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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:CAPN5-ACER3 (FusionGDB2 ID:12885)

Fusion Gene Summary for CAPN5-ACER3

Fusion gene summary

Fusion gene information	Fusion gene name: CAPN5-ACER3
	Fusion gene ID: 12885
		Hgene	Tgene
	Gene symbol	CAPN5	ACER3
	Gene ID	726	55331
	Gene name	calpain 5	alkaline ceramidase 3
	Synonyms	ADNIV\|HTRA3\|VRNI\|nCL-3	APHC\|PHCA\|PLDECO
	Cytomap	11q13.5	11q13.5
	Type of gene	protein-coding	protein-coding
	Description	calpain-5calpain htra-3new calpain 3testis tissue sperm-binding protein Li 91mP	alkaline ceramidase 3alkCDase 3alkaline CDase 3alkaline dihydroceramidase SB89alkaline phytoceramidasephytoceramidase, alkaline
	Modification date	20200313	20200320
	UniProtAcc	O15484	Q9NUN7
	Ensembl transtripts involved in fusion gene	ENST00000278559, ENST00000456580, ENST00000529629, ENST00000531028,	ENST00000532485, ENST00000530182, ENST00000526597, ENST00000533873, ENST00000538157, ENST00000544113,
Fusion gene scores	* DoF score	8 X 5 X 5=200	13 X 10 X 5=650
	# samples	8	15
	** MAII score	log2(8/200*10)=-1.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/650*10)=-2.11547721741994 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: CAPN5 [Title/Abstract] AND ACER3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	CAPN5(76778141)-ACER3(76687332), # 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	ACER3	GO:0043067	regulation of programmed cell death	20068046
Tgene	ACER3	GO:0046512	sphingosine biosynthetic process	20068046
Tgene	ACER3	GO:0046514	ceramide catabolic process	30575723
Tgene	ACER3	GO:0071602	phytosphingosine biosynthetic process	11356846\|20068046

Fusion 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.

Fusion gene breakpoints across ACER3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	STAD	TCGA-IN-AB1V	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+

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Fusion Gene ORF analysis for CAPN5-ACER3

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5UTR-3CDS	ENST00000278559	ENST00000532485	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-3CDS	ENST00000456580	ENST00000532485	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-3CDS	ENST00000529629	ENST00000532485	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-3CDS	ENST00000531028	ENST00000532485	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-3UTR	ENST00000278559	ENST00000530182	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-3UTR	ENST00000456580	ENST00000530182	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-3UTR	ENST00000529629	ENST00000530182	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-3UTR	ENST00000531028	ENST00000530182	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000278559	ENST00000526597	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000278559	ENST00000533873	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000278559	ENST00000538157	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000456580	ENST00000526597	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000456580	ENST00000533873	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000456580	ENST00000538157	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000529629	ENST00000526597	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000529629	ENST00000533873	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000529629	ENST00000538157	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000531028	ENST00000526597	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000531028	ENST00000533873	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-5UTR	ENST00000531028	ENST00000538157	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-intron	ENST00000278559	ENST00000544113	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-intron	ENST00000456580	ENST00000544113	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-intron	ENST00000529629	ENST00000544113	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+
5UTR-intron	ENST00000531028	ENST00000544113	CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

DeepORF 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.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for CAPN5-ACER3

FusionAI 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.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+	0.025649808	0.9743502
CAPN5	chr11	76778141	+	ACER3	chr11	76687332	+	0.025649808	0.9743502

Distribution 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.

Distribution 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-ACER3

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:76778141/:76687332)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
CAPN5 O15484	ACER3 Q9NUN7
FUNCTION: Calcium-regulated non-lysosomal thiol-protease. {ECO:0000250}.	FUNCTION: Endoplasmic reticulum and Golgi ceramidase that catalyzes the hydrolysis of unsaturated long-chain C18:1-, C20:1- and C20:4-ceramides, dihydroceramides and phytoceramides into sphingoid bases like sphingosine and free fatty acids at alkaline pH (PubMed:20068046, PubMed:26792856, PubMed:20207939, PubMed:11356846, PubMed:30575723). Ceramides, sphingosine, and its phosphorylated form sphingosine-1-phosphate are bioactive lipids that mediate cellular signaling pathways regulating several biological processes including cell proliferation, apoptosis and differentiation (PubMed:20068046). Controls the generation of sphingosine in erythrocytes, and thereby sphingosine-1-phosphate in plasma (PubMed:20207939). Through the regulation of ceramides and sphingosine-1-phosphate homeostasis in the brain may play a role in neurons survival and function (By similarity). By regulating the levels of proinflammatory ceramides in immune cells and tissues, may modulate the inflammatory response (By similarity). {ECO:0000250\|UniProtKB:Q9D099, ECO:0000269\|PubMed:11356846, ECO:0000269\|PubMed:20068046, ECO:0000269\|PubMed:20207939, ECO:0000269\|PubMed:26792856, ECO:0000269\|PubMed:30575723, ECO:0000303\|PubMed:20068046}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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Fusion Gene Sequence for CAPN5-ACER3

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 CAPN5-ACER3

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for CAPN5-ACER3

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for CAPN5-ACER3

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source