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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-COL1A1 (FusionGDB2 ID:HG5935TG1277)

Fusion Gene Summary for RBM3-COL1A1

check button Fusion gene summary
Fusion gene informationFusion gene name: RBM3-COL1A1
Fusion gene ID: hg5935tg1277
HgeneTgene
Gene symbol

RBM3

COL1A1

Gene ID

5935

1277

Gene nameRNA binding motif protein 3collagen type I alpha 1 chain
SynonymsIS1-RNPL|RNPLCAFYD|EDSARTH1|EDSC|OI1|OI2|OI3|OI4
Cytomap('RBM3')('COL1A1')

Xp11.23

17q21.33

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein 3RNA binding motif (RNP1, RRM) protein 3collagen alpha-1(I) chainalpha-1 type I collagenalpha1(I) procollagencollagen alpha 1 chain type Icollagen alpha-1(I) chain preproproteincollagen of skin, tendon and bone, alpha-1 chaincollagen, type I, alpha 1pro-alpha-1 collagen type 1type I pro
Modification date2020032720200322
UniProtAcc.

P02452

Ensembl transtripts involved in fusion geneENST00000430348, ENST00000354480, 
ENST00000376755, ENST00000376759, 
ENST00000466764, 
Fusion gene scores* DoF score9 X 10 X 2=18044 X 105 X 13=60060
# samples 1080
** MAII scorelog2(10/180*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(80/60060*10)=-6.23026066466979
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RBM3 [Title/Abstract] AND COL1A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRBM3(48434090)-COL1A1(48264909), # samples:9
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
TgeneCOL1A1

GO:0010718

positive regulation of epithelial to mesenchymal transition

20018240

TgeneCOL1A1

GO:0030335

positive regulation of cell migration

20018240

TgeneCOL1A1

GO:0034504

protein localization to nucleus

20018240

TgeneCOL1A1

GO:0045893

positive regulation of transcription, DNA-templated

20018240

TgeneCOL1A1

GO:0090263

positive regulation of canonical Wnt signaling pathway

20018240



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-A2-A4S1-01ARBM3chrX

48434090

+COL1A1chr17

48264909

-
ChimerDB4HNSCTCGA-CN-5370RBM3chrX

48434090

+COL1A1chr17

48264909

-
ChimerDB4HNSCTCGA-CQ-7072RBM3chrX

48434090

+COL1A1chr17

48264909

-
ChimerDB4HNSCTCGA-HD-7831RBM3chrX

48434090

+COL1A1chr17

48264909

-
ChimerDB4LUSCTCGA-85-8582RBM3chrX

48434090

+COL1A1chr17

48264909

-
ChimerDB4PAADTCGA-IB-7893RBM3chrX

48434090

+COL1A1chr17

48264909

-
ChimerDB4SARCTCGA-WK-A8Y0-01ARBM3chrX

48434090

+COL1A1chr17

48264909

-
ChimerDB4SKCMTCGA-W3-A828-06ARBM3chrX

48434090

+COL1A1chr17

48264909

-
ChimerDB4TGCTTCGA-XE-AANIRBM3chrX

48434090

+COL1A1chr17

48264909

-


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Fusion Gene ORF analysis for RBM3-COL1A1

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
5UTR-intronENST00000430348ENST00000225964RBM3chrX

48434090

+COL1A1chr17

48264909

-
intron-intronENST00000354480ENST00000225964RBM3chrX

48434090

+COL1A1chr17

48264909

-
intron-intronENST00000376755ENST00000225964RBM3chrX

48434090

+COL1A1chr17

48264909

-
intron-intronENST00000376759ENST00000225964RBM3chrX

48434090

+COL1A1chr17

48264909

-
intron-intronENST00000466764ENST00000225964RBM3chrX

48434090

+COL1A1chr17

48264909

-

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-COL1A1


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 RBM3-COL1A1


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/:48434090/:48264909)
- 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
.COL1A1

P02452

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: Type I collagen is a member of group I collagen (fibrillar forming collagen).

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-COL1A1


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-COL1A1


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-COL1A1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneCOL1A1P02452DB00048Collagenase clostridium histolyticumBinderBiotechApproved|Investigational
TgeneCOL1A1P02452DB12872Vonicog AlfaBinderBiotechApproved|Investigational
TgeneCOL1A1P02452DB13133Von Willebrand Factor HumanBinderBiotechApproved|Investigational
TgeneCOL1A1P02452DB11338Clove oilBiotechApproved|Nutraceutical
TgeneCOL1A1P02452DB04866HalofuginoneSmall moleculeInvestigational|Vet_approved

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Related Diseases for RBM3-COL1A1


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
TgeneC0268358Osteogenesis imperfecta, dominant perinatal lethal38CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0268362Osteogenesis imperfecta type III (disorder)17CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0023931Lobstein Disease15CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0268363Osteogenesis imperfecta type IV (disorder)12GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0023890Liver Cirrhosis4CTD_human
TgeneC0239946Fibrosis, Liver4CTD_human
TgeneC4551623EHLERS-DANLOS SYNDROME, ARTHROCHALASIA TYPE, 14CTD_human;GENOMICS_ENGLAND
TgeneC4552122EHLERS-DANLOS SYNDROME, CLASSIC TYPE, 14GENOMICS_ENGLAND;UNIPROT
TgeneC0020497Cortical Congenital Hyperostosis3CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0023893Liver Cirrhosis, Experimental3CTD_human
TgeneC0268345EHLERS-DANLOS SYNDROME, ARTHROCHALASIA TYPE2ORPHANET
TgeneC0000786Spontaneous abortion1CTD_human
TgeneC0000822Abortion, Tubal1CTD_human
TgeneC0002949Aneurysm, Dissecting1CTD_human
TgeneC0003504Aortic Valve Insufficiency1CTD_human
TgeneC0004364Autoimmune Diseases1CTD_human
TgeneC0005398Cholestasis, Extrahepatic1CTD_human
TgeneC0005779Blood Coagulation Disorders1GENOMICS_ENGLAND
TgeneC0006663Calcinosis1CTD_human
TgeneC0008311Cholangitis1CTD_human
TgeneC0013720Ehlers-Danlos Syndrome1GENOMICS_ENGLAND
TgeneC0016059Fibrosis1CTD_human
TgeneC0018824Heart valve disease1CTD_human
TgeneC0020538Hypertensive disease1CTD_human
TgeneC0022548Keloid1CTD_human
TgeneC0027719Nephrosclerosis1CTD_human
TgeneC0027726Nephrotic Syndrome1CTD_human
TgeneC0029172Oral Submucous Fibrosis1CTD_human
TgeneC0029434Osteogenesis Imperfecta1CTD_human;GENOMICS_ENGLAND
TgeneC0149721Left Ventricular Hypertrophy1CTD_human
TgeneC0220679Ehlers-Danlos Syndrome, Autosomal Dominant, Type Unspecified1ORPHANET
TgeneC0263628Tumoral calcinosis1CTD_human
TgeneC0340643Dissection of aorta1CTD_human
TgeneC0521174Microcalcification1CTD_human
TgeneC1458140Bleeding tendency1GENOMICS_ENGLAND
TgeneC1619692Nephrogenic Fibrosing Dermopathy1CTD_human
TgeneC1623038Cirrhosis1CTD_human
TgeneC1846545Autoimmune Lymphoproliferative Syndrome Type 2B1GENOMICS_ENGLAND
TgeneC3830362Early Pregnancy Loss1CTD_human
TgeneC4277533Dissection, Blood Vessel1CTD_human
TgeneC4552766Miscarriage1CTD_human