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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:CAPN1-SPDYC (FusionGDB2 ID:12894)

Fusion Gene Summary for CAPN1-SPDYC

check button Fusion gene summary
Fusion gene informationFusion gene name: CAPN1-SPDYC
Fusion gene ID: 12894
HgeneTgene
Gene symbol

CAPN1

SPDYC

Gene ID

823

387778

Gene namecalpain 1speedy/RINGO cell cycle regulator family member C
SynonymsCANP|CANP1|CANPL1|SPG76|muCANP|muCLRINGOC|Ringo2
Cytomap

11q13.1

11q13.1

Type of geneprotein-codingprotein-coding
Descriptioncalpain-1 catalytic subunitCANP 1calcium-activated neutral proteinase 1calpain 1, (mu/I) large subunitcalpain mu-typecalpain, large polypeptide L1calpain-1 large subunitcell proliferation-inducing gene 30 proteincell proliferation-inducing proteinspeedy protein CRINGO ChSpy/Ringo Crapid inducer of G2/M progression in oocytes Cspeedy homolog C
Modification date2020032220200313
UniProtAcc

P07384

.
Ensembl transtripts involved in fusion geneENST00000533820, ENST00000533129, 
ENST00000524773, ENST00000279247, 
ENST00000527469, ENST00000527323, 
ENST00000377185, 
Fusion gene scores* DoF score13 X 11 X 8=11441 X 1 X 1=1
# samples 131
** MAII scorelog2(13/1144*10)=-3.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(1/1*10)=3.32192809488736
Context

PubMed: CAPN1 [Title/Abstract] AND SPDYC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCAPN1(64953809)-SPDYC(64939717), # samples:3
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
HgeneCAPN1

GO:0006508

proteolysis

2400579|2407243|16411745|21531719

HgeneCAPN1

GO:0050790

regulation of catalytic activity

8954105|9271093

HgeneCAPN1

GO:0097264

self proteolysis

8769305|8954105


check buttonFusion gene breakpoints across CAPN1 (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 SPDYC (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
ChimerDB4LIHCTCGA-BC-A10Y-01ACAPN1chr11

64953809

+SPDYCchr11

64939717

+
ChimerDB4LIHCTCGA-BC-A10Y-01ACAPN1chr11

64953809

+SPDYCchr11

64939717

+
ChimerDB4LIHCTCGA-BC-A10Y-01ACAPN1chr11

64953809

-SPDYCchr11

64939717

+


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Fusion Gene ORF analysis for CAPN1-SPDYC

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
In-frameENST00000533820ENST00000377185CAPN1chr11

64953809

+SPDYCchr11

64939717

+
In-frameENST00000533129ENST00000377185CAPN1chr11

64953809

+SPDYCchr11

64939717

+
In-frameENST00000524773ENST00000377185CAPN1chr11

64953809

+SPDYCchr11

64939717

+
In-frameENST00000279247ENST00000377185CAPN1chr11

64953809

+SPDYCchr11

64939717

+
intron-3CDSENST00000527469ENST00000377185CAPN1chr11

64953809

+SPDYCchr11

64939717

+
In-frameENST00000527323ENST00000377185CAPN1chr11

64953809

+SPDYCchr11

64939717

+

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 CAPN1-SPDYC


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)
CAPN1chr1164953809+SPDYCchr1164939716+2.37E-050.9999764
CAPN1chr1164953809+SPDYCchr1164939716+2.37E-050.9999764

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 CAPN1-SPDYC


check button Go to

FGviewer for the breakpoints of chr11:64953809-chr11:64939717

.
- 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
CAPN1

P07384

.
FUNCTION: Calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction (PubMed:21531719, PubMed:2400579). Proteolytically cleaves CTBP1 at 'Asn-375', 'Gly-387' and 'His-409' (PubMed:23707407). {ECO:0000269|PubMed:21531719, ECO:0000269|PubMed:23707407, ECO:0000269|PubMed:2400579}.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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+62299_106253.0715.0Calcium bindingNote=1
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+62299_106253.0715.0Calcium bindingNote=1
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+52199_106253.0715.0Calcium bindingNote=1
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+62299_106253.0715.0Calcium bindingNote=1
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+62299_106253.0715.0Calcium bindingNote=1

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+622302_333253.0715.0Calcium bindingNote=2
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+622598_609253.0715.0Calcium bindingNote=3
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+622628_639253.0715.0Calcium bindingNote=4
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+622302_333253.0715.0Calcium bindingNote=2
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+622598_609253.0715.0Calcium bindingNote=3
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+622628_639253.0715.0Calcium bindingNote=4
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+521302_333253.0715.0Calcium bindingNote=2
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+521598_609253.0715.0Calcium bindingNote=3
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+521628_639253.0715.0Calcium bindingNote=4
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+622302_333253.0715.0Calcium bindingNote=2
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+622598_609253.0715.0Calcium bindingNote=3
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+622628_639253.0715.0Calcium bindingNote=4
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+622302_333253.0715.0Calcium bindingNote=2
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+622598_609253.0715.0Calcium bindingNote=3
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+622628_639253.0715.0Calcium bindingNote=4
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+622541_576253.0715.0DomainEF-hand 1
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+62255_354253.0715.0DomainCalpain catalytic
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+622585_618253.0715.0DomainEF-hand 2
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+622615_650253.0715.0DomainEF-hand 3
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+622680_714253.0715.0DomainEF-hand 4
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+622541_576253.0715.0DomainEF-hand 1
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+62255_354253.0715.0DomainCalpain catalytic
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+622585_618253.0715.0DomainEF-hand 2
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+622615_650253.0715.0DomainEF-hand 3
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+622680_714253.0715.0DomainEF-hand 4
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+521541_576253.0715.0DomainEF-hand 1
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+52155_354253.0715.0DomainCalpain catalytic
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+521585_618253.0715.0DomainEF-hand 2
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+521615_650253.0715.0DomainEF-hand 3
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+521680_714253.0715.0DomainEF-hand 4
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+622541_576253.0715.0DomainEF-hand 1
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+62255_354253.0715.0DomainCalpain catalytic
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+622585_618253.0715.0DomainEF-hand 2
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+622615_650253.0715.0DomainEF-hand 3
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+622680_714253.0715.0DomainEF-hand 4
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+622541_576253.0715.0DomainEF-hand 1
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+62255_354253.0715.0DomainCalpain catalytic
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+622585_618253.0715.0DomainEF-hand 2
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+622615_650253.0715.0DomainEF-hand 3
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+622680_714253.0715.0DomainEF-hand 4
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+622355_526253.0715.0RegionNote=Domain III
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+622527_542253.0715.0RegionNote=Linker
HgeneCAPN1chr11:64953809chr11:64939717ENST00000279247+622543_713253.0715.0RegionNote=Domain IV
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+622355_526253.0715.0RegionNote=Domain III
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+622527_542253.0715.0RegionNote=Linker
HgeneCAPN1chr11:64953809chr11:64939717ENST00000524773+622543_713253.0715.0RegionNote=Domain IV
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+521355_526253.0715.0RegionNote=Domain III
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+521527_542253.0715.0RegionNote=Linker
HgeneCAPN1chr11:64953809chr11:64939717ENST00000527323+521543_713253.0715.0RegionNote=Domain IV
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+622355_526253.0715.0RegionNote=Domain III
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+622527_542253.0715.0RegionNote=Linker
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533129+622543_713253.0715.0RegionNote=Domain IV
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+622355_526253.0715.0RegionNote=Domain III
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+622527_542253.0715.0RegionNote=Linker
HgeneCAPN1chr11:64953809chr11:64939717ENST00000533820+622543_713253.0715.0RegionNote=Domain IV
TgeneSPDYCchr11:64953809chr11:64939717ENST000003771852756_18886.0294.0RegionSpeedy/Ringo box%3B Required for CDK-binding


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Fusion Gene Sequence for CAPN1-SPDYC


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 CAPN1-SPDYC


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 CAPN1-SPDYC


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 CAPN1-SPDYC


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCAPN1C4310800SPASTIC PARAPLEGIA 76, AUTOSOMAL RECESSIVE2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCAPN1C0006826Malignant Neoplasms1CTD_human
HgeneCAPN1C0025202melanoma1CTD_human
HgeneCAPN1C0027651Neoplasms1CTD_human
HgeneCAPN1C0029134Optic Neuritis1CTD_human
HgeneCAPN1C0085582Retrobulbar Neuritis1CTD_human
HgeneCAPN1C0086692Benign Neoplasm1CTD_human
HgeneCAPN1C0524679Neuropapillitis1CTD_human