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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:RBM3-ILK (FusionGDB2 ID:72393)

Fusion Gene Summary for RBM3-ILK

check button Fusion gene summary
Fusion gene informationFusion gene name: RBM3-ILK
Fusion gene ID: 72393
HgeneTgene
Gene symbol

RBM3

ILK

Gene ID

5935

3611

Gene nameRNA binding motif protein 3integrin linked kinase
SynonymsIS1-RNPL|RNPLHEL-S-28|ILK-1|ILK-2|P59|p59ILK
Cytomap

Xp11.23

11p15.4

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein 3RNA binding motif (RNP1, RRM) protein 3integrin-linked protein kinase59 kDa serine/threonine-protein kinaseepididymis secretory protein Li 28integrin-linked kinase-2
Modification date2020032720200320
UniProtAcc.

Q9H0C8

Ensembl transtripts involved in fusion geneENST00000466764, ENST00000376759, 
ENST00000430348, ENST00000376755, 
ENST00000354480, 		ENST00000299421, 
ENST00000537806, ENST00000420936, 
ENST00000528995, ENST00000396751, 
ENST00000526711, 
Fusion gene scores* DoF score9 X 10 X 2=1804 X 5 X 2=40
# samples 105
** MAII scorelog2(10/180*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/40*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: RBM3 [Title/Abstract] AND ILK [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRBM3(48434003)-ILK(6630374), # samples:1
Anticipated loss of major functional domain due to fusion event.RBM3-ILK seems lost the major protein functional domain in Tgene partner, which is a kinase due to the frame-shifted ORF.
RBM3-ILK seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
RBM3-ILK seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
TgeneILK

GO:0006468

protein phosphorylation

10871859

TgeneILK

GO:0007229

integrin-mediated signaling pathway

9366252


check buttonFusion gene breakpoints across RBM3 (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 ILK (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
ChiTaRS5.0N/AAA329557RBM3chrX

48434003

+ILKchr11

6630374

+


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Fusion Gene ORF analysis for RBM3-ILK

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
3UTR-3CDSENST00000466764ENST00000299421RBM3chrX

48434003

+ILKchr11

6630374

+
3UTR-3CDSENST00000466764ENST00000537806RBM3chrX

48434003

+ILKchr11

6630374

+
3UTR-3CDSENST00000466764ENST00000420936RBM3chrX

48434003

+ILKchr11

6630374

+
3UTR-intronENST00000466764ENST00000528995RBM3chrX

48434003

+ILKchr11

6630374

+
3UTR-intronENST00000466764ENST00000396751RBM3chrX

48434003

+ILKchr11

6630374

+
3UTR-3UTRENST00000466764ENST00000526711RBM3chrX

48434003

+ILKchr11

6630374

+
Frame-shiftENST00000376759ENST00000299421RBM3chrX

48434003

+ILKchr11

6630374

+
Frame-shiftENST00000376759ENST00000537806RBM3chrX

48434003

+ILKchr11

6630374

+
Frame-shiftENST00000376759ENST00000420936RBM3chrX

48434003

+ILKchr11

6630374

+
5CDS-intronENST00000376759ENST00000528995RBM3chrX

48434003

+ILKchr11

6630374

+
5CDS-intronENST00000376759ENST00000396751RBM3chrX

48434003

+ILKchr11

6630374

+
5CDS-3UTRENST00000376759ENST00000526711RBM3chrX

48434003

+ILKchr11

6630374

+
5UTR-3CDSENST00000430348ENST00000299421RBM3chrX

48434003

+ILKchr11

6630374

+
5UTR-3CDSENST00000430348ENST00000537806RBM3chrX

48434003

+ILKchr11

6630374

+
5UTR-3CDSENST00000430348ENST00000420936RBM3chrX

48434003

+ILKchr11

6630374

+
5UTR-intronENST00000430348ENST00000528995RBM3chrX

48434003

+ILKchr11

6630374

+
5UTR-intronENST00000430348ENST00000396751RBM3chrX

48434003

+ILKchr11

6630374

+
5UTR-3UTRENST00000430348ENST00000526711RBM3chrX

48434003

+ILKchr11

6630374

+
Frame-shiftENST00000376755ENST00000299421RBM3chrX

48434003

+ILKchr11

6630374

+
Frame-shiftENST00000376755ENST00000537806RBM3chrX

48434003

+ILKchr11

6630374

+
Frame-shiftENST00000376755ENST00000420936RBM3chrX

48434003

+ILKchr11

6630374

+
5CDS-intronENST00000376755ENST00000528995RBM3chrX

48434003

+ILKchr11

6630374

+
5CDS-intronENST00000376755ENST00000396751RBM3chrX

48434003

+ILKchr11

6630374

+
5CDS-3UTRENST00000376755ENST00000526711RBM3chrX

48434003

+ILKchr11

6630374

+
intron-3CDSENST00000354480ENST00000299421RBM3chrX

48434003

+ILKchr11

6630374

+
intron-3CDSENST00000354480ENST00000537806RBM3chrX

48434003

+ILKchr11

6630374

+
intron-3CDSENST00000354480ENST00000420936RBM3chrX

48434003

+ILKchr11

6630374

+
intron-intronENST00000354480ENST00000528995RBM3chrX

48434003

+ILKchr11

6630374

+
intron-intronENST00000354480ENST00000396751RBM3chrX

48434003

+ILKchr11

6630374

+
intron-3UTRENST00000354480ENST00000526711RBM3chrX

48434003

+ILKchr11

6630374

+

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 RBM3-ILK


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 RBM3-ILK


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.ILK

Q9H0C8

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.FUNCTION: Protein phosphatase that may play a role in regulation of cell cycle progression via dephosphorylation of its substrates whose appropriate phosphorylation states might be crucial for cell proliferation. Selectively associates with integrin linked kinase (ILK), to modulate cell adhesion and growth factor signaling. Inhibits the ILK-GSK3B signaling axis and may play an important role in inhibiting oncogenic transformation. {ECO:0000269|PubMed:14990992}.

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 RBM3-ILK


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 RBM3-ILK


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 RBM3-ILK


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 RBM3-ILK


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRBM3C0006142Malignant neoplasm of breast1CTD_human
HgeneRBM3C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneRBM3C0678222Breast Carcinoma1CTD_human
HgeneRBM3C1257931Mammary Neoplasms, Human1CTD_human
HgeneRBM3C1458155Mammary Neoplasms1CTD_human
HgeneRBM3C4704874Mammary Carcinoma, Human1CTD_human
TgeneILKC0009171Cocaine Abuse2CTD_human
TgeneILKC0236736Cocaine-Related Disorders2CTD_human
TgeneILKC0600427Cocaine Dependence2CTD_human
TgeneILKC0007787Transient Ischemic Attack1CTD_human
TgeneILKC0009376Colonic Polyps1CTD_human
TgeneILKC0014544Epilepsy1CTD_human
TgeneILKC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneILKC0039978Thoracic Diseases1CTD_human
TgeneILKC0086237Epilepsy, Cryptogenic1CTD_human
TgeneILKC0236018Aura1CTD_human
TgeneILKC0345967Malignant mesothelioma1CTD_human
TgeneILKC0472381Posterior Circulation Transient Ischemic Attack1CTD_human
TgeneILKC0751019Carotid Circulation Transient Ischemic Attack1CTD_human
TgeneILKC0751020Transient Ischemic Attack, Vertebrobasilar Circulation1CTD_human
TgeneILKC0751021Crescendo Transient Ischemic Attacks1CTD_human
TgeneILKC0751022Brain Stem Ischemia, Transient1CTD_human
TgeneILKC0751111Awakening Epilepsy1CTD_human
TgeneILKC0917805Transient Cerebral Ischemia1CTD_human
TgeneILKC1527335Transient Ischemic Attack, Anterior Circulation1CTD_human