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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:CTLA4-CD28 (FusionGDB2 ID:HG1493TG940)

Fusion Gene Summary for CTLA4-CD28

Fusion gene summary

Fusion gene information	Fusion gene name: CTLA4-CD28
	Fusion gene ID: hg1493tg940
		Hgene	Tgene
	Gene symbol	CTLA4	CD28
	Gene ID	1493	940
	Gene name	cytotoxic T-lymphocyte associated protein 4	CD28 molecule
	Synonyms	ALPS5\|CD\|CD152\|CELIAC3\|CTLA-4\|GRD4\|GSE\|IDDM12	Tp44
	Cytomap	('CTLA4')('CD28') 2q33.2	2q33.2
	Type of gene	protein-coding	protein-coding
	Description	cytotoxic T-lymphocyte protein 4CD152 isoformceliac disease 3cytotoxic T lymphocyte associated antigen 4 short spliced formcytotoxic T-lymphocyte-associated serine esterase-4insulin-dependent diabetes mellitus 12ligand and transmembrane spliced cyto	T-cell-specific surface glycoprotein CD28CD28 antigen
	Modification date	20200329	20200313
	UniProtAcc	.	P10747
	Ensembl transtripts involved in fusion gene	ENST00000295854, ENST00000302823, ENST00000427473, ENST00000472206, ENST00000487393,
Fusion gene scores	* DoF score	1 X 3 X 1=3	2 X 4 X 1=8
	# samples	1	1
	** MAII score	log2(1/3*10)=1.73696559416621	log2(1/8*10)=0.321928094887362
Context	PubMed: CTLA4 [Title/Abstract] AND CD28 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint
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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	CTLA4	GO:0045590	negative regulation of regulatory T cell differentiation	18641304
Tgene	CD28	GO:0032733	positive regulation of interleukin-10 production	8617933
Tgene	CD28	GO:0032753	positive regulation of interleukin-4 production	8617933
Tgene	CD28	GO:0042102	positive regulation of T cell proliferation	3159820\|8617933
Tgene	CD28	GO:0045066	regulatory T cell differentiation	18641304
Tgene	CD28	GO:0045086	positive regulation of interleukin-2 biosynthetic process	3875683
Tgene	CD28	GO:0045840	positive regulation of mitotic nuclear division	3159820

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerKB4	.	.	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
ChimerKB4	.	.	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
ChimerKB4	.	.	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+

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Fusion Gene ORF analysis for CTLA4-CD28

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
intron-intron	ENST00000295854	ENST00000324106	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000295854	ENST00000324106	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000295854	ENST00000324106	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000295854	ENST00000374478	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000295854	ENST00000374478	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000295854	ENST00000374478	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000295854	ENST00000374481	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000295854	ENST00000374481	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000295854	ENST00000374481	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000295854	ENST00000458610	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000295854	ENST00000458610	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000295854	ENST00000458610	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000302823	ENST00000324106	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000302823	ENST00000324106	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000302823	ENST00000324106	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000302823	ENST00000374478	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000302823	ENST00000374478	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000302823	ENST00000374478	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000302823	ENST00000374481	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000302823	ENST00000374481	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000302823	ENST00000374481	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000302823	ENST00000458610	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000302823	ENST00000458610	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000302823	ENST00000458610	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000427473	ENST00000324106	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000427473	ENST00000324106	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000427473	ENST00000324106	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000427473	ENST00000374478	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000427473	ENST00000374478	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000427473	ENST00000374478	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000427473	ENST00000374481	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000427473	ENST00000374481	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000427473	ENST00000374481	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000427473	ENST00000458610	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000427473	ENST00000458610	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000427473	ENST00000458610	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000472206	ENST00000324106	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000472206	ENST00000324106	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000472206	ENST00000324106	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000472206	ENST00000374478	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000472206	ENST00000374478	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000472206	ENST00000374478	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000472206	ENST00000374481	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000472206	ENST00000374481	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000472206	ENST00000374481	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000472206	ENST00000458610	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000472206	ENST00000458610	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000472206	ENST00000458610	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000487393	ENST00000324106	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000487393	ENST00000324106	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000487393	ENST00000324106	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000487393	ENST00000374478	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000487393	ENST00000374478	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000487393	ENST00000374478	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000487393	ENST00000374481	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000487393	ENST00000374481	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000487393	ENST00000374481	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+
intron-intron	ENST00000487393	ENST00000458610	CTLA4	chr2	204732510	+	CD28	chr2	204732510	+
intron-intron	ENST00000487393	ENST00000458610	CTLA4	chr2	204735308	+	CD28	chr2	204735308	+
intron-intron	ENST00000487393	ENST00000458610	CTLA4	chr2	204736100	+	CD28	chr2	204736100	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

DeepORF 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.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for CTLA4-CD28

FusionAI 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.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

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Fusion Protein Features for CTLA4-CD28

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:/:)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	CD28 P10747
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: Involved in T-cell activation, the induction of cell proliferation and cytokine production and promotion of T-cell survival. Enhances the production of IL4 and IL10 in T-cells in conjunction with TCR/CD3 ligation and CD40L costimulation (PubMed:8617933). Isoform 3 enhances CD40L-mediated activation of NF-kappa-B and kinases MAPK8 and PAK2 in T-cells (PubMed:15067037). {ECO:0000269\|PubMed:15067037, ECO:0000269\|PubMed:8617933}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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Fusion Gene Sequence for CTLA4-CD28

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 CTLA4-CD28

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for CTLA4-CD28

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for CTLA4-CD28

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	CTLA4	C0018213	Graves Disease	3	CTD_human
Hgene	CTLA4	C0036341	Schizophrenia	3	PSYGENET
Hgene	CTLA4	C0003873	Rheumatoid Arthritis	2	CTD_human
Hgene	CTLA4	C0005586	Bipolar Disorder	2	PSYGENET
Hgene	CTLA4	C0041696	Unipolar Depression	2	PSYGENET
Hgene	CTLA4	C1269683	Major Depressive Disorder	2	PSYGENET
Hgene	CTLA4	C4015214	CTLA4 Haploinsufficiency	2	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Hgene	CTLA4	C0002171	Alopecia Areata	1	CTD_human
Hgene	CTLA4	C0004368	Autoimmune state	1	GENOMICS_ENGLAND
Hgene	CTLA4	C0009447	Common Variable Immunodeficiency	1	GENOMICS_ENGLAND
Hgene	CTLA4	C0018133	Graft-vs-Host Disease	1	CTD_human
Hgene	CTLA4	C0021831	Intestinal Diseases	1	GENOMICS_ENGLAND
Hgene	CTLA4	C0023493	Adult T-Cell Lymphoma/Leukemia	1	CTD_human
Hgene	CTLA4	C0024141	Lupus Erythematosus, Systemic	1	CTD_human;ORPHANET
Hgene	CTLA4	C0025202	melanoma	1	CTD_human
Hgene	CTLA4	C0026948	Mycosis Fungoides	1	ORPHANET
Hgene	CTLA4	C0029172	Oral Submucous Fibrosis	1	CTD_human
Hgene	CTLA4	C0036920	Sezary Syndrome	1	ORPHANET
Hgene	CTLA4	C0079773	Lymphoma, T-Cell, Cutaneous	1	CTD_human
Hgene	CTLA4	C0086438	Hypogammaglobulinemia	1	GENOMICS_ENGLAND
Hgene	CTLA4	C0087031	Juvenile-Onset Still Disease	1	CTD_human
Hgene	CTLA4	C0376407	Granulomatous Slack Skin	1	CTD_human
Hgene	CTLA4	C0494261	Combined immunodeficiency	1	GENOMICS_ENGLAND
Hgene	CTLA4	C0497156	Lymphadenopathy	1	GENOMICS_ENGLAND
Hgene	CTLA4	C1844666	Immune dysregulation	1	GENOMICS_ENGLAND
Hgene	CTLA4	C3495559	Juvenile arthritis	1	CTD_human
Hgene	CTLA4	C3495801	Granulomatosis with polyangiitis	1	ORPHANET
Hgene	CTLA4	C3714758	Juvenile psoriatic arthritis	1	CTD_human
Hgene	CTLA4	C4316788	Abnormality of the intestine	1	GENOMICS_ENGLAND
Hgene	CTLA4	C4552091	Polyarthritis, Juvenile, Rheumatoid Factor Negative	1	CTD_human
Hgene	CTLA4	C4704862	Polyarthritis, Juvenile, Rheumatoid Factor Positive	1	CTD_human
Hgene	CTLA4	C4721453	Peripheral Nervous System Diseases	1	CTD_human
Hgene	CTLA4	C4728035	CTLA4 deficiency	1	GENOMICS_ENGLAND
Tgene		C0003873	Rheumatoid Arthritis	3	CTD_human
Tgene		C0004364	Autoimmune Diseases	2	CTD_human
Tgene		C0079773	Lymphoma, T-Cell, Cutaneous	2	CTD_human
Tgene		C0376407	Granulomatous Slack Skin	2	CTD_human
Tgene		C0005138	Berylliosis	1	CTD_human
Tgene		C0019693	HIV Infections	1	CTD_human
Tgene		C0023493	Adult T-Cell Lymphoma/Leukemia	1	CTD_human
Tgene		C0026948	Mycosis Fungoides	1	ORPHANET
Tgene		C0036920	Sezary Syndrome	1	ORPHANET
Tgene		C0079774	Peripheral T-Cell Lymphoma	1	CTD_human
Tgene		C0263454	Chloracne	1	CTD_human
Tgene		C2350873	Beryllium Disease	1	CTD_human
Tgene		C4505456	HIV Coinfection	1	CTD_human

Fusion Gene Studies in Kim Lab

Fusion gene:CTLA4-CD28 (FusionGDB2 ID:HG1493TG940)

Fusion Gene Summary for CTLA4-CD28

Fusion Gene ORF analysis for CTLA4-CD28

Fusion Genomic Features for CTLA4-CD28

Fusion Protein Features for CTLA4-CD28

Fusion Gene Sequence for CTLA4-CD28

Fusion Gene PPI Analysis for CTLA4-CD28

Related Drugs for CTLA4-CD28

Related Diseases for CTLA4-CD28

Fusion Gene Studies
in Kim Lab