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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 7240

FusionGeneSummary for CIITA_PRDM16

check button Fusion gene summary
Fusion gene informationFusion gene name: CIITA_PRDM16
Fusion gene ID: 7240
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

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 containingPR domain zinc finger protein 16MDS1/EVI1-like gene 1PR domain 16PR domain containing 16transcription factor MEL1
Modification date2018052320180522
UniProtAcc

P33076

Q9HAZ2

Ensembl transtripts involved in fusion geneENST00000324288, ENST00000381835, 
ENST00000537380, 
ENST00000511072, 
ENST00000442529, ENST00000378398, 
ENST00000441472, ENST00000378391, 
ENST00000514189, ENST00000270722, 
ENST00000512462, 
Fusion gene scores* DoF score3 X 3 X 3=275 X 4 X 4=80
# samples 35
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(5/80*10)=-0.678071905112638
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]

Functional or gene categories assigned by FusionGDB annotation
* 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 from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVDLBCTCGA-GS-A9TZ-01ACIITAchr16

10971239

+PRDM16chr1

3301716

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
Frame-shitENST00000324288ENST00000511072CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000324288ENST00000442529CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000324288ENST00000378398CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000324288ENST00000441472CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000324288ENST00000378391CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000324288ENST00000514189CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000324288ENST00000270722CIITAchr16

10971239

+PRDM16chr1

3301716

+
5CDS-3UTRENST00000324288ENST00000512462CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000381835ENST00000511072CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000381835ENST00000442529CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000381835ENST00000378398CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000381835ENST00000441472CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000381835ENST00000378391CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000381835ENST00000514189CIITAchr16

10971239

+PRDM16chr1

3301716

+
Frame-shitENST00000381835ENST00000270722CIITAchr16

10971239

+PRDM16chr1

3301716

+
5CDS-3UTRENST00000381835ENST00000512462CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000511072CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000442529CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000378398CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000441472CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000378391CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000514189CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3CDSENST00000537380ENST00000270722CIITAchr16

10971239

+PRDM16chr1

3301716

+
3UTR-3UTRENST00000537380ENST00000512462CIITAchr16

10971239

+PRDM16chr1

3301716

+

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FusionProtFeatures for CIITA_PRDM16


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CIITA

P33076

PRDM16

Q9HAZ2

Essential for transcriptional activity of the HLA classII promoter; activation is via the proximal promoter. No DNAbinding of in vitro translated CIITA was detected. May act in acoactivator-like fashion through protein-protein interactions bycontacting factors binding to the proximal MHC class II promoter,to elements of the transcription machinery, or both. Alternativelyit may activate HLA class II transcription by modifying proteinsthat bind to the MHC class II promoter. Also mediates enhanced MHCclass I transcription; the promoter element requirements forCIITA-mediated transcription are distinct from those ofconstitutive MHC class I transcription, and CIITA can functionallyreplace TAF1 at these genes. Exhibits intrinsic GTP-stimulatedacetyltransferase activity. Exhibits serine/threonine proteinkinase activity: can phosphorylate the TFIID component TAF7, theRAP74 subunit of the general transcription factor TFIIF, histoneH2B at 'Ser-37' and other histones (in vitro).{ECO:0000269|PubMed:11172716, ECO:0000269|PubMed:16600381,ECO:0000269|PubMed:17493635, ECO:0000269|PubMed:24036077}. Binds DNA and functions as a transcriptional regulator.Functions in the differentiation of brown adipose tissue (BAT)which is specialized in dissipating chemical energy in the form ofheat in response to cold or excess feeding while white adiposetissue (WAT) is specialized in the storage of excess energy andthe control of systemic metabolism. Together with CEBPB, regulatesthe differentiation of myoblastic precursors into brown adiposecells. Functions also as a repressor of TGF-beta signaling.Isoform 4 may regulate granulocytes differentiation.{ECO:0000269|PubMed:12816872, ECO:0000269|PubMed:14656887,ECO:0000269|PubMed:19049980}.

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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FusionGeneSequence for CIITA_PRDM16


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI 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
CIITANCOA1, RFXANK, RFX5, XPO1, MAPK1, CDK1, MAPK3, HDAC2, HDAC1, SMARCA4, HDAC4, HDAC5, SIN3B, GSK3B, PSMC5, PSMC2, PSMC3, GTF2B, TAF9, CUL3, PPARG, EP300, EP400, TBP, TRIM22, PML, CCNT1PRDM16SMAD2, SMAD3, SKI, TFAP4, SPDEF


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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RelatedDrugs for CIITA_PRDM16


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for CIITA_PRDM16


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCIITAC2931418Bare lymphocyte syndrome 22CTD_human;ORPHANET;UNIPROT
HgeneCIITAC0001403Addison Disease1CTD_human
TgenePRDM16C0149931Migraine Disorders1CTD_human
TgenePRDM16C3809288LEFT VENTRICULAR NONCOMPACTION 81ORPHANET;UNIPROT