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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:CUL4A-PCID2 (FusionGDB2 ID:HG8451TG55795)

Fusion Gene Summary for CUL4A-PCID2

check button Fusion gene summary
Fusion gene informationFusion gene name: CUL4A-PCID2
Fusion gene ID: hg8451tg55795
HgeneTgene
Gene symbol

CUL4A

PCID2

Gene ID

8451

55795

Gene namecullin 4APCI domain containing 2
Synonyms-F10
Cytomap('CUL4A')('PCID2')

13q34

13q34

Type of geneprotein-codingprotein-coding
Descriptioncullin-4ACUL-4APCI domain-containing protein 2CSN12-like protein
Modification date2020032720200313
UniProtAcc

Q13619

.
Ensembl transtripts involved in fusion geneENST00000463426, ENST00000326335, 
ENST00000375440, ENST00000375441, 
ENST00000451881, 
Fusion gene scores* DoF score12 X 16 X 11=21129 X 6 X 7=378
# samples 1910
** MAII scorelog2(19/2112*10)=-3.47453851102751
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/378*10)=-1.91838623444635
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CUL4A [Title/Abstract] AND PCID2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCUL4A(113873362)-PCID2(113850534), # samples:2
Anticipated loss of major functional domain due to fusion event.CUL4A-PCID2 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.
CUL4A-PCID2 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.
* 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
HgeneCUL4A

GO:0016567

protein ubiquitination

26431207


check buttonFusion gene breakpoints across CUL4A (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 PCID2 (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
* 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
ChimerDB4ESCATCGA-LN-A5U6CUL4Achr13

113873362

+PCID2chr13

113850534

-
ChimerDB4STADTCGA-BR-A4PECUL4Achr13

113873362

+PCID2chr13

113850534

-


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Fusion Gene ORF analysis for CUL4A-PCID2

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
3UTR-3CDSENST00000463426ENST00000337344CUL4Achr13

113873362

+PCID2chr13

113850534

-
3UTR-3CDSENST00000463426ENST00000375477CUL4Achr13

113873362

+PCID2chr13

113850534

-
3UTR-3CDSENST00000463426ENST00000375479CUL4Achr13

113873362

+PCID2chr13

113850534

-
3UTR-intronENST00000463426ENST00000246505CUL4Achr13

113873362

+PCID2chr13

113850534

-
3UTR-intronENST00000463426ENST00000375457CUL4Achr13

113873362

+PCID2chr13

113850534

-
3UTR-intronENST00000463426ENST00000375459CUL4Achr13

113873362

+PCID2chr13

113850534

-
3UTR-intronENST00000463426ENST00000493650CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000326335ENST00000246505CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000326335ENST00000375457CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000326335ENST00000375459CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000326335ENST00000493650CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000375440ENST00000246505CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000375440ENST00000375457CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000375440ENST00000375459CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000375440ENST00000493650CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000375441ENST00000246505CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000375441ENST00000375457CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000375441ENST00000375459CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000375441ENST00000493650CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000451881ENST00000246505CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000451881ENST00000375457CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000451881ENST00000375459CUL4Achr13

113873362

+PCID2chr13

113850534

-
5CDS-intronENST00000451881ENST00000493650CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000326335ENST00000337344CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000326335ENST00000375477CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000326335ENST00000375479CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000375440ENST00000337344CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000375440ENST00000375477CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000375440ENST00000375479CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000375441ENST00000337344CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000375441ENST00000375477CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000375441ENST00000375479CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000451881ENST00000337344CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000451881ENST00000375477CUL4Achr13

113873362

+PCID2chr13

113850534

-
In-frameENST00000451881ENST00000375479CUL4Achr13

113873362

+PCID2chr13

113850534

-

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 CUL4A-PCID2


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.
genomic feature

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Fusion Protein Features for CUL4A-PCID2


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/chr13:113873362/chr13:113850534)
- 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
CUL4A

Q13619

.
FUNCTION: Core component of multiple cullin-RING-based E3 ubiquitin-protein ligase complexes which mediate the ubiquitination of target proteins. As a scaffold protein may contribute to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. The E3 ubiquitin-protein ligase activity of the complex is dependent on the neddylation of the cullin subunit and is inhibited by the association of the deneddylated cullin subunit with TIP120A/CAND1. The functional specificity of the E3 ubiquitin-protein ligase complex depends on the variable substrate recognition component. DCX(DET1-COP1) directs ubiquitination of JUN. DCX(DDB2) directs ubiquitination of XPC. DCX(DDB2) ubiquitinates histones H3-H4 and is required for efficient histone deposition during replication-coupled (H3.1) and replication-independent (H3.3) nucleosome assembly, probably by facilitating the transfer of H3 from ASF1A/ASF1B to other chaperones involved in histone deposition. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. In association with DDB1 and SKP2 probably is involved in ubiquitination of CDKN1B/p27kip. Is involved in ubiquitination of HOXA9. DCX(DTL) directs autoubiquitination of DTL. The DDB1-CUL4A-DTL E3 ligase complex regulates the circadian clock function by mediating the ubiquitination and degradation of CRY1 (PubMed:26431207). With CUL4B, contributes to ribosome biogenesis (PubMed:26711351). {ECO:0000269|PubMed:14578910, ECO:0000269|PubMed:14609952, ECO:0000269|PubMed:15448697, ECO:0000269|PubMed:15548678, ECO:0000269|PubMed:16537899, ECO:0000269|PubMed:16678110, ECO:0000269|PubMed:23478445, ECO:0000269|PubMed:24209620, ECO:0000269|PubMed:26431207, ECO:0000269|PubMed:26711351}.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
TgenePCID2chr13:113873362chr13:113850534ENST00000246505315210_391141560.0DomainPCI
TgenePCID2chr13:113873362chr13:113850534ENST00000337344314210_39188400.0DomainPCI
TgenePCID2chr13:113873362chr13:113850534ENST00000375457314210_39186398.0DomainPCI
TgenePCID2chr13:113873362chr13:113850534ENST00000375459315210_39186510.6666666666667DomainPCI
TgenePCID2chr13:113873362chr13:113850534ENST00000375477315210_39188518.0DomainPCI
TgenePCID2chr13:113873362chr13:113850534ENST00000375479315210_39188491.0DomainPCI

- 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 CUL4A-PCID2


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 CUL4A-PCID2


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 CUL4A-PCID2


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 CUL4A-PCID2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCUL4AC0004238Atrial Fibrillation2CTD_human
HgeneCUL4AC0235480Paroxysmal atrial fibrillation2CTD_human
HgeneCUL4AC2585653Persistent atrial fibrillation2CTD_human
HgeneCUL4AC3468561familial atrial fibrillation2CTD_human
HgeneCUL4AC0014518Toxic Epidermal Necrolysis1CTD_human
HgeneCUL4AC0038325Stevens-Johnson Syndrome1CTD_human
HgeneCUL4AC1274933Drug-Induced Stevens Johnson Syndrome1CTD_human
HgeneCUL4AC3658301Mycoplasma-Induced Stevens-Johnson Syndrome1CTD_human
HgeneCUL4AC3658302Stevens-Johnson Syndrome Toxic Epidermal Necrolysis Spectrum1CTD_human