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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:CD4-IGHG3 (FusionGDB2 ID:HG920TG3502)

Fusion Gene Summary for CD4-IGHG3

check button Fusion gene summary
Fusion gene informationFusion gene name: CD4-IGHG3
Fusion gene ID: hg920tg3502
HgeneTgene
Gene symbol

CD4

IGHG3

Gene ID

920

3502

Gene nameCD4 molecule
SynonymsCD4mut
Cytomap('CD4')('IGHG3')

12p13.31

Type of geneprotein-coding
DescriptionT-cell surface glycoprotein CD4CD4 antigen (p55)CD4 receptorT-cell surface antigen T4/Leu-3
Modification date20200313
UniProtAcc

P01730

P01860

Ensembl transtripts involved in fusion geneENST00000538827, ENST00000011653, 
ENST00000541982, 
Fusion gene scores* DoF score5 X 5 X 3=75138 X 68 X 15=140760
# samples 5115
** MAII scorelog2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(115/140760*10)=-6.93545974780529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CD4 [Title/Abstract] AND IGHG3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCD4(6924003)-IGHG3(106329461), # 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
HgeneCD4

GO:0001934

positive regulation of protein phosphorylation

24942581

HgeneCD4

GO:0006948

induction by virus of host cell-cell fusion

9166430

HgeneCD4

GO:0030217

T cell differentiation

1533274

HgeneCD4

GO:0032507

maintenance of protein location in cell

15128768

HgeneCD4

GO:0033674

positive regulation of kinase activity

24942581

HgeneCD4

GO:0035723

interleukin-15-mediated signaling pathway

24942581

HgeneCD4

GO:0043123

positive regulation of I-kappaB kinase/NF-kappaB signaling

24942581

HgeneCD4

GO:0043410

positive regulation of MAPK cascade

24942581

HgeneCD4

GO:0045058

T cell selection

9551897

HgeneCD4

GO:0045657

positive regulation of monocyte differentiation

24942581

HgeneCD4

GO:0045860

positive regulation of protein kinase activity

2118992

HgeneCD4

GO:0045893

positive regulation of transcription, DNA-templated

24942581

HgeneCD4

GO:0046598

positive regulation of viral entry into host cell

24942581

HgeneCD4

GO:0050863

regulation of T cell activation

1533274

HgeneCD4

GO:0051924

regulation of calcium ion transport

24942581

HgeneCD4

GO:0070374

positive regulation of ERK1 and ERK2 cascade

24942581

HgeneCD4

GO:0097011

cellular response to granulocyte macrophage colony-stimulating factor stimulus

24942581



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
ChimerDB4SKCMTCGA-EE-A2GH-06ACD4chr12

6924003

+IGHG3chr14

106329461

-


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Fusion Gene ORF analysis for CD4-IGHG3

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-intronENST00000538827ENST00000390551CD4chr12

6924003

+IGHG3chr14

106329461

-
5CDS-intronENST00000011653ENST00000390551CD4chr12

6924003

+IGHG3chr14

106329461

-
5CDS-intronENST00000541982ENST00000390551CD4chr12

6924003

+IGHG3chr14

106329461

-

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 CD4-IGHG3


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)


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Fusion Protein Features for CD4-IGHG3


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/:6924003/:106329461)
- 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
CD4

P01730

IGHG3

P01860

FUNCTION: Integral membrane glycoprotein that plays an essential role in the immune response and serves multiple functions in responses against both external and internal offenses. In T-cells, functions primarily as a coreceptor for MHC class II molecule:peptide complex. The antigens presented by class II peptides are derived from extracellular proteins while class I peptides are derived from cytosolic proteins. Interacts simultaneously with the T-cell receptor (TCR) and the MHC class II presented by antigen presenting cells (APCs). In turn, recruits the Src kinase LCK to the vicinity of the TCR-CD3 complex. LCK then initiates different intracellular signaling pathways by phosphorylating various substrates ultimately leading to lymphokine production, motility, adhesion and activation of T-helper cells. In other cells such as macrophages or NK cells, plays a role in differentiation/activation, cytokine expression and cell migration in a TCR/LCK-independent pathway. Participates in the development of T-helper cells in the thymus and triggers the differentiation of monocytes into functional mature macrophages. {ECO:0000269|PubMed:16951326, ECO:0000269|PubMed:24942581, ECO:0000269|PubMed:2823150, ECO:0000269|PubMed:7604010}.; FUNCTION: (Microbial infection) Primary receptor for human immunodeficiency virus-1 (HIV-1) (PubMed:2214026, PubMed:16331979, PubMed:9641677, PubMed:12089508). Down-regulated by HIV-1 Vpu (PubMed:17346169). Acts as a receptor for Human Herpes virus 7/HHV-7 (PubMed:7909607). {ECO:0000269|PubMed:12089508, ECO:0000269|PubMed:16331979, ECO:0000269|PubMed:17346169, ECO:0000269|PubMed:2214026, ECO:0000269|PubMed:7909607, ECO:0000269|PubMed:9641677}.FUNCTION: Constant region of immunoglobulin heavy chains. Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:22158414, PubMed:20176268). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268). {ECO:0000303|PubMed:17576170, ECO:0000303|PubMed:20176268, ECO:0000303|PubMed:22158414}.

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 CD4-IGHG3


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 CD4-IGHG3


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 CD4-IGHG3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneCD4P01730DB00098Antithymocyte immunoglobulin (rabbit)BiotechApproved
HgeneCD4P01730DB12698IbalizumabAntagonistBiotechApproved|Investigational

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Related Diseases for CD4-IGHG3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCD4C0013264Muscular Dystrophy, Duchenne1CTD_human
HgeneCD4C0027746Nerve Degeneration1CTD_human
HgeneCD4C0162526AIDS-Related Opportunistic Infections1CTD_human
HgeneCD4C0917713Becker Muscular Dystrophy1CTD_human
HgeneCD4C3542021Duchenne and Becker Muscular Dystrophy1CTD_human