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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:C2CD5-PBX4 (FusionGDB2 ID:HG9847TG80714)

Fusion Gene Summary for C2CD5-PBX4

check button Fusion gene summary
Fusion gene informationFusion gene name: C2CD5-PBX4
Fusion gene ID: hg9847tg80714
HgeneTgene
Gene symbol

C2CD5

PBX4

Gene ID

9847

80714

Gene nameC2 calcium dependent domain containing 5PBX homeobox 4
SynonymsCDP138|KIAA0528-
Cytomap('C2CD5')('PBX4')

12p12.1

19p13.11

Type of geneprotein-codingprotein-coding
DescriptionC2 domain-containing protein 5138 kDa C2 domain-containing phosphoproteinpre-B-cell leukemia transcription factor 4homeobox protein PBX4pre-B-cell leukemia homeobox 4
Modification date2020031320200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000544930, ENST00000333957, 
ENST00000396028, ENST00000446597, 
ENST00000536386, ENST00000545552, 
ENST00000542676, ENST00000540703, 
Fusion gene scores* DoF score10 X 8 X 6=4807 X 5 X 4=140
# samples 97
** MAII scorelog2(9/480*10)=-2.41503749927884
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/140*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: C2CD5 [Title/Abstract] AND PBX4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointC2CD5(22696995)-PBX4(19675898), # samples:1
Anticipated loss of major functional domain due to fusion event.C2CD5-PBX4 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.
C2CD5-PBX4 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.
C2CD5-PBX4 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
HgeneC2CD5

GO:0032869

cellular response to insulin stimulus

21907143


check buttonFusion gene breakpoints across C2CD5 (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 PBX4 (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
ChimerDB4STADTCGA-CD-A48C-01AC2CD5chr12

22696995

-PBX4chr19

19675898

-


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Fusion Gene ORF analysis for C2CD5-PBX4

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-3CDSENST00000544930ENST00000251203C2CD5chr12

22696995

-PBX4chr19

19675898

-
Frame-shiftENST00000333957ENST00000251203C2CD5chr12

22696995

-PBX4chr19

19675898

-
Frame-shiftENST00000396028ENST00000251203C2CD5chr12

22696995

-PBX4chr19

19675898

-
Frame-shiftENST00000446597ENST00000251203C2CD5chr12

22696995

-PBX4chr19

19675898

-
Frame-shiftENST00000536386ENST00000251203C2CD5chr12

22696995

-PBX4chr19

19675898

-
Frame-shiftENST00000545552ENST00000251203C2CD5chr12

22696995

-PBX4chr19

19675898

-
In-frameENST00000542676ENST00000251203C2CD5chr12

22696995

-PBX4chr19

19675898

-
intron-3CDSENST00000540703ENST00000251203C2CD5chr12

22696995

-PBX4chr19

19675898

-

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)
ENST00000542676C2CD5chr1222696995-ENST00000251203PBX4chr1919675898-86219358549163

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
ENST00000542676ENST00000251203C2CD5chr1222696995-PBX4chr1919675898-0.040810590.95918936

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Fusion Genomic Features for C2CD5-PBX4


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 C2CD5-PBX4


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/chr12:22696995/chr19:19675898)
- 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
..
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}.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
HgeneC2CD5chr12:22696995chr19:19675898ENST00000333957-22513_27301001.0Calcium bindingNote=1%3B low affinity
HgeneC2CD5chr12:22696995chr19:19675898ENST00000396028-22713_27301043.0Calcium bindingNote=1%3B low affinity

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneC2CD5chr12:22696995chr19:19675898ENST00000333957-22575_86301001.0Calcium bindingNote=2%3B high affinity
HgeneC2CD5chr12:22696995chr19:19675898ENST00000396028-22775_86301043.0Calcium bindingNote=2%3B high affinity
HgeneC2CD5chr12:22696995chr19:19675898ENST00000333957-2251_109301001.0DomainC2
HgeneC2CD5chr12:22696995chr19:19675898ENST00000396028-2271_109301043.0DomainC2
TgenePBX4chr12:22696995chr19:19675898ENST0000025120348210_272256375.0DNA bindingHomeobox%3B TALE-type
TgenePBX4chr12:22696995chr19:19675898ENST000002512034818_209256375.0DomainPBC


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Fusion Gene Sequence for C2CD5-PBX4


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.
>11622_11622_1_C2CD5-PBX4_C2CD5_chr12_22696995_ENST00000542676_PBX4_chr19_19675898_ENST00000251203_length(transcript)=862nt_BP=193nt
AGTTACCCCGCGCGCCTCCGCCCCTCTCCCGCCGGCCCCGCGCTCGGCGCAGACTCGTTTGTTTGTTTCTGCAGGAGCCCAAGAAGAGGC
CGAAACCGAGACCATGCCAGGGAAGCTGAAGGTGAAAATCGTGGCCGGGCGCCATTTGCCAGTGATGGACCGTGCTAGTGACCTGACTGA
TGCCTTCGTGGAGGTCTCTAACTGGTTTGGCAACAAAAGAATCCGGTATAAAAAGAACATGGGGAAGTTTCAAGAAGAGGCTACCATTTA
CACGGGTAAAACGGCTGTGGATACCACGGAAGTTGGGGTCCCAGGGAACCACGCCAGCTGCCTGTCAACACCTAGCTCCGGCTCCTCTGG
ACCCTTCCCGCTGCCCAGCGCTGGGGACGCCTTCCTCACCCTGCGGACTCTGGCCTCTCTCCAGCCTCCTCCTGGGGGAGGCTGCCTGCA
GTCCCAGGCCCAGGGTAGCTGGCAGGGGGCCACCCCCCAACCTGCAACTGCCTCACCTGCTGGAGACCCTGGCAGCATCAACTCCAGTAC
ATCTAATTAAGTTTGGGGGATAAGCAGGAAAGAGCGCTGCGTGAGCTGCCATGTATCGCCAGCCGTTGCTTTGTTACTGAACGTGCCGCC
GACGACCTCAGAAAACCCAGATGGGTGGTGGTGCCCATGAGCCCCTGCTCCTCAGCCAGGCCCGTGGCGCCGGCTCATGTGTCTGCTGCG
ACTCGAGATGGCCTGAAACGCCACTCATTCTCCCACTTCAGTTCGTTTTTTTGACAGTAATTTTATGGTAACGCTATGAATTGAATTGTC

>11622_11622_1_C2CD5-PBX4_C2CD5_chr12_22696995_ENST00000542676_PBX4_chr19_19675898_ENST00000251203_length(amino acids)=163AA_BP=45
MFVSAGAQEEAETETMPGKLKVKIVAGRHLPVMDRASDLTDAFVEVSNWFGNKRIRYKKNMGKFQEEATIYTGKTAVDTTEVGVPGNHAS

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Fusion Gene PPI Analysis for C2CD5-PBX4


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 C2CD5-PBX4


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 C2CD5-PBX4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0376634Craniofacial Abnormalities1CTD_human