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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:RAB6B-RBP1 (FusionGDB2 ID:71468)

Fusion Gene Summary for RAB6B-RBP1

check button Fusion gene summary
Fusion gene informationFusion gene name: RAB6B-RBP1
Fusion gene ID: 71468
HgeneTgene
Gene symbol

RAB6B

RBP1

Gene ID

51560

5947

Gene nameRAB6B, member RAS oncogene familyretinol binding protein 1
Synonyms-CRABP-I|CRBP|CRBP1|CRBPI|RBPC
Cytomap

3q22.1

3q23

Type of geneprotein-codingprotein-coding
Descriptionras-related protein Rab-6Bsmall GTP-binding proteinsmall GTPase RAB6Bretinol-binding protein 1CRBP-Icellular retinol binding protein 1cellular retinol-binding protein Iretinol-binding protein 1, cellular
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000285208, ENST00000486858, 
ENST00000543906, ENST00000469959, 
ENST00000483943, ENST00000492918, 
ENST00000232219, 
Fusion gene scores* DoF score4 X 3 X 3=364 X 3 X 3=36
# samples 46
** MAII scorelog2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(6/36*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: RAB6B [Title/Abstract] AND RBP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRAB6B(133583428)-RBP1(139237364), # samples:1
Anticipated loss of major functional domain due to fusion event.RAB6B-RBP1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
RAB6B-RBP1 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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 RAB6B (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 RBP1 (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
ChimerDB4GBMTCGA-28-5213-01ARAB6Bchr3

133583428

-RBP1chr3

139237364

-


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Fusion Gene ORF analysis for RAB6B-RBP1

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-intronENST00000285208ENST00000483943RAB6Bchr3

133583428

-RBP1chr3

139237364

-
5CDS-intronENST00000285208ENST00000492918RAB6Bchr3

133583428

-RBP1chr3

139237364

-
5CDS-intronENST00000486858ENST00000483943RAB6Bchr3

133583428

-RBP1chr3

139237364

-
5CDS-intronENST00000486858ENST00000492918RAB6Bchr3

133583428

-RBP1chr3

139237364

-
5CDS-intronENST00000543906ENST00000483943RAB6Bchr3

133583428

-RBP1chr3

139237364

-
5CDS-intronENST00000543906ENST00000492918RAB6Bchr3

133583428

-RBP1chr3

139237364

-
Frame-shiftENST00000486858ENST00000232219RAB6Bchr3

133583428

-RBP1chr3

139237364

-
In-frameENST00000285208ENST00000232219RAB6Bchr3

133583428

-RBP1chr3

139237364

-
In-frameENST00000543906ENST00000232219RAB6Bchr3

133583428

-RBP1chr3

139237364

-
intron-3CDSENST00000469959ENST00000232219RAB6Bchr3

133583428

-RBP1chr3

139237364

-
intron-intronENST00000469959ENST00000483943RAB6Bchr3

133583428

-RBP1chr3

139237364

-
intron-intronENST00000469959ENST00000492918RAB6Bchr3

133583428

-RBP1chr3

139237364

-

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)
ENST00000285208RAB6Bchr3133583428-ENST00000232219RBP1chr3139237364-82847923634203
ENST00000543906RAB6Bchr3133583428-ENST00000232219RBP1chr3139237364-6072584280143

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
ENST00000285208ENST00000232219RAB6Bchr3133583428-RBP1chr3139237364-0.079062250.9209377
ENST00000543906ENST00000232219RAB6Bchr3133583428-RBP1chr3139237364-0.0535932740.94640666

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Fusion Genomic Features for RAB6B-RBP1


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.
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.

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Fusion Protein Features for RAB6B-RBP1


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/chr3:133583428/chr3:139237364)
- 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
..
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: 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
HgeneRAB6Bchr3:133583428chr3:139237364ENST00000285208-2820_2743209.0Nucleotide bindingNote=GTP
HgeneRAB6Bchr3:133583428chr3:139237364ENST00000543906-2920_27431632.3333333333333Nucleotide bindingNote=GTP

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRAB6Bchr3:133583428chr3:139237364ENST00000285208-2842_5043209.0MotifEffector region
HgeneRAB6Bchr3:133583428chr3:139237364ENST00000543906-2942_50431632.3333333333333MotifEffector region
HgeneRAB6Bchr3:133583428chr3:139237364ENST00000285208-28126_12943209.0Nucleotide bindingNote=GTP
HgeneRAB6Bchr3:133583428chr3:139237364ENST00000285208-2868_7243209.0Nucleotide bindingNote=GTP
HgeneRAB6Bchr3:133583428chr3:139237364ENST00000543906-29126_129431632.3333333333333Nucleotide bindingNote=GTP
HgeneRAB6Bchr3:133583428chr3:139237364ENST00000543906-2968_72431632.3333333333333Nucleotide bindingNote=GTP


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Fusion Gene Sequence for RAB6B-RBP1


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.
>71468_71468_1_RAB6B-RBP1_RAB6B_chr3_133583428_ENST00000285208_RBP1_chr3_139237364_ENST00000232219_length(transcript)=828nt_BP=479nt
CTCCTCCGCCCCGCGCGCCGTCCCTGCGCCCCGCTCCGCCCGCGCCTCTCTCCCAGCGCCGCGCCTCGGGCGTAAAGAGCGCGCCCCTCG
CACCGCAGCCAGTGCCGACCGCAGCAGCCCAGCCCCAGCCTTCCTCCGCCTCCGCCTCTCTCTCCTCCTCCTCCTCCGCCGCCGGACACG
CAGCCGCAGGCCGGGACCGGGACGCAGCTGGGGAGTCAGGGACGCGCGCAGCCAGCCCTTCCCCCTCCGGCTCCCGCACCGCCGGCCGCC
TCCCCTCGCCCTCCTACTCTCCCCTCCCTGCTCCTTCGCTTTTTCCTCCTCCTCCTCTCCCGGCCCCGGCTGCCAGCACCATGTCCGCAG
GGGGAGATTTTGGGAATCCACTGAGAAAATTCAAGTTGGTGTTCTTGGGGGAGCAGAGCGTCGGGAAGACGTCTCTGATTACGAGGTTCA
TGTACGACAGCTTCGACAACACATACCAGACAACAGTGAGCTGGGACGGAGACAAGCTCCAGTGTGTGCAGAAGGGTGAGAAGGAGGGGC
GTGGCTGGACCCAGTGGATCGAGGGTGATGAGCTGCACCTGGAGATGAGAGTGGAAGGTGTGGTCTGCAAGCAAGTATTCAAGAAGGTGC
AGTGAGGCCCAGGCAGACAACCTTGTCCCAAGGAATCAGCAGGATGTGTGGGCCAGGATCCCCCTCTTTGCACAGCATGAGGCAAAAATG
TCCAGCCACCCCCAGGCATCTGTTAGCAGAGTCTGTCTCTTGGCTTTGTCACTTTTCCTTTTCTTAAAACAAAGCCATGCCAATAAAGTG

>71468_71468_1_RAB6B-RBP1_RAB6B_chr3_133583428_ENST00000285208_RBP1_chr3_139237364_ENST00000232219_length(amino acids)=203AA_BP=151
MRPAPPAPLSQRRASGVKSAPLAPQPVPTAAAQPQPSSASASLSSSSSAAGHAAAGRDRDAAGESGTRAASPSPSGSRTAGRLPSPSYSP
LPAPSLFPPPPLPAPAASTMSAGGDFGNPLRKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQTTVSWDGDKLQCVQKGEKEGRGWTQWIE

--------------------------------------------------------------
>71468_71468_2_RAB6B-RBP1_RAB6B_chr3_133583428_ENST00000543906_RBP1_chr3_139237364_ENST00000232219_length(transcript)=607nt_BP=258nt
ACGCGCGCAGCCAGCCCTTCCCCCTCCGGCTCCCGCACCGCCGGCCGCCTCCCCTCGCCCTCCTACTCTCCCCTCCCTGCTCCTTCGCTT
TTTCCTCCTCCTCCTCTCCCGGCCCCGGCTGCCAGCACCATGTCCGCAGGGGGAGATTTTGGGAATCCACTGAGAAAATTCAAGTTGGTG
TTCTTGGGGGAGCAGAGCGTCGGGAAGACGTCTCTGATTACGAGGTTCATGTACGACAGCTTCGACAACACATACCAGACAACAGTGAGC
TGGGACGGAGACAAGCTCCAGTGTGTGCAGAAGGGTGAGAAGGAGGGGCGTGGCTGGACCCAGTGGATCGAGGGTGATGAGCTGCACCTG
GAGATGAGAGTGGAAGGTGTGGTCTGCAAGCAAGTATTCAAGAAGGTGCAGTGAGGCCCAGGCAGACAACCTTGTCCCAAGGAATCAGCA
GGATGTGTGGGCCAGGATCCCCCTCTTTGCACAGCATGAGGCAAAAATGTCCAGCCACCCCCAGGCATCTGTTAGCAGAGTCTGTCTCTT

>71468_71468_2_RAB6B-RBP1_RAB6B_chr3_133583428_ENST00000543906_RBP1_chr3_139237364_ENST00000232219_length(amino acids)=143AA_BP=1
MSAWASLHLLEYLLADHTFHSHLQVQLITLDPLGPATPLLLTLLHTLELVSVPAHCCLVCVVEAVVHEPRNQRRLPDALLPQEHQLEFSQ

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

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Fusion Gene PPI Analysis for RAB6B-RBP1


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 RAB6B-RBP1


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 RAB6B-RBP1


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