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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-PRDM16 (FusionGDB2 ID:HG4261TG63976)

Fusion Gene Summary for CIITA-PRDM16

check button Fusion gene summary
Fusion gene informationFusion gene name: CIITA-PRDM16
Fusion gene ID: hg4261tg63976
HgeneTgene
Gene symbol

CIITA

PRDM16

Gene ID

4261

63976

Gene nameclass II major histocompatibility complex transactivatorPR/SET domain 16
SynonymsC2TA|CIITAIV|MHC2TA|NLRACMD1LL|KMT8F|LVNC8|MEL1|PFM13
Cytomap('CIITA')('PRDM16')

16p13.13

1p36.32

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 containinghistone-lysine N-methyltransferase PRDM16MDS1/EVI1-like gene 1PR domain 16PR domain containing 16PR domain zinc finger protein 16transcription factor MEL1
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000537380, ENST00000324288, 
ENST00000381835, 
Fusion gene scores* DoF score6 X 6 X 5=1809 X 8 X 7=504
# samples 69
** MAII scorelog2(6/180*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/504*10)=-2.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CIITA [Title/Abstract] AND PRDM16 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCIITA(10971239)-PRDM16(3301716), # samples:2
Anticipated loss of major functional domain due to fusion event.CIITA-PRDM16 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
CIITA-PRDM16 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CIITA-PRDM16 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
CIITA-PRDM16 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
CIITA-PRDM16 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
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

TgenePRDM16

GO:0000122

negative regulation of transcription by RNA polymerase II

19049980

TgenePRDM16

GO:0030512

negative regulation of transforming growth factor beta receptor signaling pathway

14656887

TgenePRDM16

GO:0045892

negative regulation of transcription, DNA-templated

12816872

TgenePRDM16

GO:0045893

positive regulation of transcription, DNA-templated

25578880



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
ChimerDB4DLBCTCGA-GS-A9TZ-01ACIITAchr16

10971239

-PRDM16chr1

3301716

+
ChimerDB4DLBCTCGA-GS-A9TZCIITAchr16

10971239

+PRDM16chr1

3301715

+
ChimerDB4DLBCTCGA-GS-A9TZCIITAchr16

10971239

+PRDM16chr1

3301716

+


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Fusion Gene ORF analysis for CIITA-PRDM16

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-3CDSENST00000537380ENST00000270722CIITAchr16

10971239

+PRDM16chr1

3301715

+
3UTR-3CDSENST00000537380ENST00000270722CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000378391CIITAchr16

10971239

+PRDM16chr1

3301715

+
3UTR-3CDSENST00000537380ENST00000378391CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000378398CIITAchr16

10971239

+PRDM16chr1

3301715

+
3UTR-3CDSENST00000537380ENST00000378398CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000441472CIITAchr16

10971239

+PRDM16chr1

3301715

+
3UTR-3CDSENST00000537380ENST00000441472CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000442529CIITAchr16

10971239

+PRDM16chr1

3301715

+
3UTR-3CDSENST00000537380ENST00000442529CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000511072CIITAchr16

10971239

+PRDM16chr1

3301715

+
3UTR-3CDSENST00000537380ENST00000511072CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000514189CIITAchr16

10971239

+PRDM16chr1

3301715

+
3UTR-3CDSENST00000537380ENST00000514189CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3UTRENST00000537380ENST00000512462CIITAchr16

10971239

+PRDM16chr1

3301715

+
3UTR-3UTRENST00000537380ENST00000512462CIITAchr16

10971239

+PRDM16chr1

3301716

+
5CDS-3UTRENST00000324288ENST00000512462CIITAchr16

10971239

+PRDM16chr1

3301715

+
5CDS-3UTRENST00000324288ENST00000512462CIITAchr16

10971239

+PRDM16chr1

3301716

+
5CDS-3UTRENST00000381835ENST00000512462CIITAchr16

10971239

+PRDM16chr1

3301715

+
5CDS-3UTRENST00000381835ENST00000512462CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000324288ENST00000270722CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000324288ENST00000270722CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000324288ENST00000378391CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000324288ENST00000378391CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000324288ENST00000378398CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000324288ENST00000378398CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000324288ENST00000441472CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000324288ENST00000441472CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000324288ENST00000442529CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000324288ENST00000442529CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000324288ENST00000511072CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000324288ENST00000511072CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000324288ENST00000514189CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000324288ENST00000514189CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000381835ENST00000270722CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000381835ENST00000270722CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000381835ENST00000378391CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000381835ENST00000378391CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000381835ENST00000378398CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000381835ENST00000378398CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000381835ENST00000441472CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000381835ENST00000441472CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000381835ENST00000442529CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000381835ENST00000442529CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000381835ENST00000511072CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000381835ENST00000511072CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shiftENST00000381835ENST00000514189CIITAchr16

10971239

+PRDM16chr1

3301715

+
Frame-shiftENST00000381835ENST00000514189CIITAchr16

10971239

+PRDM16chr1

3301716

+

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-PRDM16


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)
CIITAchr1610971239+PRDM16chr13301715+0.0172582250.9827418
CIITAchr1610971239+PRDM16chr13301715+0.0172582250.9827418


check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for CIITA-PRDM16


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/:10971239/:3301716)
- 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

- 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-PRDM16


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-PRDM16


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-PRDM16


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 CIITA-PRDM16


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
TgeneC0007852Cervical Migraine Syndrome1CTD_human
TgeneC0018984Hemicrania migraine1CTD_human
TgeneC0149931Migraine Disorders1CTD_human
TgeneC0270858Abdominal Migraine1CTD_human
TgeneC0338489Status Migrainosus1CTD_human
TgeneC0340427Familial dilated cardiomyopathy1ORPHANET
TgeneC0521664Acute Confusional Migraine1CTD_human
TgeneC0700438Sick Headaches1CTD_human
TgeneC1842870Chromosome 1p36 Deletion Syndrome1ORPHANET
TgeneC1960469Left ventricular noncompaction1ORPHANET
TgeneC3809288LEFT VENTRICULAR NONCOMPACTION 81CTD_human;GENOMICS_ENGLAND;UNIPROT