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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:CTSL-ZFR2 (FusionGDB2 ID:20528)

Fusion Gene Summary for CTSL-ZFR2

check button Fusion gene summary
Fusion gene informationFusion gene name: CTSL-ZFR2
Fusion gene ID: 20528
HgeneTgene
Gene symbol

CTSL

ZFR2

Gene ID

1514

23217

Gene namecathepsin Lzinc finger RNA binding protein 2
SynonymsCATL|CTSL1|MEPKIAA1086
Cytomap

9q21.33

19p13.3

Type of geneprotein-codingprotein-coding
Descriptioncathepsin L1major excreted proteinzinc finger RNA-binding protein 2
Modification date2020032020200313
UniProtAcc

P07711

.
Ensembl transtripts involved in fusion geneENST00000340342, ENST00000343150, 
ENST00000495822, ENST00000342020, 
ENST00000262961, ENST00000439086, 
ENST00000591712, ENST00000591965, 
ENST00000592398, 
Fusion gene scores* DoF score4 X 6 X 1=244 X 4 X 3=48
# samples 65
** MAII scorelog2(6/24*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(5/48*10)=0.0588936890535686
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CTSL [Title/Abstract] AND ZFR2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCTSL(90346304)-ZFR2(3845467), # 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
HgeneCTSL

GO:0006508

proteolysis

8811434|21326229

HgeneCTSL

GO:0030574

collagen catabolic process

22952693

HgeneCTSL

GO:0051603

proteolysis involved in cellular protein catabolic process

22952693


check buttonFusion gene breakpoints across CTSL (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 ZFR2 (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
ChiTaRS5.0N/ABC012612CTSLchr9

90346304

+ZFR2chr19

3845467

+


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Fusion Gene ORF analysis for CTSL-ZFR2

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-intronENST00000340342ENST00000262961CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000340342ENST00000439086CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000340342ENST00000591712CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000340342ENST00000591965CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000340342ENST00000592398CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000343150ENST00000262961CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000343150ENST00000439086CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000343150ENST00000591712CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000343150ENST00000591965CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000343150ENST00000592398CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000495822ENST00000262961CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000495822ENST00000439086CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000495822ENST00000591712CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000495822ENST00000591965CTSLchr9

90346304

+ZFR2chr19

3845467

+
5CDS-intronENST00000495822ENST00000592398CTSLchr9

90346304

+ZFR2chr19

3845467

+
intron-intronENST00000342020ENST00000262961CTSLchr9

90346304

+ZFR2chr19

3845467

+
intron-intronENST00000342020ENST00000439086CTSLchr9

90346304

+ZFR2chr19

3845467

+
intron-intronENST00000342020ENST00000591712CTSLchr9

90346304

+ZFR2chr19

3845467

+
intron-intronENST00000342020ENST00000591965CTSLchr9

90346304

+ZFR2chr19

3845467

+
intron-intronENST00000342020ENST00000592398CTSLchr9

90346304

+ZFR2chr19

3845467

+

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 CTSL-ZFR2


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 CTSL-ZFR2


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/:90346304/:3845467)
- 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
CTSL

P07711

.
FUNCTION: Thiol protease important for the overall degradation of proteins in lysosomes (Probable). Plays a critical for normal cellular functions such as general protein turnover, antigen processing and bone remodeling. Involved in the solubilization of cross-linked TG/thyroglobulin and in the subsequent release of thyroid hormone thyroxine (T4) by limited proteolysis of TG/thyroglobulin in the thyroid follicle lumen (By similarity). In neuroendocrine chromaffin cells secretory vesicles, catalyzes the prohormone proenkephalin processing to the active enkephalin peptide neurotransmitter (By similarity). In thymus, regulates CD4(+) T cell positive selection by generating the major histocompatibility complex class II (MHCII) bound peptide ligands presented by cortical thymic epithelial cells. Also mediates invariant chain processing in cortical thymic epithelial cells (By similarity). Major elastin-degrading enzyme at neutral pH. Accumulates as a mature and active enzyme in the extracellular space of antigen presenting cells (APCs) to regulate degradation of the extracellular matrix in the course of inflammation (By similarity). Secreted form generates endostatin from COL18A1 (PubMed:10716919). Critical for cardiac morphology and function. Plays an important role in hair follicle morphogenesis and cycling, as well as epidermal differentiation (By similarity). Required for maximal stimulation of steroidogenesis by TIMP1 (By similarity). {ECO:0000250|UniProtKB:P06797, ECO:0000250|UniProtKB:P07154, ECO:0000250|UniProtKB:P25975, ECO:0000269|PubMed:10716919, ECO:0000305}.; FUNCTION: [Isoform 2]: Functions in the regulation of cell cycle progression through proteolytic processing of the CUX1 transcription factor (PubMed:15099520). Translation initiation at downstream start sites allows the synthesis of isoforms that are devoid of a signal peptide and localize to the nucleus where they cleave the CUX1 transcription factor and modify its DNA binding properties (PubMed:15099520). {ECO:0000269|PubMed:15099520}.; FUNCTION: (Microbial infection) Facilitates human coronaviruses SARS-CoV and SARS-CoV-2 infections via proteolysis of coronavirus spike (S) glycoproteins in lysosome for entry into host cell (PubMed:32142651, PubMed:32221306, PubMed:16339146, PubMed:18562523). Proteolysis within lysosomes is sufficient to activate membrane fusion by coronaviruses SARS-CoV and EMC (HCoV-EMC) S as well as Zaire ebolavirus glycoproteins (PubMed:16081529, PubMed:26953343, PubMed:18562523). {ECO:0000269|PubMed:16081529, ECO:0000269|PubMed:16339146, ECO:0000269|PubMed:18562523, ECO:0000269|PubMed:26953343, ECO:0000269|PubMed:32142651, ECO:0000269|PubMed:32221306, ECO:0000269|PubMed:32855215}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 CTSL-ZFR2


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 CTSL-ZFR2


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 CTSL-ZFR2


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 CTSL-ZFR2


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