* DoF score13 X 7 X 7=6379 X 9 X 5=405
# samples 1610
** MAII scorelog2(16/637*10)=-1.99322146736894
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/405*10)=-2.01792190799726
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: DENND1B [Title/Abstract] AND RGL1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointDENND1B(197741998)-RGL1(183666538), # samples:2
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

check buttonFusion gene breakpoints across DENND1B (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 RGL1 (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
ChimerDB4LUSCTCGA-18-3407-01ADENND1Bchr1

197741998

-RGL1chr1

183666538

+
ChimerDB4LUSCTCGA-18-3407DENND1Bchr1

197741998

-RGL1chr1

183666538

+


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Fusion Gene ORF analysis for DENND1B-RGL1

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-5UTRENST00000367396ENST00000536277DENND1Bchr1

197741998

-RGL1chr1

183666538

+
5CDS-intronENST00000367396ENST00000304685DENND1Bchr1

197741998

-RGL1chr1

183666538

+
5CDS-intronENST00000367396ENST00000360851DENND1Bchr1

197741998

-RGL1chr1

183666538

+
5CDS-intronENST00000367396ENST00000539189DENND1Bchr1

197741998

-RGL1chr1

183666538

+
5UTR-5UTRENST00000235453ENST00000536277DENND1Bchr1

197741998

-RGL1chr1

183666538

+
5UTR-5UTRENST00000477581ENST00000536277DENND1Bchr1

197741998

-RGL1chr1

183666538

+
5UTR-intronENST00000235453ENST00000304685DENND1Bchr1

197741998

-RGL1chr1

183666538

+
5UTR-intronENST00000235453ENST00000360851DENND1Bchr1

197741998

-RGL1chr1

183666538

+
5UTR-intronENST00000235453ENST00000539189DENND1Bchr1

197741998

-RGL1chr1

183666538

+
5UTR-intronENST00000477581ENST00000304685DENND1Bchr1

197741998

-RGL1chr1

183666538

+
5UTR-intronENST00000477581ENST00000360851DENND1Bchr1

197741998

-RGL1chr1

183666538

+
5UTR-intronENST00000477581ENST00000539189DENND1Bchr1

197741998

-RGL1chr1

183666538

+
intron-5UTRENST00000400967ENST00000536277DENND1Bchr1

197741998

-RGL1chr1

183666538

+
intron-intronENST00000400967ENST00000304685DENND1Bchr1

197741998

-RGL1chr1

183666538

+
intron-intronENST00000400967ENST00000360851DENND1Bchr1

197741998

-RGL1chr1

183666538

+
intron-intronENST00000400967ENST00000539189DENND1Bchr1

197741998

-RGL1chr1

183666538

+

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 DENND1B-RGL1


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)
DENND1Bchr1197741997-RGL1chr1183666537+1.36E-050.9999864
DENND1Bchr1197741997-RGL1chr1183666537+1.36E-050.9999864
DENND1Bchr1197741997-RGL1chr1183666537+1.36E-050.9999864
DENND1Bchr1197741997-RGL1chr1183666537+1.36E-050.9999864

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.
genomic feature of top 1%

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Fusion Protein Features for DENND1B-RGL1


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/:197741998/:183666538)
- 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
DENND1B

Q6P3S1

.
FUNCTION: Guanine nucleotide exchange factor (GEF) for RAB35 that acts as a regulator of T-cell receptor (TCR) internalization in TH2 cells (PubMed:20154091, PubMed:20937701, PubMed:24520163, PubMed:26774822). Acts by promoting the exchange of GDP to GTP, converting inactive GDP-bound RAB35 into its active GTP-bound form (PubMed:20154091, PubMed:20937701). Plays a role in clathrin-mediated endocytosis (PubMed:20154091). Controls cytokine production in TH2 lymphocytes by controlling the rate of TCR internalization and routing to endosomes: acts by mediating clathrin-mediated endocytosis of TCR via its interaction with the adapter protein complex 2 (AP-2) and GEF activity (PubMed:26774822). Dysregulation leads to impaired TCR down-modulation and recycling, affecting cytokine production in TH2 cells (PubMed:26774822). {ECO:0000269|PubMed:20154091, ECO:0000269|PubMed:20937701, ECO:0000269|PubMed:24520163, ECO:0000269|PubMed:26774822}.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}.

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 DENND1B-RGL1


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 DENND1B-RGL1


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 DENND1B-RGL1


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 DENND1B-RGL1


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