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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:CDK15-GOLGA4 (FusionGDB2 ID:15189)

Fusion Gene Summary for CDK15-GOLGA4

check button Fusion gene summary
Fusion gene informationFusion gene name: CDK15-GOLGA4
Fusion gene ID: 15189
HgeneTgene
Gene symbol

CDK15

GOLGA4

Gene ID

65061

2803

Gene namecyclin dependent kinase 15golgin A4
SynonymsALS2CR7|PFTAIRE2|PFTK2CRPF46|GCP2|GOLG|MU-RMS-40.18|p230
Cytomap

2q33.1

3p22.2

Type of geneprotein-codingprotein-coding
Descriptioncyclin-dependent kinase 15PFTAIRE protein kinase 2amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 7amyotrophic lateral sclerosis 2 chromosomal region candidate gene 7 proteincell division protein kinase 15serine/threonine protgolgin subfamily A member 4256 kDa golgin72.1 proteincentrosome-related protein F46golgi autoantigen, golgin subfamily a, 4golgin-240golgin-245protein 72.1trans-Golgi p230
Modification date2020031320200313
UniProtAcc

Q96Q40

Q13439

Ensembl transtripts involved in fusion geneENST00000410091, ENST00000260967, 
ENST00000374598, ENST00000434439, 
ENST00000450471, ENST00000488419, 
ENST00000361924, ENST00000435830, 
ENST00000356847, ENST00000444882, 
Fusion gene scores* DoF score3 X 3 X 2=1814 X 16 X 6=1344
# samples 315
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(15/1344*10)=-3.16349873228288
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CDK15 [Title/Abstract] AND GOLGA4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDK15(202655383)-GOLGA4(37330726), # 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
TgeneGOLGA4

GO:0043001

Golgi to plasma membrane protein transport

15265687

TgeneGOLGA4

GO:0045773

positive regulation of axon extension

22705394


check buttonFusion gene breakpoints across CDK15 (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 GOLGA4 (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
ChimerDB4Non-CancerTCGA-CG-5730-11ACDK15chr2

202655383

+GOLGA4chr3

37330726

+


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Fusion Gene ORF analysis for CDK15-GOLGA4

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-3CDSENST00000410091ENST00000361924CDK15chr2

202655383

+GOLGA4chr3

37330726

+
5UTR-3UTRENST00000410091ENST00000435830CDK15chr2

202655383

+GOLGA4chr3

37330726

+
5UTR-intronENST00000410091ENST00000356847CDK15chr2

202655383

+GOLGA4chr3

37330726

+
5UTR-intronENST00000410091ENST00000444882CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-3CDSENST00000260967ENST00000361924CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-3CDSENST00000374598ENST00000361924CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-3CDSENST00000434439ENST00000361924CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-3CDSENST00000450471ENST00000361924CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-3CDSENST00000488419ENST00000361924CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-3UTRENST00000260967ENST00000435830CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-3UTRENST00000374598ENST00000435830CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-3UTRENST00000434439ENST00000435830CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-3UTRENST00000450471ENST00000435830CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-3UTRENST00000488419ENST00000435830CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-intronENST00000260967ENST00000356847CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-intronENST00000260967ENST00000444882CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-intronENST00000374598ENST00000356847CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-intronENST00000374598ENST00000444882CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-intronENST00000434439ENST00000356847CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-intronENST00000434439ENST00000444882CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-intronENST00000450471ENST00000356847CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-intronENST00000450471ENST00000444882CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-intronENST00000488419ENST00000356847CDK15chr2

202655383

+GOLGA4chr3

37330726

+
intron-intronENST00000488419ENST00000444882CDK15chr2

202655383

+GOLGA4chr3

37330726

+

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 CDK15-GOLGA4


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)
CDK15chr2202655383+GOLGA4chr337330725+0.0119806740.9880193
CDK15chr2202655383+GOLGA4chr337330725+0.0119806740.9880193

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 CDK15-GOLGA4


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/:202655383/:37330726)
- 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
CDK15

Q96Q40

GOLGA4

Q13439

FUNCTION: Serine/threonine-protein kinase that acts like an antiapoptotic protein that counters TRAIL/TNFSF10-induced apoptosis by inducing phosphorylation of BIRC5 at 'Thr-34'. {ECO:0000269|PubMed:24866247}.FUNCTION: Involved in vesicular trafficking at the Golgi apparatus level. May play a role in delivery of transport vesicles containing GPI-linked proteins from the trans-Golgi network through its interaction with MACF1. Involved in endosome-to-Golgi trafficking (PubMed:29084197). {ECO:0000269|PubMed:15265687, ECO:0000269|PubMed:29084197}.

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 CDK15-GOLGA4


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 CDK15-GOLGA4


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 CDK15-GOLGA4


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 CDK15-GOLGA4


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