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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:MPRIP-COPS3 (FusionGDB2 ID:54775)

Fusion Gene Summary for MPRIP-COPS3

check button Fusion gene summary
Fusion gene informationFusion gene name: MPRIP-COPS3
Fusion gene ID: 54775
HgeneTgene
Gene symbol

MPRIP

COPS3

Gene ID

23164

8533

Gene namemyosin phosphatase Rho interacting proteinCOP9 signalosome subunit 3
SynonymsM-RIP|MRIP|RHOIP3|RIP3|p116RipCSN3|SGN3
Cytomap

17p11.2

17p11.2

Type of geneprotein-codingprotein-coding
Descriptionmyosin phosphatase Rho-interacting proteinRho interacting protein 3COP9 signalosome complex subunit 3COP9 complex subunit 3COP9 constitutive photomorphogenic homolog subunit 3JAB1-containing signalosome subunit 3signalosome subunit 3
Modification date2020031320200327
UniProtAcc

Q6WCQ1

Q9UNS2

Ensembl transtripts involved in fusion geneENST00000395807, ENST00000341712, 
ENST00000395804, ENST00000395811, 
ENST00000444976, ENST00000395806, 
ENST00000268717, ENST00000439936, 
ENST00000539941, 
Fusion gene scores* DoF score24 X 12 X 11=31687 X 6 X 5=210
# samples 237
** MAII scorelog2(23/3168*10)=-3.78386656913523
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/210*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MPRIP [Title/Abstract] AND COPS3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMPRIP(16981390)-COPS3(17150465), # samples:2
Anticipated loss of major functional domain due to fusion event.MPRIP-COPS3 seems lost the major protein functional domain in Hgene partner, which is a essential gene 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
TgeneCOPS3

GO:0000338

protein deneddylation

19141280


check buttonFusion gene breakpoints across MPRIP (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 COPS3 (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
ChimerDB4KIRPTCGA-HE-A5NK-01AMPRIPchr17

16981390

-COPS3chr17

17150465

-
ChimerDB4KIRPTCGA-HE-A5NK-01AMPRIPchr17

16981390

+COPS3chr17

17150465

-


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Fusion Gene ORF analysis for MPRIP-COPS3

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-3CDSENST00000395807ENST00000268717MPRIPchr17

16981390

+COPS3chr17

17150465

-
3UTR-3CDSENST00000395807ENST00000439936MPRIPchr17

16981390

+COPS3chr17

17150465

-
3UTR-3CDSENST00000395807ENST00000539941MPRIPchr17

16981390

+COPS3chr17

17150465

-
Frame-shiftENST00000341712ENST00000268717MPRIPchr17

16981390

+COPS3chr17

17150465

-
Frame-shiftENST00000341712ENST00000539941MPRIPchr17

16981390

+COPS3chr17

17150465

-
Frame-shiftENST00000395804ENST00000268717MPRIPchr17

16981390

+COPS3chr17

17150465

-
Frame-shiftENST00000395804ENST00000539941MPRIPchr17

16981390

+COPS3chr17

17150465

-
Frame-shiftENST00000395811ENST00000268717MPRIPchr17

16981390

+COPS3chr17

17150465

-
Frame-shiftENST00000395811ENST00000539941MPRIPchr17

16981390

+COPS3chr17

17150465

-
Frame-shiftENST00000444976ENST00000268717MPRIPchr17

16981390

+COPS3chr17

17150465

-
Frame-shiftENST00000444976ENST00000539941MPRIPchr17

16981390

+COPS3chr17

17150465

-
In-frameENST00000341712ENST00000439936MPRIPchr17

16981390

+COPS3chr17

17150465

-
In-frameENST00000395804ENST00000439936MPRIPchr17

16981390

+COPS3chr17

17150465

-
In-frameENST00000395811ENST00000439936MPRIPchr17

16981390

+COPS3chr17

17150465

-
In-frameENST00000444976ENST00000439936MPRIPchr17

16981390

+COPS3chr17

17150465

-
intron-3CDSENST00000395806ENST00000268717MPRIPchr17

16981390

+COPS3chr17

17150465

-
intron-3CDSENST00000395806ENST00000439936MPRIPchr17

16981390

+COPS3chr17

17150465

-
intron-3CDSENST00000395806ENST00000539941MPRIPchr17

16981390

+COPS3chr17

17150465

-

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)
ENST00000395811MPRIPchr1716981390+ENST00000439936COPS3chr1717150465-63435689409106
ENST00000444976MPRIPchr1716981390+ENST00000439936COPS3chr1717150465-62534780400106
ENST00000395804MPRIPchr1716981390+ENST00000439936COPS3chr1717150465-60132356376106
ENST00000341712MPRIPchr1716981390+ENST00000439936COPS3chr1717150465-5452670320106

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
ENST00000395811ENST00000439936MPRIPchr1716981390+COPS3chr1717150465-0.0193532930.9806467
ENST00000444976ENST00000439936MPRIPchr1716981390+COPS3chr1717150465-0.0189299530.98107004
ENST00000395804ENST00000439936MPRIPchr1716981390+COPS3chr1717150465-0.0151282630.9848718
ENST00000341712ENST00000439936MPRIPchr1716981390+COPS3chr1717150465-0.0230173020.9769827

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Fusion Genomic Features for MPRIP-COPS3


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 MPRIP-COPS3


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/chr17:16981390/chr17:17150465)
- 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
MPRIP

Q6WCQ1

COPS3

Q9UNS2

FUNCTION: Targets myosin phosphatase to the actin cytoskeleton. Required for the regulation of the actin cytoskeleton by RhoA and ROCK1. Depletion leads to an increased number of stress fibers in smooth muscle cells through stabilization of actin fibers by phosphorylated myosin. Overexpression of MRIP as well as its F-actin-binding region leads to disassembly of stress fibers in neuronal cells. {ECO:0000250|UniProtKB:P97434, ECO:0000269|PubMed:15545284, ECO:0000269|PubMed:16257966}.FUNCTION: Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, c-jun/JUN, IkappaBalpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively. {ECO:0000269|PubMed:11285227, ECO:0000269|PubMed:11337588, ECO:0000269|PubMed:12628923, ECO:0000269|PubMed:12732143, ECO:0000269|PubMed:9535219}.

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
HgeneMPRIPchr17:16981390chr17:17150465ENST00000341712+324673_977891231.0Coiled coilOntology_term=ECO:0000255
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395804+323673_977891026.0Coiled coilOntology_term=ECO:0000255
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395811+323673_977891039.0Coiled coilOntology_term=ECO:0000255
HgeneMPRIPchr17:16981390chr17:17150465ENST00000444976+322673_977891001.0Coiled coilOntology_term=ECO:0000255
HgeneMPRIPchr17:16981390chr17:17150465ENST00000341712+324179_252891231.0Compositional biasNote=Ser-rich
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395804+323179_252891026.0Compositional biasNote=Ser-rich
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395811+323179_252891039.0Compositional biasNote=Ser-rich
HgeneMPRIPchr17:16981390chr17:17150465ENST00000444976+322179_252891001.0Compositional biasNote=Ser-rich
HgeneMPRIPchr17:16981390chr17:17150465ENST00000341712+324387_483891231.0DomainPH 2
HgeneMPRIPchr17:16981390chr17:17150465ENST00000341712+32443_150891231.0DomainPH 1
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395804+323387_483891026.0DomainPH 2
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395804+32343_150891026.0DomainPH 1
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395811+323387_483891039.0DomainPH 2
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395811+32343_150891039.0DomainPH 1
HgeneMPRIPchr17:16981390chr17:17150465ENST00000444976+322387_483891001.0DomainPH 2
HgeneMPRIPchr17:16981390chr17:17150465ENST00000444976+32243_150891001.0DomainPH 1
TgeneCOPS3chr17:16981390chr17:17150465ENST000002687171012197_365406424.0DomainPCI
TgeneCOPS3chr17:16981390chr17:17150465ENST000005399411012197_365386404.0DomainPCI


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Fusion Gene Sequence for MPRIP-COPS3


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.
>54775_54775_1_MPRIP-COPS3_MPRIP_chr17_16981390_ENST00000341712_COPS3_chr17_17150465_ENST00000439936_length(transcript)=545nt_BP=267nt
ATGTCGGCAGCCAAGGAGAACCCGTGCAGGAAATTCCAGGCCAACATCTTCAACAAGAGCAAGTGTCAGAACTGCTTCAAGCCCCGCGAG
TCGCATCTGCTCAACGACGAGGACCTGACGCAGGCAAAACCCATTTATGGCGGTTGGCTGCTCCTGGCTCCAGATGGGACCGACTTTGAC
AACCCAGTGCACCGGTCTCGGAAATGGCAGCGACGGTTCTTCATCCTTTACGAGCACGGCCTCTTGCGCTACGCCCTGGATGAGATGAGT
ATGGGCTCACAAGAAGATGATTCAGGAAACAAACCATCCAGTTATTCTTGAAACTAACATCCATCCTGAGCTAAACAAGAGAAACTACCA
TCTTGGCCAGTGACAAGTGTTCGGAGGGCAGCAGAGAGGACCAAGCCTGTGTCACCTGGAGACTAAGAAATTAAGTTTTGTTTTGACATC
TTCAGTCCTGTGTGCTTTCAGAAAACCATTTTCTCTGCAAAGAAAGGAAACAGATTTGCAAACTTTAAAGTCTGTCGTGGATTTATTTAT

>54775_54775_1_MPRIP-COPS3_MPRIP_chr17_16981390_ENST00000341712_COPS3_chr17_17150465_ENST00000439936_length(amino acids)=106AA_BP=89
MSAAKENPCRKFQANIFNKSKCQNCFKPRESHLLNDEDLTQAKPIYGGWLLLAPDGTDFDNPVHRSRKWQRRFFILYEHGLLRYALDEMS

--------------------------------------------------------------
>54775_54775_2_MPRIP-COPS3_MPRIP_chr17_16981390_ENST00000395804_COPS3_chr17_17150465_ENST00000439936_length(transcript)=601nt_BP=323nt
GCCAGGCCGGCCAGGCCTGCGCCGCCGCCGCCGCCGCCGTCGCCGCCGCGCCGACCATGTCGGCAGCCAAGGAGAACCCGTGCAGGAAAT
TCCAGGCCAACATCTTCAACAAGAGCAAGTGTCAGAACTGCTTCAAGCCCCGCGAGTCGCATCTGCTCAACGACGAGGACCTGACGCAGG
CAAAACCCATTTATGGCGGTTGGCTGCTCCTGGCTCCAGATGGGACCGACTTTGACAACCCAGTGCACCGGTCTCGGAAATGGCAGCGAC
GGTTCTTCATCCTTTACGAGCACGGCCTCTTGCGCTACGCCCTGGATGAGATGAGTATGGGCTCACAAGAAGATGATTCAGGAAACAAAC
CATCCAGTTATTCTTGAAACTAACATCCATCCTGAGCTAAACAAGAGAAACTACCATCTTGGCCAGTGACAAGTGTTCGGAGGGCAGCAG
AGAGGACCAAGCCTGTGTCACCTGGAGACTAAGAAATTAAGTTTTGTTTTGACATCTTCAGTCCTGTGTGCTTTCAGAAAACCATTTTCT

>54775_54775_2_MPRIP-COPS3_MPRIP_chr17_16981390_ENST00000395804_COPS3_chr17_17150465_ENST00000439936_length(amino acids)=106AA_BP=89
MSAAKENPCRKFQANIFNKSKCQNCFKPRESHLLNDEDLTQAKPIYGGWLLLAPDGTDFDNPVHRSRKWQRRFFILYEHGLLRYALDEMS

--------------------------------------------------------------
>54775_54775_3_MPRIP-COPS3_MPRIP_chr17_16981390_ENST00000395811_COPS3_chr17_17150465_ENST00000439936_length(transcript)=634nt_BP=356nt
GCGGCCGCGCTGAGCCCCTAGCCCGCCGGGAGCGCCAGGCCGGCCAGGCCTGCGCCGCCGCCGCCGCCGCCGTCGCCGCCGCGCCGACCA
TGTCGGCAGCCAAGGAGAACCCGTGCAGGAAATTCCAGGCCAACATCTTCAACAAGAGCAAGTGTCAGAACTGCTTCAAGCCCCGCGAGT
CGCATCTGCTCAACGACGAGGACCTGACGCAGGCAAAACCCATTTATGGCGGTTGGCTGCTCCTGGCTCCAGATGGGACCGACTTTGACA
ACCCAGTGCACCGGTCTCGGAAATGGCAGCGACGGTTCTTCATCCTTTACGAGCACGGCCTCTTGCGCTACGCCCTGGATGAGATGAGTA
TGGGCTCACAAGAAGATGATTCAGGAAACAAACCATCCAGTTATTCTTGAAACTAACATCCATCCTGAGCTAAACAAGAGAAACTACCAT
CTTGGCCAGTGACAAGTGTTCGGAGGGCAGCAGAGAGGACCAAGCCTGTGTCACCTGGAGACTAAGAAATTAAGTTTTGTTTTGACATCT
TCAGTCCTGTGTGCTTTCAGAAAACCATTTTCTCTGCAAAGAAAGGAAACAGATTTGCAAACTTTAAAGTCTGTCGTGGATTTATTTATC

>54775_54775_3_MPRIP-COPS3_MPRIP_chr17_16981390_ENST00000395811_COPS3_chr17_17150465_ENST00000439936_length(amino acids)=106AA_BP=89
MSAAKENPCRKFQANIFNKSKCQNCFKPRESHLLNDEDLTQAKPIYGGWLLLAPDGTDFDNPVHRSRKWQRRFFILYEHGLLRYALDEMS

--------------------------------------------------------------
>54775_54775_4_MPRIP-COPS3_MPRIP_chr17_16981390_ENST00000444976_COPS3_chr17_17150465_ENST00000439936_length(transcript)=625nt_BP=347nt
CTGAGCCCCTAGCCCGCCGGGAGCGCCAGGCCGGCCAGGCCTGCGCCGCCGCCGCCGCCGCCGTCGCCGCCGCGCCGACCATGTCGGCAG
CCAAGGAGAACCCGTGCAGGAAATTCCAGGCCAACATCTTCAACAAGAGCAAGTGTCAGAACTGCTTCAAGCCCCGCGAGTCGCATCTGC
TCAACGACGAGGACCTGACGCAGGCAAAACCCATTTATGGCGGTTGGCTGCTCCTGGCTCCAGATGGGACCGACTTTGACAACCCAGTGC
ACCGGTCTCGGAAATGGCAGCGACGGTTCTTCATCCTTTACGAGCACGGCCTCTTGCGCTACGCCCTGGATGAGATGAGTATGGGCTCAC
AAGAAGATGATTCAGGAAACAAACCATCCAGTTATTCTTGAAACTAACATCCATCCTGAGCTAAACAAGAGAAACTACCATCTTGGCCAG
TGACAAGTGTTCGGAGGGCAGCAGAGAGGACCAAGCCTGTGTCACCTGGAGACTAAGAAATTAAGTTTTGTTTTGACATCTTCAGTCCTG

>54775_54775_4_MPRIP-COPS3_MPRIP_chr17_16981390_ENST00000444976_COPS3_chr17_17150465_ENST00000439936_length(amino acids)=106AA_BP=89
MSAAKENPCRKFQANIFNKSKCQNCFKPRESHLLNDEDLTQAKPIYGGWLLLAPDGTDFDNPVHRSRKWQRRFFILYEHGLLRYALDEMS

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

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Fusion Gene PPI Analysis for MPRIP-COPS3


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
HgeneMPRIPchr17:16981390chr17:17150465ENST00000341712+3242_38389.01231.0F-actin
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395804+3232_38389.01026.0F-actin
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395811+3232_38389.01039.0F-actin
HgeneMPRIPchr17:16981390chr17:17150465ENST00000444976+3222_38389.01001.0F-actin
HgeneMPRIPchr17:16981390chr17:17150465ENST00000341712+324824_87989.01231.0PPP1R12A
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395804+323824_87989.01026.0PPP1R12A
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395811+323824_87989.01039.0PPP1R12A
HgeneMPRIPchr17:16981390chr17:17150465ENST00000444976+322824_87989.01001.0PPP1R12A
HgeneMPRIPchr17:16981390chr17:17150465ENST00000341712+324546_82489.01231.0RHOA
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395804+323546_82489.01026.0RHOA
HgeneMPRIPchr17:16981390chr17:17150465ENST00000395811+323546_82489.01039.0RHOA
HgeneMPRIPchr17:16981390chr17:17150465ENST00000444976+322546_82489.01001.0RHOA


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 MPRIP-COPS3


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 MPRIP-COPS3


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