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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:RCBTB2-RB1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RCBTB2-RB1
FusionPDB ID: 73139
FusionGDB2.0 ID: 73139
HgeneTgene
Gene symbol

RCBTB2

RB1

Gene ID

1102

5925

Gene nameRCC1 and BTB domain containing protein 2RB transcriptional corepressor 1
SynonymsCHC1L|RLGOSRC|PPP1R130|RB|p105-Rb|p110-RB1|pRb|pp110
Cytomap

13q14.2

13q14.2

Type of geneprotein-codingprotein-coding
DescriptionRCC1 and BTB domain-containing protein 2RCC1-like G exchanging factor RLGregulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2retinoblastoma-associated proteinGOS563 exon 17 substitution mutation causes premature stopexon 17 tumor GOS561 substitution mutation causes premature stopprepro-retinoblastoma-associated proteinprotein phosphatase 1, regulatory subunit 130retinoblas
Modification date2020031320200329
UniProtAcc.

RB1CC1

Ensembl transtripts involved in fusion geneENST idsENST00000344532, ENST00000430805, 
ENST00000544492, ENST00000481144, 
ENST00000544904, 
ENST00000484879, 
ENST00000267163, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score5 X 6 X 5=15013 X 16 X 11=2288
# samples 527
** MAII scorelog2(5/150*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(27/2288*10)=-3.08305573972756
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: RCBTB2 [Title/Abstract] AND RB1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RCBTB2(49070255)-RB1(48939061), # samples:1
RCBTB2(49070327)-RB1(48939030), # samples:1
Anticipated loss of major functional domain due to fusion event.RCBTB2-RB1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
RCBTB2-RB1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
RCBTB2-RB1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
RCBTB2-RB1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
RCBTB2-RB1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
RCBTB2-RB1 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
RCBTB2-RB1 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
RCBTB2-RB1 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
TgeneRB1

GO:0043550

regulation of lipid kinase activity

16286473

TgeneRB1

GO:0045892

negative regulation of transcription, DNA-templated

10783144|12065415|19223331

TgeneRB1

GO:2000679

positive regulation of transcription regulatory region DNA binding

25100735


check buttonFusion gene breakpoints across RCBTB2 (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 RB1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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-D8-A1XJ-01ARCBTB2chr13

49070255

-RB1chr13

48939061

+
ChimerDB4BRCATCGA-D8-A1XJ-01ARCBTB2chr13

49070327

-RB1chr13

48939030

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000544492RCBTB2chr1349070327-ENST00000267163RB1chr1348939030+500511644713089872

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
ENST00000544492ENST00000267163RCBTB2chr1349070327-RB1chr1348939030+0.0003647380.9996352

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>73139_73139_1_RCBTB2-RB1_RCBTB2_chr13_49070327_ENST00000544492_RB1_chr13_48939030_ENST00000267163_length(amino acids)=872AA_BP=230
MSGVTTETGSLDSATVATSQPLAEWQLCKASVSRGIIEIAACHSTHTSAAKTQGGHVYMWGQCRGQSVILPHLTHFSCTDDVFACFATPA
VTWRLLSVEPDDHLTVAESLKREFDNPDTADLKFLVDGKYIYAHKVLLKIRCEHFRSSLEDNEDDIVEMSEFSYPVYRAFLEYLYTDSIS
LSPEEAVGLLDLATFYRENRLKKLCQQTIKQGICEENAIALLSAAVKYDAQVKNVYFKNFIPFMNSLGLVTSNGLPEVENLSKRYEEIYL
KNKDLDARLFLDHDKTLQTDSIDSFETQRTPRKSNLDEEVNVIPPHTPVRTVMNTIQQLMMILNSASDQPSENLISYFNNCTVNPKESIL
KRVKDIGYIFKEKFAKAVGQGCVEIGSQRYKLGVRLYYRVMESMLKSEEERLSIQNFSKLLNDNIFHMSLLACALEVVMATYSRSTSQNL
DSGTDLSFPWILNVLNLKAFDFYKVIESFIKAEGNLTREMIKHLERCEHRIMESLAWLSDSPLFDLIKQSKDREGPTDHLESACPLNLPL
QNNHTAADMYLSPVRSPKKKGSTTRVNSTANAETQATSAFQTQKPLKSTSLSLFYKKVYRLAYLRLNTLCERLLSEHPELEHIIWTLFQH
TLQNEYELMRDRHLDQIMMCSMYGICKVKNIDLKFKIIVTAYKDLPHAVQETFKRVLIKEEEYDSIIVFYNSVFMQRLKTNILQYASTRP
PTLSPIPHIPRSPYKFPSSPLRIPGGNIYISPLKSPYKISEGLPTPTKMTPRSRILVSIGESFGTSEKFQKINQMVCNSDRVLKRSAEGS

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Fusion Protein Functional Features


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/chr13:49070255/chr13:48939061)
- 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
.RB1

RB1CC1

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.1594

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRCBTB2chr13:49070327chr13:48939030ENST00000344532-1415394_457505.0552.0DomainBTB
HgeneRCBTB2chr13:49070327chr13:48939030ENST00000344532-1415117_169505.0552.0RepeatRCC1 2
HgeneRCBTB2chr13:49070327chr13:48939030ENST00000344532-1415171_222505.0552.0RepeatRCC1 3
HgeneRCBTB2chr13:49070327chr13:48939030ENST00000344532-1415223_274505.0552.0RepeatRCC1 4
HgeneRCBTB2chr13:49070327chr13:48939030ENST00000344532-1415276_326505.0552.0RepeatRCC1 5
HgeneRCBTB2chr13:49070327chr13:48939030ENST00000344532-1415328_382505.0552.0RepeatRCC1 6
HgeneRCBTB2chr13:49070327chr13:48939030ENST00000344532-141564_115505.0552.0RepeatRCC1 1
TgeneRB1chr13:49070327chr13:48939030ENST00000267163727860_876287.0929.0MotifBipartite nuclear localization signal
TgeneRB1chr13:49070327chr13:48939030ENST00000267163727373_579287.0929.0RegionNote=Domain A
TgeneRB1chr13:49070327chr13:48939030ENST00000267163727373_771287.0929.0RegionNote=Pocket%3B binds T and E1A
TgeneRB1chr13:49070327chr13:48939030ENST00000267163727580_639287.0929.0RegionNote=Spacer
TgeneRB1chr13:49070327chr13:48939030ENST00000267163727640_771287.0929.0RegionNote=Domain B

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneRB1chr13:49070327chr13:48939030ENST0000026716372710_18287.0929.0Compositional biasNote=Poly-Ala
TgeneRB1chr13:49070327chr13:48939030ENST0000026716372720_29287.0929.0Compositional biasNote=Poly-Pro


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
RCBTB2
RB1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to RCBTB2-RB1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to RCBTB2-RB1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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