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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:RIF1-BICD1 (FusionGDB2 ID:HG55183TG636)

Fusion Gene Summary for RIF1-BICD1

check button Fusion gene summary
Fusion gene informationFusion gene name: RIF1-BICD1
Fusion gene ID: hg55183tg636
HgeneTgene
Gene symbol

RIF1

BICD1

Gene ID

55183

636

Gene namereplication timing regulatory factor 1BICD cargo adaptor 1
Synonyms-BICD|bic-D 1
Cytomap('RIF1')('BICD1')

2q23.3

12p11.21

Type of geneprotein-codingprotein-coding
Descriptiontelomere-associated protein RIF1RAP1 interacting factor homolograp1-interacting factor 1 homologprotein bicaudal D homolog 1bicaudal D homolog 1cytoskeleton-like bicaudal D protein homolog 1
Modification date2020032220200313
UniProtAcc.

Q96G01

Ensembl transtripts involved in fusion geneENST00000243326, ENST00000428287, 
ENST00000430328, ENST00000433166, 
ENST00000444746, ENST00000453091, 
ENST00000457745, 
Fusion gene scores* DoF score6 X 6 X 4=14413 X 12 X 6=936
# samples 614
** MAII scorelog2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/936*10)=-2.74108170263844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RIF1 [Title/Abstract] AND BICD1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRIF1(152315048)-BICD1(32400457), # 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
HgeneRIF1

GO:0006974

cellular response to DNA damage stimulus

28241136

HgeneRIF1

GO:0043247

telomere maintenance in response to DNA damage

15583028

HgeneRIF1

GO:2000042

negative regulation of double-strand break repair via homologous recombination

23333306

HgeneRIF1

GO:2001034

positive regulation of double-strand break repair via nonhomologous end joining

28241136

TgeneBICD1

GO:0033365

protein localization to organelle

12447383|20089649



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
ChiTaRS5.0N/AEI792395RIF1chr2

152315048

+BICD1chr12

32400457

-


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Fusion Gene ORF analysis for RIF1-BICD1

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-intronENST00000243326ENST00000281474RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000243326ENST00000548411RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000243326ENST00000550207RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000243326ENST00000551086RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000243326ENST00000551848RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000428287ENST00000281474RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000428287ENST00000548411RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000428287ENST00000550207RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000428287ENST00000551086RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000428287ENST00000551848RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000430328ENST00000281474RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000430328ENST00000548411RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000430328ENST00000550207RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000430328ENST00000551086RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000430328ENST00000551848RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000433166ENST00000281474RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000433166ENST00000548411RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000433166ENST00000550207RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000433166ENST00000551086RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000433166ENST00000551848RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000444746ENST00000281474RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000444746ENST00000548411RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000444746ENST00000550207RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000444746ENST00000551086RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000444746ENST00000551848RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000453091ENST00000281474RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000453091ENST00000548411RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000453091ENST00000550207RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000453091ENST00000551086RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000453091ENST00000551848RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000457745ENST00000281474RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000457745ENST00000548411RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000457745ENST00000550207RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000457745ENST00000551086RIF1chr2

152315048

+BICD1chr12

32400457

-
intron-intronENST00000457745ENST00000551848RIF1chr2

152315048

+BICD1chr12

32400457

-

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 RIF1-BICD1


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)


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Fusion Protein Features for RIF1-BICD1


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/:152315048/:32400457)
- 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
.BICD1

Q96G01

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: Regulates coat complex coatomer protein I (COPI)-independent Golgi-endoplasmic reticulum transport by recruiting the dynein-dynactin motor complex.

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 RIF1-BICD1


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 RIF1-BICD1


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 RIF1-BICD1


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 RIF1-BICD1


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