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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:CAPNS1-GLUL (FusionGDB2 ID:12915)

Fusion Gene Summary for CAPNS1-GLUL

check button Fusion gene summary
Fusion gene informationFusion gene name: CAPNS1-GLUL
Fusion gene ID: 12915
HgeneTgene
Gene symbol

CAPNS1

GLUL

Gene ID

826

2752

Gene namecalpain small subunit 1glutamate-ammonia ligase
SynonymsCALPAIN4|CANP|CANPS|CAPN4|CDPS|CSS1GLNS|GS|PIG43|PIG59
Cytomap

19q13.12

1q25.3

Type of geneprotein-codingprotein-coding
Descriptioncalpain small subunit 1CANP small subunitcalcium-activated neutral proteinase small subunitcalcium-dependent protease small subunit 1calcium-dependent protease, small subunitcalpain 4, small subunit (30K)calpain regulatory subunitcalpain, small polglutamine synthetasecell proliferation-inducing protein 59glutamate decarboxylaseglutamine synthasepalmitoyltransferase GLULproliferation-inducing protein 43
Modification date2020031320200313
UniProtAcc

P04632

P15104

Ensembl transtripts involved in fusion geneENST00000246533, ENST00000587718, 
ENST00000588780, ENST00000588815, 
ENST00000590874, ENST00000589146, 
ENST00000339526, ENST00000491322, 
ENST00000311223, ENST00000331872, 
ENST00000417584, 
Fusion gene scores* DoF score29 X 25 X 9=652518 X 16 X 6=1728
# samples 3120
** MAII scorelog2(31/6525*10)=-4.39563778107037
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(20/1728*10)=-3.11103131238874
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CAPNS1 [Title/Abstract] AND GLUL [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCAPNS1(36633235)-GLUL(182355537), # samples:1
Anticipated loss of major functional domain due to fusion event.CAPNS1-GLUL seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
CAPNS1-GLUL seems lost the major protein functional domain in Tgene 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
TgeneGLUL

GO:0008283

cell proliferation

18662667

TgeneGLUL

GO:0010594

regulation of endothelial cell migration

30158707

TgeneGLUL

GO:0018345

protein palmitoylation

30158707

TgeneGLUL

GO:1903670

regulation of sprouting angiogenesis

30158707


check buttonFusion gene breakpoints across CAPNS1 (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 GLUL (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
ChimerDB4BRCATCGA-AR-A0U3-01ACAPNS1chr19

36633235

+GLULchr1

182355537

-


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Fusion Gene ORF analysis for CAPNS1-GLUL

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
5CDS-5UTRENST00000246533ENST00000339526CAPNS1chr19

36633235

+GLULchr1

182355537

-
5CDS-5UTRENST00000246533ENST00000491322CAPNS1chr19

36633235

+GLULchr1

182355537

-
5CDS-5UTRENST00000587718ENST00000339526CAPNS1chr19

36633235

+GLULchr1

182355537

-
5CDS-5UTRENST00000587718ENST00000491322CAPNS1chr19

36633235

+GLULchr1

182355537

-
5CDS-5UTRENST00000588780ENST00000339526CAPNS1chr19

36633235

+GLULchr1

182355537

-
5CDS-5UTRENST00000588780ENST00000491322CAPNS1chr19

36633235

+GLULchr1

182355537

-
5CDS-5UTRENST00000588815ENST00000339526CAPNS1chr19

36633235

+GLULchr1

182355537

-
5CDS-5UTRENST00000588815ENST00000491322CAPNS1chr19

36633235

+GLULchr1

182355537

-
5CDS-5UTRENST00000590874ENST00000339526CAPNS1chr19

36633235

+GLULchr1

182355537

-
5CDS-5UTRENST00000590874ENST00000491322CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000246533ENST00000311223CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000246533ENST00000331872CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000246533ENST00000417584CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000587718ENST00000311223CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000587718ENST00000331872CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000587718ENST00000417584CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000588780ENST00000311223CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000588780ENST00000331872CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000588780ENST00000417584CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000588815ENST00000311223CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000588815ENST00000331872CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000588815ENST00000417584CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000590874ENST00000311223CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000590874ENST00000331872CAPNS1chr19

36633235

+GLULchr1

182355537

-
Frame-shiftENST00000590874ENST00000417584CAPNS1chr19

36633235

+GLULchr1

182355537

-
intron-3CDSENST00000589146ENST00000311223CAPNS1chr19

36633235

+GLULchr1

182355537

-
intron-3CDSENST00000589146ENST00000331872CAPNS1chr19

36633235

+GLULchr1

182355537

-
intron-3CDSENST00000589146ENST00000417584CAPNS1chr19

36633235

+GLULchr1

182355537

-
intron-5UTRENST00000589146ENST00000339526CAPNS1chr19

36633235

+GLULchr1

182355537

-
intron-5UTRENST00000589146ENST00000491322CAPNS1chr19

36633235

+GLULchr1

182355537

-

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 CAPNS1-GLUL


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 CAPNS1-GLUL


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/:36633235/:182355537)
- 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
CAPNS1

P04632

GLUL

P15104

FUNCTION: Regulatory subunit of the calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction.FUNCTION: Glutamine synthetase that catalyzes the ATP-dependent conversion of glutamate and ammonia to glutamine (PubMed:30158707, PubMed:16267323). Its role depends on tissue localization: in the brain, it regulates the levels of toxic ammonia and converts neurotoxic glutamate to harmless glutamine, whereas in the liver, it is one of the enzymes responsible for the removal of ammonia (By similarity). Essential for proliferation of fetal skin fibroblasts (PubMed:18662667). Independently of its glutamine synthetase activity, required for endothelial cell migration during vascular development: acts by regulating membrane localization and activation of the GTPase RHOJ, possibly by promoting RHOJ palmitoylation (PubMed:30158707). May act as a palmitoyltransferase for RHOJ: able to autopalmitoylate and then transfer the palmitoyl group to RHOJ (PubMed:30158707). Plays a role in ribosomal 40S subunit biogenesis (PubMed:26711351). {ECO:0000250|UniProtKB:P15105, ECO:0000269|PubMed:16267323, ECO:0000269|PubMed:18662667, ECO:0000269|PubMed:26711351, ECO:0000269|PubMed:30158707}.

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 CAPNS1-GLUL


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 CAPNS1-GLUL


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 CAPNS1-GLUL


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 CAPNS1-GLUL


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