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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:CAPN5-XRRA1 (FusionGDB2 ID:12940)

Fusion Gene Summary for CAPN5-XRRA1

check button Fusion gene summary
Fusion gene informationFusion gene name: CAPN5-XRRA1
Fusion gene ID: 12940
HgeneTgene
Gene symbol

CAPN5

XRRA1

Gene ID

726

143570

Gene namecalpain 5X-ray radiation resistance associated 1
SynonymsADNIV|HTRA3|VRNI|nCL-3-
Cytomap

11q13.5

11q13.4

Type of geneprotein-codingprotein-coding
Descriptioncalpain-5calpain htra-3new calpain 3testis tissue sperm-binding protein Li 91mPX-ray radiation resistance-associated protein 1
Modification date2020031320200313
UniProtAcc

O15484

.
Ensembl transtripts involved in fusion geneENST00000531028, ENST00000278559, 
ENST00000529629, ENST00000456580, 
ENST00000340360, ENST00000321448, 
ENST00000527087, ENST00000533598, 
Fusion gene scores* DoF score8 X 5 X 5=2007 X 9 X 6=378
# samples 89
** MAII scorelog2(8/200*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/378*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CAPN5 [Title/Abstract] AND XRRA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCAPN5(76804859)-XRRA1(74554498), # samples:1
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
TgeneXRRA1

GO:0010165

response to X-ray

12908878


check buttonFusion gene breakpoints across CAPN5 (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 XRRA1 (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
ChimerDB4SKCMTCGA-YG-AA3P-06ACAPN5chr11

76804859

-XRRA1chr11

74554498

-


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Fusion Gene ORF analysis for CAPN5-XRRA1

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
intron-3CDSENST00000531028ENST00000340360CAPN5chr11

76804859

-XRRA1chr11

74554498

-
intron-3CDSENST00000531028ENST00000321448CAPN5chr11

76804859

-XRRA1chr11

74554498

-
intron-3CDSENST00000531028ENST00000527087CAPN5chr11

76804859

-XRRA1chr11

74554498

-
intron-intronENST00000531028ENST00000533598CAPN5chr11

76804859

-XRRA1chr11

74554498

-
Frame-shiftENST00000278559ENST00000340360CAPN5chr11

76804859

-XRRA1chr11

74554498

-
Frame-shiftENST00000278559ENST00000321448CAPN5chr11

76804859

-XRRA1chr11

74554498

-
In-frameENST00000278559ENST00000527087CAPN5chr11

76804859

-XRRA1chr11

74554498

-
5CDS-intronENST00000278559ENST00000533598CAPN5chr11

76804859

-XRRA1chr11

74554498

-
Frame-shiftENST00000529629ENST00000340360CAPN5chr11

76804859

-XRRA1chr11

74554498

-
Frame-shiftENST00000529629ENST00000321448CAPN5chr11

76804859

-XRRA1chr11

74554498

-
In-frameENST00000529629ENST00000527087CAPN5chr11

76804859

-XRRA1chr11

74554498

-
5CDS-intronENST00000529629ENST00000533598CAPN5chr11

76804859

-XRRA1chr11

74554498

-
Frame-shiftENST00000456580ENST00000340360CAPN5chr11

76804859

-XRRA1chr11

74554498

-
Frame-shiftENST00000456580ENST00000321448CAPN5chr11

76804859

-XRRA1chr11

74554498

-
In-frameENST00000456580ENST00000527087CAPN5chr11

76804859

-XRRA1chr11

74554498

-
5CDS-intronENST00000456580ENST00000533598CAPN5chr11

76804859

-XRRA1chr11

74554498

-

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)
ENST00000278559CAPN5chr1176804859-ENST00000527087XRRA1chr1174554498-97248663524153
ENST00000529629CAPN5chr1176804859-ENST00000527087XRRA1chr1174554498-100952343561172
ENST00000456580CAPN5chr1176804859-ENST00000527087XRRA1chr1174554498-104055411592193

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
ENST00000278559ENST00000527087CAPN5chr1176804859-XRRA1chr1174554498-0.32832320.6716768
ENST00000529629ENST00000527087CAPN5chr1176804859-XRRA1chr1174554498-0.325024070.674976
ENST00000456580ENST00000527087CAPN5chr1176804859-XRRA1chr1174554498-0.498056920.50194305

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Fusion Genomic Features for CAPN5-XRRA1


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 CAPN5-XRRA1


check button Go to

FGviewer for the breakpoints of chr11:76804859-chr11:74554498

.
- 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
CAPN5

O15484

.
FUNCTION: Calcium-regulated non-lysosomal thiol-protease. {ECO:0000250}.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
TgeneXRRA1chr11:76804859chr11:74554498ENST000003214481416723_745433.3333333333333518.0Coiled coilOntology_term=ECO:0000255
TgeneXRRA1chr11:76804859chr11:74554498ENST000003403601719723_745708.3333333333334793.0Coiled coilOntology_term=ECO:0000255
TgeneXRRA1chr11:76804859chr11:74554498ENST000005270871315723_745586.0599.0Coiled coilOntology_term=ECO:0000255

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCAPN5chr11:76804859chr11:74554498ENST00000278559-31326_34399.0641.0DomainCalpain catalytic
HgeneCAPN5chr11:76804859chr11:74554498ENST00000278559-313499_61499.0641.0DomainC2
HgeneCAPN5chr11:76804859chr11:74554498ENST00000529629-41426_34399.0641.0DomainCalpain catalytic
HgeneCAPN5chr11:76804859chr11:74554498ENST00000529629-414499_61499.0641.0DomainC2
HgeneCAPN5chr11:76804859chr11:74554498ENST00000278559-313344_49699.0641.0RegionNote=Domain III
HgeneCAPN5chr11:76804859chr11:74554498ENST00000529629-414344_49699.0641.0RegionNote=Domain III
TgeneXRRA1chr11:76804859chr11:74554498ENST000003214481416104_125433.3333333333333518.0RepeatNote=LRR 1
TgeneXRRA1chr11:76804859chr11:74554498ENST000003214481416141_155433.3333333333333518.0RepeatNote=LRR 2
TgeneXRRA1chr11:76804859chr11:74554498ENST000003214481416164_184433.3333333333333518.0RepeatNote=LRR 3
TgeneXRRA1chr11:76804859chr11:74554498ENST000003214481416188_209433.3333333333333518.0RepeatNote=LRR 4
TgeneXRRA1chr11:76804859chr11:74554498ENST000003214481416229_250433.3333333333333518.0RepeatNote=LRR 5
TgeneXRRA1chr11:76804859chr11:74554498ENST000003214481416254_275433.3333333333333518.0RepeatNote=LRR 6
TgeneXRRA1chr11:76804859chr11:74554498ENST000003403601719104_125708.3333333333334793.0RepeatNote=LRR 1
TgeneXRRA1chr11:76804859chr11:74554498ENST000003403601719141_155708.3333333333334793.0RepeatNote=LRR 2
TgeneXRRA1chr11:76804859chr11:74554498ENST000003403601719164_184708.3333333333334793.0RepeatNote=LRR 3
TgeneXRRA1chr11:76804859chr11:74554498ENST000003403601719188_209708.3333333333334793.0RepeatNote=LRR 4
TgeneXRRA1chr11:76804859chr11:74554498ENST000003403601719229_250708.3333333333334793.0RepeatNote=LRR 5
TgeneXRRA1chr11:76804859chr11:74554498ENST000003403601719254_275708.3333333333334793.0RepeatNote=LRR 6
TgeneXRRA1chr11:76804859chr11:74554498ENST000005270871315104_125586.0599.0RepeatNote=LRR 1
TgeneXRRA1chr11:76804859chr11:74554498ENST000005270871315141_155586.0599.0RepeatNote=LRR 2
TgeneXRRA1chr11:76804859chr11:74554498ENST000005270871315164_184586.0599.0RepeatNote=LRR 3
TgeneXRRA1chr11:76804859chr11:74554498ENST000005270871315188_209586.0599.0RepeatNote=LRR 4
TgeneXRRA1chr11:76804859chr11:74554498ENST000005270871315229_250586.0599.0RepeatNote=LRR 5
TgeneXRRA1chr11:76804859chr11:74554498ENST000005270871315254_275586.0599.0RepeatNote=LRR 6


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Fusion Gene Sequence for CAPN5-XRRA1


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.
>In-frame_ENST00000278559_ENST00000527087_TCGA-YG-AA3P-06A_CAPN5_chr11_76804859_-_XRRA1_chr11_74554498_length(transcript)=972nt_BP=486nt
GAATGCGAGCGCCAGCCCCCGCCGCAGGCCAGTCCCAGCTGGATCTCCGGCCAGAGCCCGAGGCTGCTGCGCCGGGCGGCTGCAGCCTCC
GCTCCAGCGCCCGCGCCGTGCCCTGCATCCCGGGAGCCCGGCTGGACCCGCGGCGGCTCGGCCGGTGTTCCCCCTCCCCTCCCTGGGGCA
GCAGCCACCATGTTCTCGTGTGTGAAGCCCTATGAGGACCAGAACTACTCAGCCCTGAGGCGGGACTGCCGGCGCAGGAAGGTGCTCTTC
GAGGACCCCCTCTTCCCCGCCACTGACGACTCACTCTACTATAAGGGCACGCCGGGGCCCGCCGTCAGGTGGAAGCGACCCAAGGGCATC
TGCGAGGACCCCCGCCTCTTTGTGGATGGCATCAGCTCCCACGACCTGCACCAGGGCCAGGTGGGCAACTGCTGGTTTGTGGCAGCCTGC
TCGTCACTTGCCTCCCGGGAGTCGCTGTGGCAAAAGGTGCTGTCCTGCACCAGTGGACAGAACGGCGGCTGGTGAACCACAAGCAGTACC
TGGAGGCCAAGAGGCTGTTGAAGGAGTTCCAGGCACGTTACCGGCAGCTGGTGAGTGGCTCTCTGCGCACAGTGTTCGGGACTACCCCGC
TCCCCATGGCCTGCCCAGCGCTGAGTGAGAGCCAGCCCAAGTTCGGCCACTTCCTCGAGTTCATGGATGAGTTCTGCCAGGAGCCCACAG
CCAGTGACTCACAAGGCTAGAGCTGTGCATGGGGGCTGTGTGCACCACCCGGCCTGTGCCCCAGCTCTCCCCGAGGGCTCTGTGCCCTGG
ACCGCACCTCAAGGTTGACCAGCCGGCCACAGGCCTCAGAGCTCAGCTGGGCCCCACTTGCTGGCCACAAGGTGGCATCCCCTTGTCAGG

>In-frame_ENST00000278559_ENST00000527087_TCGA-YG-AA3P-06A_CAPN5_chr11_76804859_-_XRRA1_chr11_74554498_length(amino acids)=153AA_start in transcript=63_stop in transcript=524
MLRRAAAASAPAPAPCPASREPGWTRGGSAGVPPPLPGAAATMFSCVKPYEDQNYSALRRDCRRRKVLFEDPLFPATDDSLYYKGTPGPA

--------------------------------------------------------------
>In-frame_ENST00000529629_ENST00000527087_TCGA-YG-AA3P-06A_CAPN5_chr11_76804859_-_XRRA1_chr11_74554498_length(transcript)=1009nt_BP=523nt
AGCTGGATCTCCGGCCAGAGCCCGAGGCTGCTGCGCCGGGCGGCTGCAGCCTCCGCTCCAGCGCCCGCGCCGTGCCCTGCATCCCGGGAG
CCCGGCTGGACCCGCGGCGGCTCGGCCGATGAGAATTCTGAAGCACAAAGAGGTTAACTGCTTTGCACCTCGCTGGCCTCAGTCTCCCCA
TCTGAGGACGGGTGTTCCCCCTCCCCTCCCTGGGGCAGCAGCCACCATGTTCTCGTGTGTGAAGCCCTATGAGGACCAGAACTACTCAGC
CCTGAGGCGGGACTGCCGGCGCAGGAAGGTGCTCTTCGAGGACCCCCTCTTCCCCGCCACTGACGACTCACTCTACTATAAGGGCACGCC
GGGGCCCGCCGTCAGGTGGAAGCGACCCAAGGGCATCTGCGAGGACCCCCGCCTCTTTGTGGATGGCATCAGCTCCCACGACCTGCACCA
GGGCCAGGTGGGCAACTGCTGGTTTGTGGCAGCCTGCTCGTCACTTGCCTCCCGGGAGTCGCTGTGGCAAAAGGTGCTGTCCTGCACCAG
TGGACAGAACGGCGGCTGGTGAACCACAAGCAGTACCTGGAGGCCAAGAGGCTGTTGAAGGAGTTCCAGGCACGTTACCGGCAGCTGGTG
AGTGGCTCTCTGCGCACAGTGTTCGGGACTACCCCGCTCCCCATGGCCTGCCCAGCGCTGAGTGAGAGCCAGCCCAAGTTCGGCCACTTC
CTCGAGTTCATGGATGAGTTCTGCCAGGAGCCCACAGCCAGTGACTCACAAGGCTAGAGCTGTGCATGGGGGCTGTGTGCACCACCCGGC
CTGTGCCCCAGCTCTCCCCGAGGGCTCTGTGCCCTGGACCGCACCTCAAGGTTGACCAGCCGGCCACAGGCCTCAGAGCTCAGCTGGGCC
CCACTTGCTGGCCACAAGGTGGCATCCCCTTGTCAGGATCTCCCCTCCTTGGCCCAGGCATGACCTGGTGCCTGGCCCAGCGGCAATAAA

>In-frame_ENST00000529629_ENST00000527087_TCGA-YG-AA3P-06A_CAPN5_chr11_76804859_-_XRRA1_chr11_74554498_length(amino acids)=172AA_start in transcript=43_stop in transcript=561
MQPPLQRPRRALHPGSPAGPAAARPMRILKHKEVNCFAPRWPQSPHLRTGVPPPLPGAAATMFSCVKPYEDQNYSALRRDCRRRKVLFED

--------------------------------------------------------------
>In-frame_ENST00000456580_ENST00000527087_TCGA-YG-AA3P-06A_CAPN5_chr11_76804859_-_XRRA1_chr11_74554498_length(transcript)=1040nt_BP=554nt
AGAGCCCGAGGCTGCTGCGCCGGGCGGCTGCAGCCTCCGCTCCAGCGCCCGCGCCGTGCCCTGCATCCCGGGAGCCCGGCTGGACCCGCG
GCGGCTCGGCCGGTGTTCCCCCTCCCCTCCCTGGGGCAGCAGCCACCATGTTCTCGTGTGTGAAGCCCTATGAGGACCAGAACTACTCAG
CCCTGAGGCGGGACTGCCGGCGCAGGAAGGTGCTCTTCGAGGACCCCCTCTTCCCCGCCACTGACGACTCACTCTACTATAAGGGCACGC
CGGGGCCCGCCGTCAGGTGGAAGCGACCCAAGTACAGTGGCCATTCGCTGGCCCCTCACAGGCCTGGCTGGGGAGATGCACGGAGAATGG
AGAATGTCCCCAGGCCTGGGAGCTCAGGGTGTCCGTCCTCCTCGCTCAGGGCCCGGGACCTGGGCATCTGCGAGGACCCCCGCCTCTTTG
TGGATGGCATCAGCTCCCACGACCTGCACCAGGGCCAGGTGGGCAACTGCTGGTTTGTGGCAGCCTGCTCGTCACTTGCCTCCCGGGAGT
CGCTGTGGCAAAAGGTGCTGTCCTGCACCAGTGGACAGAACGGCGGCTGGTGAACCACAAGCAGTACCTGGAGGCCAAGAGGCTGTTGAA
GGAGTTCCAGGCACGTTACCGGCAGCTGGTGAGTGGCTCTCTGCGCACAGTGTTCGGGACTACCCCGCTCCCCATGGCCTGCCCAGCGCT
GAGTGAGAGCCAGCCCAAGTTCGGCCACTTCCTCGAGTTCATGGATGAGTTCTGCCAGGAGCCCACAGCCAGTGACTCACAAGGCTAGAG
CTGTGCATGGGGGCTGTGTGCACCACCCGGCCTGTGCCCCAGCTCTCCCCGAGGGCTCTGTGCCCTGGACCGCACCTCAAGGTTGACCAG
CCGGCCACAGGCCTCAGAGCTCAGCTGGGCCCCACTTGCTGGCCACAAGGTGGCATCCCCTTGTCAGGATCTCCCCTCCTTGGCCCAGGC

>In-frame_ENST00000456580_ENST00000527087_TCGA-YG-AA3P-06A_CAPN5_chr11_76804859_-_XRRA1_chr11_74554498_length(amino acids)=193AA_start in transcript=11_stop in transcript=592
MLRRAAAASAPAPAPCPASREPGWTRGGSAGVPPPLPGAAATMFSCVKPYEDQNYSALRRDCRRRKVLFEDPLFPATDDSLYYKGTPGPA
VRWKRPKYSGHSLAPHRPGWGDARRMENVPRPGSSGCPSSSLRARDLGICEDPRLFVDGISSHDLHQGQVGNCWFVAACSSLASRESLWQ

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Fusion Gene PPI Analysis for CAPN5-XRRA1


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 CAPN5-XRRA1


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 CAPN5-XRRA1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCAPN5C0242852Proliferative vitreoretinopathy1CTD_human;ORPHANET;UNIPROT
HgeneCAPN5C4721549Autosomal dominant neovascular inflammatory vitreoretinopathy1ORPHANET