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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:CTSB-EIF4A2 (FusionGDB2 ID:20462)

Fusion Gene Summary for CTSB-EIF4A2

check button Fusion gene summary
Fusion gene informationFusion gene name: CTSB-EIF4A2
Fusion gene ID: 20462
HgeneTgene
Gene symbol

CTSB

EIF4A2

Gene ID

1508

1974

Gene namecathepsin Beukaryotic translation initiation factor 4A2
SynonymsAPPS|CPSB|RECEUPBM-010|DDX2B|EIF4A|EIF4F|eIF-4A-II|eIF4A-II
Cytomap

8p23.1

3q27.3

Type of geneprotein-codingprotein-coding
Descriptioncathepsin BAPP secretaseamyloid precursor protein secretasecathepsin B1cysteine proteaseepididymis secretory sperm binding proteineukaryotic initiation factor 4A-IIATP-dependent RNA helicase eIF4A-2
Modification date2020031320200322
UniProtAcc

P07858

Q14240

Ensembl transtripts involved in fusion geneENST00000530640, ENST00000345125, 
ENST00000353047, ENST00000415599, 
ENST00000434271, ENST00000453527, 
ENST00000525076, ENST00000531089, 
ENST00000533455, ENST00000534510, 
ENST00000356531, ENST00000440191, 
ENST00000323963, 
Fusion gene scores* DoF score24 X 19 X 10=456013 X 14 X 6=1092
# samples 2516
** MAII scorelog2(25/4560*10)=-4.18903382439002
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1092*10)=-2.77082904603249
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CTSB [Title/Abstract] AND EIF4A2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCTSB(11701564)-EIF4A2(186501336), # 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
HgeneCTSB

GO:0006508

proteolysis

7890620|8811434

HgeneCTSB

GO:0030574

collagen catabolic process

22952693

HgeneCTSB

GO:0051603

proteolysis involved in cellular protein catabolic process

22952693

TgeneEIF4A2

GO:1900260

negative regulation of RNA-directed 5'-3' RNA polymerase activity

11922617


check buttonFusion gene breakpoints across CTSB (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 EIF4A2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4THCATCGA-DJ-A3V6-01ACTSBchr8

11701564

-EIF4A2chr3

186501336

+
ChimerDB4THCATCGA-DJ-A3VM-01ACTSBchr8

11701564

-EIF4A2chr3

186501336

+
ChimerDB4THCATCGA-ET-A40Q-01ACTSBchr8

11701564

-EIF4A2chr3

186501336

+


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Fusion Gene ORF analysis for CTSB-EIF4A2

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-intronENST00000530640ENST00000356531CTSBchr8

11701564

-EIF4A2chr3

186501336

+
5CDS-intronENST00000530640ENST00000440191CTSBchr8

11701564

-EIF4A2chr3

186501336

+
In-frameENST00000530640ENST00000323963CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-3CDSENST00000345125ENST00000323963CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-3CDSENST00000353047ENST00000323963CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-3CDSENST00000415599ENST00000323963CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-3CDSENST00000434271ENST00000323963CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-3CDSENST00000453527ENST00000323963CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-3CDSENST00000525076ENST00000323963CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-3CDSENST00000531089ENST00000323963CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-3CDSENST00000533455ENST00000323963CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-3CDSENST00000534510ENST00000323963CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000345125ENST00000356531CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000345125ENST00000440191CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000353047ENST00000356531CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000353047ENST00000440191CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000415599ENST00000356531CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000415599ENST00000440191CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000434271ENST00000356531CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000434271ENST00000440191CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000453527ENST00000356531CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000453527ENST00000440191CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000525076ENST00000356531CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000525076ENST00000440191CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000531089ENST00000356531CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000531089ENST00000440191CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000533455ENST00000356531CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000533455ENST00000440191CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000534510ENST00000356531CTSBchr8

11701564

-EIF4A2chr3

186501336

+
intron-intronENST00000534510ENST00000440191CTSBchr8

11701564

-EIF4A2chr3

186501336

+

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)
ENST00000530640CTSBchr811701564-ENST00000323963EIF4A2chr3186501336+3308138914532676407

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
ENST00000530640ENST00000323963CTSBchr811701564-EIF4A2chr3186501336+0.0010664410.9989335

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Fusion Genomic Features for CTSB-EIF4A2


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)
CTSBchr811701561-EIF4A2chr3186501335+0.042747370.9572527
CTSBchr811701561-EIF4A2chr3186501335+0.042747370.9572527

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.
genomic feature

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.
genomic feature of top 1%

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Fusion Protein Features for CTSB-EIF4A2


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/chr8:11701564/chr3:186501336)
- 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
CTSB

P07858

EIF4A2

Q14240

FUNCTION: Thiol protease which is believed to participate in intracellular degradation and turnover of proteins (PubMed:12220505). Cleaves matrix extracellular phosphoglycoprotein MEPE (PubMed:12220505). Involved in the solubilization of cross-linked TG/thyroglobulin in the thyroid follicle lumen (By similarity). Has also been implicated in tumor invasion and metastasis (PubMed:3972105). {ECO:0000250|UniProtKB:P10605, ECO:0000269|PubMed:12220505, ECO:0000269|PubMed:3972105}.FUNCTION: ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.

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
TgeneEIF4A2chr8:11701564chr3:186501336ENST00000323963-111246_4079408.0DomainHelicase C-terminal
TgeneEIF4A2chr8:11701564chr3:186501336ENST00000323963-11164_2359408.0DomainHelicase ATP-binding
TgeneEIF4A2chr8:11701564chr3:186501336ENST00000440191011246_4070409.0DomainHelicase C-terminal
TgeneEIF4A2chr8:11701564chr3:186501336ENST0000044019101164_2350409.0DomainHelicase ATP-binding
TgeneEIF4A2chr8:11701564chr3:186501336ENST00000323963-111183_1869408.0MotifNote=DEAD box
TgeneEIF4A2chr8:11701564chr3:186501336ENST00000323963-11133_619408.0MotifNote=Q motif
TgeneEIF4A2chr8:11701564chr3:186501336ENST00000440191011183_1860409.0MotifNote=DEAD box
TgeneEIF4A2chr8:11701564chr3:186501336ENST0000044019101133_610409.0MotifNote=Q motif
TgeneEIF4A2chr8:11701564chr3:186501336ENST00000323963-11177_849408.0Nucleotide bindingATP
TgeneEIF4A2chr8:11701564chr3:186501336ENST0000044019101177_840409.0Nucleotide bindingATP

- 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 CTSB-EIF4A2


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.
>20462_20462_1_CTSB-EIF4A2_CTSB_chr8_11701564_ENST00000530640_EIF4A2_chr3_186501336_ENST00000323963_length(transcript)=3308nt_BP=1389nt
GGCCGGGGCTGGCCCAGGCTACGGCGGCTGCAGGGCTCCGGCAACCGCTCCGGCAACGCCAACCGCTCCGCTGCGCGCAGGCTGGGCTGC
AGGCTCTCGGCTGCAGCGCTGGGTGGATCTAGGATCCGGCTTCCAACATGTGGCAGCTCTGGGCCTCCCTCTGCTGCCTGCTGGTGTTGG
CCAATGCCCGGAGCAGGCCCTCTTTCCATCCCCTGTCGGATGAGCTGGTCAACTATGTCAACAAACGGAATACCACGTGGCAGGCCGGGC
ACAACTTCTACAACGTGGACATGAGCTACTTGAAGAGGCTATGTGGTACCTTCCTGGGTGGGCCCAAGCCACCCCAGAGAGTTATGTTTA
CCGAGGACCTGAAGCTGCCTGCAAGCTTCGATGCACGGGAACAATGGCCACAGTGTCCCACCATCAAAGAGATCAGAGACCAGGGCTCCT
GTGGCTCCTGCTGGGCCTTCGGGGCTGTGGAAGCCATCTCTGACCGGATCTGCATCCACACCAATGCGCACGTCAGCGTGGAGGTGTCGG
CGGAGGACCTGCTCACATGCTGTGGCAGCATGTGTGGGGACGGCTGTAATGGTGGCTATCCTGCTGAAGCTTGGAACTTCTGGACAAGAA
AAGGCCTGGTTTCTGGTGGCCTCTATGAATCCCATGTAGGGTGCAGACCGTACTCCATCCCTCCCTGTGAGCACCACGTCAACGGCTCCC
GGCCCCCATGCACGGGGGAGGGAGATACCCCCAAGTGTAGCAAGATCTGTGAGCCTGGCTACAGCCCGACCTACAAACAGGACAAGCACT
ACGGATACAATTCCTACAGCGTCTCCAATAGCGAGAAGGACATCATGGCCGAGATCTACAAAAACGGCCCCGTGGAGGGAGCTTTCTCTG
TGTATTCGGACTTCCTGCTCTACAAGTCAGGAGTGTACCAACACGTCACCGGAGAGATGATGGGTGGCCATGCCATCCGCATCCTGGGCT
GGGGAGTGGAGAATGGCACACCCTACTGGCTGGTTGCCAACTCCTGGAACACTGACTGGGGTGACAATGGCTTCTTTAAAATACTCAGAG
GACAGGATCACTGTGGAATCGAATCAGAAGTGGTGGCTGGAATTCCACGCACCGATCAGTACTGGGAAAAGATCTAATCTGCCGTGGGCC
TGTCGTGCCAGTCCTGGGGGCGAGATCGGGAGAATCACGTCCTGGAACTGCATGTTCTTGCGACTCTTGGGACTTCATCTTAACTTCTCG
CTGCCCCAGCCATGTTTTCAACCATGGCATCCCTCCCCCAATTAGTTCCCTGTCATCCTCGTCAACCTTCTCTGTAAGTGCCTGGTAAGC
TTGCCCTTGCTTAAGAACTCAAAACATAGCTGTGCTCTATATAAAAAACGGGTGGTTGGGCGCCGCTGTCTTTTCAGTCGGGCGCTGAGT
GGTTTTTCGGATCATGTCTGGTGGCTCCGCGGATTATAACAGAGAACATGGCGGCCCAGAGGGAATGGACCCCGATGGTGTCATCGAGAG
CAACTGGAATGAGATTGTTGATAACTTTGATGATATGAATTTAAAGGAGTCTCTCCTTCGTGGCATCTATGCTTACGGTTTTGAGAAGCC
TTCCGCTATTCAGCAGAGAGCTATTATTCCCTGTATTAAAGGGTATGATGTGATTGCTCAAGCTCAGTCAGGTACTGGCAAGACAGCCAC
ATTTGCTATTTCCATCCTGCAACAGTTGGAGATTGAGTTCAAGGAGACCCAAGCACTAGTATTGGCCCCCACCAGAGAACTGGCTCAACA
GATCCAAAAGGTAATTCTGGCACTTGGAGACTATATGGGAGCCACTTGTCATGCCTGCATTGGTGGAACAAATGTTCGAAATGAAATGCA
AAAACTGCAGGCTGAAGCACCACATATTGTTGTTGGTACACCCGGGAGAGTGTTTGATATGTTAAACAGAAGATACCTTTCTCCAAAATG
GATCAAAATGTTTGTTTTGGATGAAGCAGATGAAATGTTGAGCCGTGGTTTTAAGGATCAAATCTATGAGATTTTCCAAAAACTAAACAC
AAGTATTCAGGTTGTGTTGCTTTCTGCCACAATGCCAACTGATGTGTTGGAAGTGACCAAAAAATTCATGAGAGATCCAATTCGAATTCT
GGTGAAAAAGGAAGAATTGACCCTTGAAGGAATCAAACAGTTTTATATTAATGTTGAGAGAGAGGAATGGAAGTTGGATACACTTTGTGA
CTTGTACGAGACACTGACCATTACACAGGCTGTTATTTTTCTCAATACGAGGCGCAAGGTGGACTGGCTGACTGAGAAGATGCATGCCAG
AGACTTCACAGTTTCTGCTCTGCATGGTGACATGGACCAGAAGGAGAGAGATGTTATCATGAGGGAATTCCGGTCAGGGTCAAGTCGTGT
TCTGATCACTACTGACTTGTTGGCTCGCGGGATTGATGTGCAACAAGTGTCTTTGGTTATAAATTATGATCTACCTACCAATCGTGAAAA
CTATATTCACAGAATTGGCAGAGGGGGTCGATTTGGGAGGAAAGGTGTGGCTATAAACTTTGTTACTGAAGAAGACAAGAGGATTCTTCG
TGACATTGAGACTTTCTACAATACTACAGTGGAGGAGATGCCCATGAATGTGGCTGACCTTATTTAATTCCTGGGATGAGAGTTTTGGAT
GCAGTGCTCGCTGTTGCTGAATAGGCGATCACAACGTGCATTGTGCTTCTTTCTTTGGGAATATTTGAATCTTGTCTCAATGCTCATAAC
GGATCAGAAATACAGATTTTGATAGCAAAGCGACGTTAGTCGTGAGCTCTTGTGAGGAAAGTCATTGGCTTTATCCTCTTTAGAGTTAGA
CTGTTGGGGTGGGTATAAAAGATGGGGTCTGTAAAATCTTTCTTTCTTAGAAATTTATTTCCTAGTTCTGTAGAAATGGTTGTATTAGAT
GTTCTCTATCATTTAATAATATACTTGTGGACTAAAAGATATAAGTGCTGTATAAAATCAGCCAATTATGTTAAACTAGCATATCTGCCT
TTATTGTGTTTGTCATTAGCCTGAGTAGAAAGGCCTTTAAAATTTTTTTAGAAAGCATTTGAATGCATTTTGTTTGGTATTGTATTTATT
CAATAAAGTATTTAATTAGTGCTAAGTGTGAACTGGACCCTGTTGCTAAGCCCCAGCAAGCAATCCTAGGTAGGGTTTAATCCCCAGTAA

>20462_20462_1_CTSB-EIF4A2_CTSB_chr8_11701564_ENST00000530640_EIF4A2_chr3_186501336_ENST00000323963_length(amino acids)=407AA_BP=
MSGGSADYNREHGGPEGMDPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAIS
ILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMF
VLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYET
LTITQAVIFLNTRRKVDWLTEKMHARDFTVSALHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHR

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Fusion Gene PPI Analysis for CTSB-EIF4A2


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 CTSB-EIF4A2


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 CTSB-EIF4A2


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