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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:CIITA-IL2 (FusionGDB2 ID:HG4261TG3558)

Fusion Gene Summary for CIITA-IL2

check button Fusion gene summary
Fusion gene informationFusion gene name: CIITA-IL2
Fusion gene ID: hg4261tg3558
HgeneTgene
Gene symbol

CIITA

IL2

Gene ID

4261

3558

Gene nameclass II major histocompatibility complex transactivatorinterleukin 2
SynonymsC2TA|CIITAIV|MHC2TA|NLRAIL-2|TCGF|lymphokine
Cytomap('CIITA')('IL2')

16p13.13

4q27

Type of geneprotein-codingprotein-coding
DescriptionMHC class II transactivatorMHC class II transactivator type IMHC class II transactivator type IIINLR family, acid domain containingnucleotide-binding oligomerization domain, leucine rich repeat and acid domain containinginterleukin-2T cell growth factoraldesleukininvolved in regulation of T-cell clonal expansion
Modification date2020032020200322
UniProtAcc.

P60568

Ensembl transtripts involved in fusion geneENST00000324288, ENST00000381835, 
ENST00000537380, 
Fusion gene scores* DoF score6 X 6 X 5=1801 X 1 X 1=1
# samples 61
** MAII scorelog2(6/180*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(1/1*10)=3.32192809488736
Context

PubMed: CIITA [Title/Abstract] AND IL2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCIITA(11032360)-IL2(123373359), # 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
HgeneCIITA

GO:0034341

response to interferon-gamma

19041327

HgeneCIITA

GO:0045345

positive regulation of MHC class I biosynthetic process

20639463

HgeneCIITA

GO:0045892

negative regulation of transcription, DNA-templated

19041327

HgeneCIITA

GO:0045893

positive regulation of transcription, DNA-templated

19041327

HgeneCIITA

GO:0045944

positive regulation of transcription by RNA polymerase II

20639463

HgeneCIITA

GO:0046677

response to antibiotic

107465

TgeneIL2

GO:0002366

leukocyte activation involved in immune response

16204630

TgeneIL2

GO:0002903

negative regulation of B cell apoptotic process

9184696

TgeneIL2

GO:0030890

positive regulation of B cell proliferation

9184696

TgeneIL2

GO:0032740

positive regulation of interleukin-17 production

16482511

TgeneIL2

GO:0042104

positive regulation of activated T cell proliferation

1830926|10072077

TgeneIL2

GO:0042531

positive regulation of tyrosine phosphorylation of STAT protein

19088061



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


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Fusion Gene ORF analysis for CIITA-IL2

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

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 CIITA-IL2


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 CIITA-IL2


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/:11032360/:123373359)
- 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
.IL2

P60568

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: Produced by T-cells in response to antigenic or mitogenic stimulation, this protein is required for T-cell proliferation and other activities crucial to regulation of the immune response. Can stimulate B-cells, monocytes, lymphokine-activated killer cells, natural killer cells, and glioma cells.

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 CIITA-IL2


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 CIITA-IL2


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 CIITA-IL2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneIL2P60568DB00852PseudoephedrineInhibitorSmall moleculeApproved
TgeneIL2P60568DB01327CefazolinInhibitorSmall moleculeApproved
TgeneIL2P60568DB05299keyhole limpet hemocyaninBiotechApproved|Investigational

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Related Diseases for CIITA-IL2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCIITAC2931418Bare lymphocyte syndrome 25CTD_human;ORPHANET;UNIPROT
HgeneCIITAC0001403Addison Disease1CTD_human
HgeneCIITAC1859534Bare Lymphocyte Syndrome, Type II, Complementation Group A1GENOMICS_ENGLAND
HgeneCIITAC2930967Gastro-enteropancreatic neuroendocrine tumor1CTD_human
TgeneC0025202melanoma22CTD_human
TgeneC0022665Kidney Neoplasm4CTD_human
TgeneC0740457Malignant neoplasm of kidney4CTD_human
TgeneC0024121Lung Neoplasms3CTD_human
TgeneC0027659Neoplasms, Experimental3CTD_human
TgeneC0036341Schizophrenia3PSYGENET
TgeneC0242379Malignant neoplasm of lung3CTD_human
TgeneC0004352Autistic Disorder2CTD_human
TgeneC0005684Malignant neoplasm of urinary bladder2CTD_human
TgeneC0005695Bladder Neoplasm2CTD_human
TgeneC0017658Glomerulonephritis2CTD_human
TgeneC0162820Dermatitis, Allergic Contact2CTD_human
TgeneC1704377Bright Disease2CTD_human
TgeneC0001175Acquired Immunodeficiency Syndrome1CTD_human
TgeneC0002622Amnesia1CTD_human
TgeneC0002871Anemia1CTD_human
TgeneC0003123Anorexia1CTD_human
TgeneC0004093Asthenia1CTD_human
TgeneC0006118Brain Neoplasms1CTD_human
TgeneC0006826Malignant Neoplasms1CTD_human
TgeneC0011574Involutional Depression1CTD_human
TgeneC0011609Drug Eruptions1CTD_human
TgeneC0014324Entamoebiasis1CTD_human
TgeneC0015967Fever1CTD_human
TgeneC0017636Glioblastoma1CTD_human
TgeneC0019693HIV Infections1CTD_human
TgeneC0020649Hypotension1CTD_human
TgeneC0023418leukemia1CTD_human
TgeneC0023493Adult T-Cell Lymphoma/Leukemia1CTD_human
TgeneC0023530Leukopenia1CTD_human
TgeneC0023903Liver neoplasms1CTD_human
TgeneC0027627Neoplasm Metastasis1CTD_human
TgeneC0027651Neoplasms1CTD_human
TgeneC0027726Nephrotic Syndrome1CTD_human
TgeneC0030193Pain1CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0036349Paranoid Schizophrenia1PSYGENET
TgeneC0042237Malignant Vaginal Neoplasm1CTD_human
TgeneC0042258Vaginal Neoplasms1CTD_human
TgeneC0086692Benign Neoplasm1CTD_human
TgeneC0153633Malignant neoplasm of brain1CTD_human
TgeneC0233750Hysterical amnesia1CTD_human
TgeneC0233796Temporary Amnesia1CTD_human
TgeneC0234230Pain, Burning1CTD_human
TgeneC0234238Ache1CTD_human
TgeneC0234254Radiating pain1CTD_human
TgeneC0236795Dissociative Amnesia1CTD_human
TgeneC0241910Autoimmune Chronic Hepatitis1CTD_human
TgeneC0242594Residual Cancer1CTD_human
TgeneC0242596Neoplasm, Residual1CTD_human
TgeneC0262497Global Amnesia1CTD_human
TgeneC0334588Giant Cell Glioblastoma1CTD_human
TgeneC0345904Malignant neoplasm of liver1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC0406537Morbilliform Drug Reaction1CTD_human
TgeneC0458257Pain, Splitting1CTD_human
TgeneC0458259Pain, Crushing1CTD_human
TgeneC0496899Benign neoplasm of brain, unspecified1CTD_human
TgeneC0543478Residual Tumor1CTD_human
TgeneC0750906Tactile Amnesia1CTD_human
TgeneC0750907Amnestic State1CTD_human
TgeneC0750974Brain Tumor, Primary1CTD_human
TgeneC0750977Recurrent Brain Neoplasm1CTD_human
TgeneC0750979Primary malignant neoplasm of brain1CTD_human
TgeneC0751217Hyperkinesia, Generalized1CTD_human
TgeneC0751407Pain, Migratory1CTD_human
TgeneC0751408Suffering, Physical1CTD_human
TgeneC1269683Major Depressive Disorder1CTD_human
TgeneC1527390Neoplasms, Intracranial1CTD_human
TgeneC1571983Involutional paraphrenia1CTD_human
TgeneC1571984Psychosis, Involutional1CTD_human
TgeneC1621958Glioblastoma Multiforme1CTD_human
TgeneC3887506Hyperkinesia1CTD_human
TgeneC4316791Entamoeba histolytica Infection1CTD_human
TgeneC4505456HIV Coinfection1CTD_human