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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:CDK5RAP1-ZMIZ2 (FusionGDB2 ID:15266)

Fusion Gene Summary for CDK5RAP1-ZMIZ2

check button Fusion gene summary
Fusion gene informationFusion gene name: CDK5RAP1-ZMIZ2
Fusion gene ID: 15266
HgeneTgene
Gene symbol

CDK5RAP1

ZMIZ2

Gene ID

51654

83637

Gene nameCDK5 regulatory subunit associated protein 1zinc finger MIZ-type containing 2
SynonymsC20orf34|C42|CGI-05|HSPC167NET27|TRAFIP20|ZIMP7|hZIMP7
Cytomap

20q11.21

7p13

Type of geneprotein-codingprotein-coding
DescriptionCDK5 regulatory subunit-associated protein 1CDK5 activator-binding protein C42zinc finger MIZ domain-containing protein 2PIAS-like protein Zimp7
Modification date2020031320200313
UniProtAcc

Q96SZ6

.
Ensembl transtripts involved in fusion geneENST00000339269, ENST00000346416, 
ENST00000357886, ENST00000473997, 
ENST00000477105, ENST00000544843, 
ENST00000265346, ENST00000309315, 
ENST00000413916, ENST00000433667, 
ENST00000441627, ENST00000463931, 
Fusion gene scores* DoF score7 X 6 X 5=2102 X 2 X 2=8
# samples 72
** MAII scorelog2(7/210*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/8*10)=1.32192809488736
Context

PubMed: CDK5RAP1 [Title/Abstract] AND ZMIZ2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDK5RAP1(31989234)-ZMIZ2(44798880), # 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
HgeneCDK5RAP1

GO:0045736

negative regulation of cyclin-dependent protein serine/threonine kinase activity

11882646

TgeneZMIZ2

GO:0007179

transforming growth factor beta receptor signaling pathway

16777850

TgeneZMIZ2

GO:0045944

positive regulation of transcription by RNA polymerase II

16051670

TgeneZMIZ2

GO:0060395

SMAD protein signal transduction

16777850


check buttonFusion gene breakpoints across CDK5RAP1 (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 ZMIZ2 (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
ChimerDB4BRCATCGA-BH-A0DI-01ACDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+


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Fusion Gene ORF analysis for CDK5RAP1-ZMIZ2

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
5UTR-3CDSENST00000339269ENST00000265346CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000339269ENST00000309315CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000339269ENST00000413916CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000339269ENST00000433667CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000339269ENST00000441627CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000346416ENST00000265346CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000346416ENST00000309315CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000346416ENST00000413916CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000346416ENST00000433667CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000346416ENST00000441627CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000357886ENST00000265346CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000357886ENST00000309315CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000357886ENST00000413916CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000357886ENST00000433667CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000357886ENST00000441627CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000473997ENST00000265346CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000473997ENST00000309315CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000473997ENST00000413916CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000473997ENST00000433667CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000473997ENST00000441627CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000477105ENST00000265346CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000477105ENST00000309315CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000477105ENST00000413916CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000477105ENST00000433667CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000477105ENST00000441627CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000544843ENST00000265346CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000544843ENST00000309315CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000544843ENST00000413916CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000544843ENST00000433667CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-3CDSENST00000544843ENST00000441627CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-intronENST00000339269ENST00000463931CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-intronENST00000346416ENST00000463931CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-intronENST00000357886ENST00000463931CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-intronENST00000473997ENST00000463931CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-intronENST00000477105ENST00000463931CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+
5UTR-intronENST00000544843ENST00000463931CDK5RAP1chr20

31989234

-ZMIZ2chr7

44798880

+

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 CDK5RAP1-ZMIZ2


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)
CDK5RAP1chr2031989233-ZMIZ2chr744798879+5.07E-081
CDK5RAP1chr2031989233-ZMIZ2chr744798879+5.07E-081

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.
genomic feature of top 1%

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Fusion Protein Features for CDK5RAP1-ZMIZ2


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/:31989234/:44798880)
- 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
CDK5RAP1

Q96SZ6

.
FUNCTION: Methylthiotransferase that catalyzes the conversion of N6-(dimethylallyl)adenosine (i(6)A) to 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 (adjacent to the 3'-end of the anticodon) of four mitochondrial DNA-encoded tRNAs (Ser(UCN), Phe, Tyr and Trp) (PubMed:22422838, PubMed:25738458, PubMed:28981754). Essential for efficient and highly accurate protein translation by the ribosome (PubMed:22422838, PubMed:25738458, PubMed:28981754). Specifically inhibits CDK5 activation by CDK5R1 (PubMed:11882646). Essential for efficient mitochondrial protein synthesis and respiratory chain; shows pathological consequences in mitochondrial disease (PubMed:25738458). {ECO:0000269|PubMed:11882646, ECO:0000269|PubMed:22422838, ECO:0000269|PubMed:25738458, ECO:0000269|PubMed:28981754}.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 CDK5RAP1-ZMIZ2


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 CDK5RAP1-ZMIZ2


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 CDK5RAP1-ZMIZ2


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 CDK5RAP1-ZMIZ2


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