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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:CDK5RAP1-CDH4

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CDK5RAP1-CDH4
FusionPDB ID: 15260
FusionGDB2.0 ID: 15260
HgeneTgene
Gene symbol

CDK5RAP1

CDH4

Gene ID

51654

1002

Gene nameCDK5 regulatory subunit associated protein 1cadherin 4
SynonymsC20orf34|C42|CGI-05|HSPC167CAD4|R-CAD|RCAD
Cytomap

20q11.21

20q13.33

Type of geneprotein-codingprotein-coding
DescriptionCDK5 regulatory subunit-associated protein 1CDK5 activator-binding protein C42cadherin-4R-cadherincadherin 4, type 1, R-cadherin (retinal)cadherin 4, type 1, preproproteinretinal cadherin
Modification date2020031320200313
UniProtAcc

Q96SZ6

P55283

Ensembl transtripts involved in fusion geneENST idsENST00000477105, ENST00000473997, 
ENST00000346416, ENST00000357886, 
ENST00000544843, ENST00000339269, 
ENST00000360469, ENST00000543233, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 6 X 5=21016 X 14 X 7=1568
# samples 721
** MAII scorelog2(7/210*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(21/1568*10)=-2.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: CDK5RAP1 [Title/Abstract] AND CDH4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CDK5RAP1(31967267)-CDH4(60503248), # samples:1
Anticipated loss of major functional domain due to fusion event.CDK5RAP1-CDH4 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CDK5RAP1-CDH4 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CDK5RAP1-CDH4 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
CDK5RAP1-CDH4 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
CDK5RAP1-CDH4 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CDK5RAP1-CDH4 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
CDK5RAP1-CDH4 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
* 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


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.
all structure

check buttonFusion gene breakpoints across CDH4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4LUADTCGA-75-6211-01ACDK5RAP1chr20

31967267

-CDH4chr20

60503248

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000346416CDK5RAP1chr2031967267-ENST00000360469CDH4chr2060503248+591312611421374410
ENST00000346416CDK5RAP1chr2031967267-ENST00000543233CDH4chr2060503248+254712611421374410
ENST00000357886CDK5RAP1chr2031967267-ENST00000360469CDH4chr2060503248+595513031421416424
ENST00000357886CDK5RAP1chr2031967267-ENST00000543233CDH4chr2060503248+258913031421416424
ENST00000544843CDK5RAP1chr2031967267-ENST00000360469CDH4chr2060503248+587112191001332410
ENST00000544843CDK5RAP1chr2031967267-ENST00000543233CDH4chr2060503248+250512191001332410

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
ENST00000346416ENST00000360469CDK5RAP1chr2031967267-CDH4chr2060503248+0.0528756450.9471243
ENST00000346416ENST00000543233CDK5RAP1chr2031967267-CDH4chr2060503248+0.033640420.96635956
ENST00000357886ENST00000360469CDK5RAP1chr2031967267-CDH4chr2060503248+0.0591409020.94085914
ENST00000357886ENST00000543233CDK5RAP1chr2031967267-CDH4chr2060503248+0.045391930.9546081
ENST00000544843ENST00000360469CDK5RAP1chr2031967267-CDH4chr2060503248+0.0527404550.9472595
ENST00000544843ENST00000543233CDK5RAP1chr2031967267-CDH4chr2060503248+0.037573150.9624269

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>15260_15260_1_CDK5RAP1-CDH4_CDK5RAP1_chr20_31967267_ENST00000346416_CDH4_chr20_60503248_ENST00000360469_length(amino acids)=410AA_BP=373
MFSAMHPLQCVLQVQRSLGWGPLASVSWLSLRMCRAHSSLSSTMCPSPERQEDGARKDFSSRLAAGPTFQHFLKSASAPQEKLSSEVEDP
PPYLMMDELLGRQRKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKALKTRRPRSRVPL
RIGILGCMAERLKEEILNREKMVDILAGPDAYRDLPRLLAVAESGQQAANVLLSLDETYADVMPVQTSASATSAFVSIMRGCDNMCSYCI
VPFTRGRERSRPIASILEEVKKLSEQGLKEVTLLGQNVNSFRDNSEVQFNSAVPTNLSRGFTTNYKTKQGGLRFAHLLDQVSRVDPEMRI

--------------------------------------------------------------

>15260_15260_2_CDK5RAP1-CDH4_CDK5RAP1_chr20_31967267_ENST00000346416_CDH4_chr20_60503248_ENST00000543233_length(amino acids)=410AA_BP=373
MFSAMHPLQCVLQVQRSLGWGPLASVSWLSLRMCRAHSSLSSTMCPSPERQEDGARKDFSSRLAAGPTFQHFLKSASAPQEKLSSEVEDP
PPYLMMDELLGRQRKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKALKTRRPRSRVPL
RIGILGCMAERLKEEILNREKMVDILAGPDAYRDLPRLLAVAESGQQAANVLLSLDETYADVMPVQTSASATSAFVSIMRGCDNMCSYCI
VPFTRGRERSRPIASILEEVKKLSEQGLKEVTLLGQNVNSFRDNSEVQFNSAVPTNLSRGFTTNYKTKQGGLRFAHLLDQVSRVDPEMRI

--------------------------------------------------------------

>15260_15260_3_CDK5RAP1-CDH4_CDK5RAP1_chr20_31967267_ENST00000357886_CDH4_chr20_60503248_ENST00000360469_length(amino acids)=424AA_BP=387
MFSAMHPLQCVLQVQRSLGWGPLASVSWLSLRMCRAHSSLSSTMCPSPERQEDGARKDFSSRLAAGPTFQHFLKSASAPQEKLSSEVEDP
PPYLMMDELLGRQRKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKALKTRRPRSRVPL
RIGILGCMAERLKEEILNREKMVDILAGPDAYRDLPRLLAVAESGQQAANVLLSLDETYADVMPVQTSASATSAFVSIMRGCDNMCSYCI
VPFTRGRERSRPIASILEEVKKLSEQVFLPPRPPKVLGLQGLKEVTLLGQNVNSFRDNSEVQFNSAVPTNLSRGFTTNYKTKQGGLRFAH

--------------------------------------------------------------

>15260_15260_4_CDK5RAP1-CDH4_CDK5RAP1_chr20_31967267_ENST00000357886_CDH4_chr20_60503248_ENST00000543233_length(amino acids)=424AA_BP=387
MFSAMHPLQCVLQVQRSLGWGPLASVSWLSLRMCRAHSSLSSTMCPSPERQEDGARKDFSSRLAAGPTFQHFLKSASAPQEKLSSEVEDP
PPYLMMDELLGRQRKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKALKTRRPRSRVPL
RIGILGCMAERLKEEILNREKMVDILAGPDAYRDLPRLLAVAESGQQAANVLLSLDETYADVMPVQTSASATSAFVSIMRGCDNMCSYCI
VPFTRGRERSRPIASILEEVKKLSEQVFLPPRPPKVLGLQGLKEVTLLGQNVNSFRDNSEVQFNSAVPTNLSRGFTTNYKTKQGGLRFAH

--------------------------------------------------------------

>15260_15260_5_CDK5RAP1-CDH4_CDK5RAP1_chr20_31967267_ENST00000544843_CDH4_chr20_60503248_ENST00000360469_length(amino acids)=410AA_BP=373
MFSAMHPLQCVLQVQRSLGWGPLASVSWLSLRMCRAHSSLSSTMCPSPERQEDGARKDFSSRLAAGPTFQHFLKSASAPQEKLSSEVEDP
PPYLMMDELLGRQRKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKALKTRRPRSRVPL
RIGILGCMAERLKEEILNREKMVDILAGPDAYRDLPRLLAVAESGQQAANVLLSLDETYADVMPVQTSASATSAFVSIMRGCDNMCSYCI
VPFTRGRERSRPIASILEEVKKLSEQGLKEVTLLGQNVNSFRDNSEVQFNSAVPTNLSRGFTTNYKTKQGGLRFAHLLDQVSRVDPEMRI

--------------------------------------------------------------

>15260_15260_6_CDK5RAP1-CDH4_CDK5RAP1_chr20_31967267_ENST00000544843_CDH4_chr20_60503248_ENST00000543233_length(amino acids)=410AA_BP=373
MFSAMHPLQCVLQVQRSLGWGPLASVSWLSLRMCRAHSSLSSTMCPSPERQEDGARKDFSSRLAAGPTFQHFLKSASAPQEKLSSEVEDP
PPYLMMDELLGRQRKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKALKTRRPRSRVPL
RIGILGCMAERLKEEILNREKMVDILAGPDAYRDLPRLLAVAESGQQAANVLLSLDETYADVMPVQTSASATSAFVSIMRGCDNMCSYCI
VPFTRGRERSRPIASILEEVKKLSEQGLKEVTLLGQNVNSFRDNSEVQFNSAVPTNLSRGFTTNYKTKQGGLRFAHLLDQVSRVDPEMRI

--------------------------------------------------------------

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Fusion Protein Functional Features


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/chr20:31967267/chr20:60503248)
- 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

CDH4

P55283

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: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. May play an important role in retinal development.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000346416-814100_220369.0588.0DomainMTTase N-terminal
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000357886-915100_220383.0602.0DomainMTTase N-terminal
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000544843-812100_220369.0427.6666666666667DomainMTTase N-terminal
TgeneCDH4chr20:31967267chr20:60503248ENST000003604691016873_888590.3333333333334917.0Compositional biasNote=Ser-rich
TgeneCDH4chr20:31967267chr20:60503248ENST00000543233915873_888516.3333333333334843.0Compositional biasNote=Ser-rich
TgeneCDH4chr20:31967267chr20:60503248ENST000003604691016614_724590.3333333333334917.0DomainCadherin 5
TgeneCDH4chr20:31967267chr20:60503248ENST00000543233915614_724516.3333333333334843.0DomainCadherin 5
TgeneCDH4chr20:31967267chr20:60503248ENST000003604691016757_916590.3333333333334917.0Topological domainCytoplasmic
TgeneCDH4chr20:31967267chr20:60503248ENST00000543233915757_916516.3333333333334843.0Topological domainCytoplasmic
TgeneCDH4chr20:31967267chr20:60503248ENST000003604691016735_756590.3333333333334917.0TransmembraneHelical
TgeneCDH4chr20:31967267chr20:60503248ENST00000543233915735_756516.3333333333334843.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000339269-113100_2200511.0DomainMTTase N-terminal
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000339269-113244_5120511.0DomainRadical SAM core
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000339269-113515_5900511.0DomainTRAM
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000346416-814244_512369.0588.0DomainRadical SAM core
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000346416-814515_590369.0588.0DomainTRAM
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000357886-915244_512383.0602.0DomainRadical SAM core
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000357886-915515_590383.0602.0DomainTRAM
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000544843-812244_512369.0427.6666666666667DomainRadical SAM core
HgeneCDK5RAP1chr20:31967267chr20:60503248ENST00000544843-812515_590369.0427.6666666666667DomainTRAM
TgeneCDH4chr20:31967267chr20:60503248ENST000003604691016170_277590.3333333333334917.0DomainCadherin 1
TgeneCDH4chr20:31967267chr20:60503248ENST000003604691016278_392590.3333333333334917.0DomainCadherin 2
TgeneCDH4chr20:31967267chr20:60503248ENST000003604691016393_507590.3333333333334917.0DomainCadherin 3
TgeneCDH4chr20:31967267chr20:60503248ENST000003604691016508_613590.3333333333334917.0DomainCadherin 4
TgeneCDH4chr20:31967267chr20:60503248ENST00000543233915170_277516.3333333333334843.0DomainCadherin 1
TgeneCDH4chr20:31967267chr20:60503248ENST00000543233915278_392516.3333333333334843.0DomainCadherin 2
TgeneCDH4chr20:31967267chr20:60503248ENST00000543233915393_507516.3333333333334843.0DomainCadherin 3
TgeneCDH4chr20:31967267chr20:60503248ENST00000543233915508_613516.3333333333334843.0DomainCadherin 4
TgeneCDH4chr20:31967267chr20:60503248ENST000003604691016170_734590.3333333333334917.0Topological domainExtracellular
TgeneCDH4chr20:31967267chr20:60503248ENST00000543233915170_734516.3333333333334843.0Topological domainExtracellular


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
CDK5RAP1
CDH4


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to CDK5RAP1-CDH4


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to CDK5RAP1-CDH4


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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