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Center for Computational Systems Medicine level2
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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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:CNRIP1-PPP3R1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CNRIP1-PPP3R1
FusionPDB ID: 17846
FusionGDB2.0 ID: 17846
HgeneTgene
Gene symbol

CNRIP1

PPP3R1

Gene ID

25927

5534

Gene namecannabinoid receptor interacting protein 1protein phosphatase 3 regulatory subunit B, alpha
SynonymsC2orf32|CRIP-1|CRIP1CALNB1|CNB|CNB1
Cytomap

2p14

2p14

Type of geneprotein-codingprotein-coding
DescriptionCB1 cannabinoid receptor-interacting protein 1cannabinoid receptor CB1-interacting protein 1calcineurin subunit B type 1calcineurin B, type I (19kDa)protein phosphatase 2B regulatory subunit 1protein phosphatase 2B regulatory subunit B alphaprotein phosphatase 3 (formerly 2B), regulatory subunit B (19kD), alpha isoform (calcineurin B, type I
Modification date2020031320200313
UniProtAcc

Q96F85

.
Ensembl transtripts involved in fusion geneENST idsENST00000263655, ENST00000409559, 
ENST00000481714, ENST00000409862, 
ENST00000409377, ENST00000234310, 
ENST00000409752, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score3 X 2 X 3=185 X 4 X 4=80
# samples 46
** MAII scorelog2(4/18*10)=1.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(6/80*10)=-0.415037499278844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: CNRIP1 [Title/Abstract] AND PPP3R1 [Title/Abstract] AND fusion [Title/Abstract]

A rare genomic duplication in 2p14 underlies autosomal dominant hearing loss DFNA58 (pmid: 32337552)
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PPP3R1(68413600)-CNRIP1(68544439), # samples:2
CNRIP1(68544289)-PPP3R1(68444263), # samples:9
Anticipated loss of major functional domain due to fusion event.CNRIP1-PPP3R1 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.
CNRIP1-PPP3R1 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.
PPP3R1-CNRIP1 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.
PPP3R1-CNRIP1 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.
PPP3R1-CNRIP1 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
TgenePPP3R1

GO:0033173

calcineurin-NFAT signaling cascade

22688515

TgenePPP3R1

GO:0045944

positive regulation of transcription by RNA polymerase II

22688515


check buttonFusion gene breakpoints across CNRIP1 (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 PPP3R1 (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
ChimerDB4Non-Cancer61NCNRIP1chr2

68544288

-PPP3R1chr2

68444263

-
ChimerDB4Non-CancerSPNT_115CNRIP1chr2

68544288

-PPP3R1chr2

68444263

-
ChimerDB4Non-CancerTCGA-06-0675-11ACNRIP1chr2

68544289

-PPP3R1chr2

68444263

-
ChimerDB4Non-CancerTCGA-06-0678-11ACNRIP1chr2

68544289

-PPP3R1chr2

68444263

-
ChimerDB4Non-CancerTCGA-06-0680-11ACNRIP1chr2

68544289

-PPP3R1chr2

68444263

-
ChimerDB4Non-CancerTCGA-06-0681-11ACNRIP1chr2

68544289

-PPP3R1chr2

68444263

-
ChimerDB4Non-CancerTCGA-55-6972-11ACNRIP1chr2

68544289

-PPP3R1chr2

68444263

-
ChimerDB4Non-CancerTCGA-BH-A0DD-11ACNRIP1chr2

68544289

-PPP3R1chr2

68444263

-
ChimerDB4Non-CancerTCGA-BH-A1EO-11ACNRIP1chr2

68544289

-PPP3R1chr2

68444263

-
ChimerDB4Non-CancerTCGA-E2-A1LS-11ACNRIP1chr2

68544289

-PPP3R1chr2

68444263

-
ChimerDB4Non-CancerTCGA-E9-A1RC-11ACNRIP1chr2

68544289

-PPP3R1chr2

68444263

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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)
ENST00000409559CNRIP1chr268544288-ENST00000234310PPP3R1chr268444263-29463300839279
ENST00000409559CNRIP1chr268544288-ENST00000409752PPP3R1chr268444263-9993300839279
ENST00000263655CNRIP1chr268544288-ENST00000234310PPP3R1chr268444263-35529366061445279
ENST00000263655CNRIP1chr268544288-ENST00000409752PPP3R1chr268444263-16059366061445279
ENST00000409559CNRIP1chr268544289-ENST00000234310PPP3R1chr268444263-29463300839279
ENST00000409559CNRIP1chr268544289-ENST00000409752PPP3R1chr268444263-9993300839279
ENST00000263655CNRIP1chr268544289-ENST00000234310PPP3R1chr268444263-35529366061445279
ENST00000263655CNRIP1chr268544289-ENST00000409752PPP3R1chr268444263-16059366061445279

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
ENST00000409559ENST00000234310CNRIP1chr268544288-PPP3R1chr268444263-4.58E-050.9999542
ENST00000409559ENST00000409752CNRIP1chr268544288-PPP3R1chr268444263-0.0001370320.9998629
ENST00000263655ENST00000234310CNRIP1chr268544288-PPP3R1chr268444263-5.84E-050.9999416
ENST00000263655ENST00000409752CNRIP1chr268544288-PPP3R1chr268444263-0.0003721720.9996278
ENST00000409559ENST00000234310CNRIP1chr268544289-PPP3R1chr268444263-4.58E-050.9999542
ENST00000409559ENST00000409752CNRIP1chr268544289-PPP3R1chr268444263-0.0001370320.9998629
ENST00000263655ENST00000234310CNRIP1chr268544289-PPP3R1chr268444263-5.84E-050.9999416
ENST00000263655ENST00000409752CNRIP1chr268544289-PPP3R1chr268444263-0.0003721720.9996278

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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

>17846_17846_1_CNRIP1-PPP3R1_CNRIP1_chr2_68544288_ENST00000263655_PPP3R1_chr2_68444263_ENST00000234310_length(amino acids)=279AA_BP=0
MGDLPGLVRLSIALRIQPNDGPVFYKVDGQRFGQNRTIKLLTGSSYKVEVKIKPSTLQVENISIGGVLVPLELKSKEPDGDRVVYTGTYD
TEGVTPTKSGERQPIQITMPGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVD
FKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLD

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

>17846_17846_2_CNRIP1-PPP3R1_CNRIP1_chr2_68544288_ENST00000263655_PPP3R1_chr2_68444263_ENST00000409752_length(amino acids)=279AA_BP=0
MGDLPGLVRLSIALRIQPNDGPVFYKVDGQRFGQNRTIKLLTGSSYKVEVKIKPSTLQVENISIGGVLVPLELKSKEPDGDRVVYTGTYD
TEGVTPTKSGERQPIQITMPGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVD
FKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLD

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

>17846_17846_3_CNRIP1-PPP3R1_CNRIP1_chr2_68544288_ENST00000409559_PPP3R1_chr2_68444263_ENST00000234310_length(amino acids)=279AA_BP=0
MGDLPGLVRLSIALRIQPNDGPVFYKVDGQRFGQNRTIKLLTGSSYKVEVKIKPSTLQVENISIGGVLVPLELKSKEPDGDRVVYTGTYD
TEGVTPTKSGERQPIQITMPGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVD
FKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLD

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

>17846_17846_4_CNRIP1-PPP3R1_CNRIP1_chr2_68544288_ENST00000409559_PPP3R1_chr2_68444263_ENST00000409752_length(amino acids)=279AA_BP=0
MGDLPGLVRLSIALRIQPNDGPVFYKVDGQRFGQNRTIKLLTGSSYKVEVKIKPSTLQVENISIGGVLVPLELKSKEPDGDRVVYTGTYD
TEGVTPTKSGERQPIQITMPGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVD
FKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLD

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

>17846_17846_5_CNRIP1-PPP3R1_CNRIP1_chr2_68544289_ENST00000263655_PPP3R1_chr2_68444263_ENST00000234310_length(amino acids)=279AA_BP=0
MGDLPGLVRLSIALRIQPNDGPVFYKVDGQRFGQNRTIKLLTGSSYKVEVKIKPSTLQVENISIGGVLVPLELKSKEPDGDRVVYTGTYD
TEGVTPTKSGERQPIQITMPGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVD
FKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLD

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

>17846_17846_6_CNRIP1-PPP3R1_CNRIP1_chr2_68544289_ENST00000263655_PPP3R1_chr2_68444263_ENST00000409752_length(amino acids)=279AA_BP=0
MGDLPGLVRLSIALRIQPNDGPVFYKVDGQRFGQNRTIKLLTGSSYKVEVKIKPSTLQVENISIGGVLVPLELKSKEPDGDRVVYTGTYD
TEGVTPTKSGERQPIQITMPGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVD
FKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLD

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

>17846_17846_7_CNRIP1-PPP3R1_CNRIP1_chr2_68544289_ENST00000409559_PPP3R1_chr2_68444263_ENST00000234310_length(amino acids)=279AA_BP=0
MGDLPGLVRLSIALRIQPNDGPVFYKVDGQRFGQNRTIKLLTGSSYKVEVKIKPSTLQVENISIGGVLVPLELKSKEPDGDRVVYTGTYD
TEGVTPTKSGERQPIQITMPGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVD
FKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLD

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

>17846_17846_8_CNRIP1-PPP3R1_CNRIP1_chr2_68544289_ENST00000409559_PPP3R1_chr2_68444263_ENST00000409752_length(amino acids)=279AA_BP=0
MGDLPGLVRLSIALRIQPNDGPVFYKVDGQRFGQNRTIKLLTGSSYKVEVKIKPSTLQVENISIGGVLVPLELKSKEPDGDRVVYTGTYD
TEGVTPTKSGERQPIQITMPGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVD
FKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLD

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

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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/chr2:68413600/chr2:68544439)
- 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
CNRIP1

Q96F85

.
FUNCTION: [Isoform 1]: Suppresses cannabinoid receptor CNR1-mediated tonic inhibition of voltage-gated calcium channels. {ECO:0000269|PubMed:17895407}.; FUNCTION: [Isoform 2]: Does not suppress cannabinoid receptor CNR1-mediated tonic inhibition of voltage-gated calcium channels. {ECO:0000269|PubMed:17895407}.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.

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
TgenePPP3R1chr2:68544288chr2:68444263ENST0000023431006100_1111.0171.0Calcium binding3
TgenePPP3R1chr2:68544288chr2:68444263ENST0000023431006141_1521.0171.0Calcium binding4
TgenePPP3R1chr2:68544288chr2:68444263ENST000002343100631_421.0171.0Calcium binding1
TgenePPP3R1chr2:68544288chr2:68444263ENST000002343100663_741.0171.0Calcium binding2
TgenePPP3R1chr2:68544289chr2:68444263ENST0000023431006100_1111.0171.0Calcium binding3
TgenePPP3R1chr2:68544289chr2:68444263ENST0000023431006141_1521.0171.0Calcium binding4
TgenePPP3R1chr2:68544289chr2:68444263ENST000002343100631_421.0171.0Calcium binding1
TgenePPP3R1chr2:68544289chr2:68444263ENST000002343100663_741.0171.0Calcium binding2
TgenePPP3R1chr2:68544288chr2:68444263ENST0000023431006128_1631.0171.0DomainEF-hand 4
TgenePPP3R1chr2:68544288chr2:68444263ENST000002343100618_511.0171.0DomainEF-hand 1
TgenePPP3R1chr2:68544288chr2:68444263ENST000002343100650_851.0171.0DomainEF-hand 2
TgenePPP3R1chr2:68544288chr2:68444263ENST000002343100687_1221.0171.0DomainEF-hand 3
TgenePPP3R1chr2:68544289chr2:68444263ENST0000023431006128_1631.0171.0DomainEF-hand 4
TgenePPP3R1chr2:68544289chr2:68444263ENST000002343100618_511.0171.0DomainEF-hand 1
TgenePPP3R1chr2:68544289chr2:68444263ENST000002343100650_851.0171.0DomainEF-hand 2
TgenePPP3R1chr2:68544289chr2:68444263ENST000002343100687_1221.0171.0DomainEF-hand 3
TgenePPP3R1chr2:68544288chr2:68444263ENST0000023431006131_1361.0171.0RegionCalcineurin A binding
TgenePPP3R1chr2:68544289chr2:68444263ENST0000023431006131_1361.0171.0RegionCalcineurin A binding

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>482_CNRIP1_68544289_PPP3R1_68444263_ranked_0.pdbCNRIP16854428968544289ENST00000409752PPP3R1chr268444263-
MGDLPGLVRLSIALRIQPNDGPVFYKVDGQRFGQNRTIKLLTGSSYKVEVKIKPSTLQVENISIGGVLVPLELKSKEPDGDRVVYTGTYD
TEGVTPTKSGERQPIQITMPGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVD
FKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLD
279


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
CNRIP1_pLDDT.png
all structure
all structure
PPP3R1_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
CNRIP1
PPP3R1


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 CNRIP1-PPP3R1


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 CNRIP1-PPP3R1


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