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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:CDKN1A-CD9 (FusionGDB2 ID:15421)

Fusion Gene Summary for CDKN1A-CD9

check button Fusion gene summary
Fusion gene informationFusion gene name: CDKN1A-CD9
Fusion gene ID: 15421
HgeneTgene
Gene symbol

CDKN1A

CD9

Gene ID

1026

928

Gene namecyclin dependent kinase inhibitor 1ACD9 molecule
SynonymsCAP20|CDKN1|CIP1|MDA-6|P21|SDI1|WAF1|p21CIP1BTCC-1|DRAP-27|MIC3|MRP-1|TSPAN-29|TSPAN29
Cytomap

6p21.2

12p13.31

Type of geneprotein-codingprotein-coding
Descriptioncyclin-dependent kinase inhibitor 1CDK-interacting protein 1CDK-interaction protein 1DNA synthesis inhibitorcyclin-dependent kinase inhibitor 1A (p21, Cip1)melanoma differentiation associated protein 6wild-type p53-activated fragment 1CD9 antigen5H9 antigenBA-2/p24 antigenCD9 antigen (p24)antigen CD9cell growth-inhibiting gene 2 proteinleukocyte antigen MIC3motility related protein-1tetraspanin-29
Modification date2020032920200327
UniProtAcc

P38936

Q8TCZ2

Ensembl transtripts involved in fusion geneENST00000448526, ENST00000244741, 
ENST00000405375, ENST00000373711, 
ENST00000478800, 		ENST00000382518, 
ENST00000009180, ENST00000382515, 
ENST00000481267, 
Fusion gene scores* DoF score6 X 7 X 3=1268 X 7 X 6=336
# samples 78
** MAII scorelog2(7/126*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/336*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CDKN1A [Title/Abstract] AND CD9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDKN1A(36646575)-CD9(6334590), # samples:2
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
HgeneCDKN1A

GO:0000082

G1/S transition of mitotic cell cycle

10208428

HgeneCDKN1A

GO:0006977

DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest

15149599

HgeneCDKN1A

GO:0007050

cell cycle arrest

15149599

HgeneCDKN1A

GO:0008285

negative regulation of cell proliferation

10208428|15149599

HgeneCDKN1A

GO:0030308

negative regulation of cell growth

10208428

HgeneCDKN1A

GO:0042326

negative regulation of phosphorylation

10208428

HgeneCDKN1A

GO:0045860

positive regulation of protein kinase activity

22869755

TgeneCD9

GO:0007155

cell adhesion

7511626

TgeneCD9

GO:0007342

fusion of sperm to egg plasma membrane involved in single fertilization

14575715

TgeneCD9

GO:0051271

negative regulation of cellular component movement

8478605

TgeneCD9

GO:0090331

negative regulation of platelet aggregation

18541721


check buttonFusion gene breakpoints across CDKN1A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across CD9 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4adenocarcinomaHM245393CDKN1Achr6

36646575

CD9chr12

6334590

ChiTaRS5.0N/AHM245393CDKN1Achr6

36646575

+CD9chr12

6334590

+


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Fusion Gene ORF analysis for CDKN1A-CD9

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
intron-3CDSENST00000448526ENST00000382518CDKN1Achr6

36646575

CD9chr12

6334590

intron-3CDSENST00000448526ENST00000009180CDKN1Achr6

36646575

CD9chr12

6334590

intron-5UTRENST00000448526ENST00000382515CDKN1Achr6

36646575

CD9chr12

6334590

intron-3UTRENST00000448526ENST00000481267CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-3CDSENST00000244741ENST00000382518CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-3CDSENST00000244741ENST00000009180CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-5UTRENST00000244741ENST00000382515CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-3UTRENST00000244741ENST00000481267CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-3CDSENST00000405375ENST00000382518CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-3CDSENST00000405375ENST00000009180CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-5UTRENST00000405375ENST00000382515CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-3UTRENST00000405375ENST00000481267CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-3CDSENST00000373711ENST00000382518CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-3CDSENST00000373711ENST00000009180CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-5UTRENST00000373711ENST00000382515CDKN1Achr6

36646575

CD9chr12

6334590

5UTR-3UTRENST00000373711ENST00000481267CDKN1Achr6

36646575

CD9chr12

6334590

3UTR-3CDSENST00000478800ENST00000382518CDKN1Achr6

36646575

CD9chr12

6334590

3UTR-3CDSENST00000478800ENST00000009180CDKN1Achr6

36646575

CD9chr12

6334590

3UTR-5UTRENST00000478800ENST00000382515CDKN1Achr6

36646575

CD9chr12

6334590

3UTR-3UTRENST00000478800ENST00000481267CDKN1Achr6

36646575

CD9chr12

6334590

intron-3CDSENST00000448526ENST00000382518CDKN1Achr6

36646575

+CD9chr12

6334590

+
intron-3CDSENST00000448526ENST00000009180CDKN1Achr6

36646575

+CD9chr12

6334590

+
intron-5UTRENST00000448526ENST00000382515CDKN1Achr6

36646575

+CD9chr12

6334590

+
intron-3UTRENST00000448526ENST00000481267CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-3CDSENST00000244741ENST00000382518CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-3CDSENST00000244741ENST00000009180CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-5UTRENST00000244741ENST00000382515CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-3UTRENST00000244741ENST00000481267CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-3CDSENST00000405375ENST00000382518CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-3CDSENST00000405375ENST00000009180CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-5UTRENST00000405375ENST00000382515CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-3UTRENST00000405375ENST00000481267CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-3CDSENST00000373711ENST00000382518CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-3CDSENST00000373711ENST00000009180CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-5UTRENST00000373711ENST00000382515CDKN1Achr6

36646575

+CD9chr12

6334590

+
5UTR-3UTRENST00000373711ENST00000481267CDKN1Achr6

36646575

+CD9chr12

6334590

+
3UTR-3CDSENST00000478800ENST00000382518CDKN1Achr6

36646575

+CD9chr12

6334590

+
3UTR-3CDSENST00000478800ENST00000009180CDKN1Achr6

36646575

+CD9chr12

6334590

+
3UTR-5UTRENST00000478800ENST00000382515CDKN1Achr6

36646575

+CD9chr12

6334590

+
3UTR-3UTRENST00000478800ENST00000481267CDKN1Achr6

36646575

+CD9chr12

6334590

+

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 CDKN1A-CD9


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)
CDKN1Achr636646575+CD9chr126334591+0.196729960.80327
CDKN1Achr636646575+CD9chr126334591+0.196729960.80327

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

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Fusion Protein Features for CDKN1A-CD9


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CDKN1A

P38936

CD9

Q8TCZ2

FUNCTION: May be involved in p53/TP53 mediated inhibition of cellular proliferation in response to DNA damage. Binds to and inhibits cyclin-dependent kinase activity, preventing phosphorylation of critical cyclin-dependent kinase substrates and blocking cell cycle progression. Functions in the nuclear localization and assembly of cyclin D-CDK4 complex and promotes its kinase activity towards RB1. At higher stoichiometric ratios, inhibits the kinase activity of the cyclin D-CDK4 complex. Inhibits DNA synthesis by DNA polymerase delta by competing with POLD3 for PCNA binding (PubMed:11595739). Plays an important role in controlling cell cycle progression and DNA damage-induced G2 arrest (PubMed:9106657). {ECO:0000269|PubMed:11595739, ECO:0000269|PubMed:8242751, ECO:0000269|PubMed:9106657}.FUNCTION: Plays a role in a late step of leukocyte extravasation helping cells to overcome the endothelial basement membrane. Acts at the same site as, but independently of, PECAM1 (By similarity). Homophilic adhesion molecule, but these interactions may not be required for cell aggregation (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 CDKN1A-CD9


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 CDKN1A-CD9


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 CDKN1A-CD9


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneCDKN1AP38936DB01169Arsenic trioxideSmall moleculeApproved|Investigational
HgeneCDKN1AP38936DB01169Arsenic trioxideSmall moleculeApproved|Investigational
HgeneCDKN1AP38936DB01169Arsenic trioxideSmall moleculeApproved|Investigational
HgeneCDKN1AP38936DB01169Arsenic trioxideSmall moleculeApproved|Investigational
HgeneCDKN1AP38936DB01169Arsenic trioxideSmall moleculeApproved|Investigational
HgeneCDKN1AP38936DB01169Arsenic trioxideSmall moleculeApproved|Investigational
HgeneCDKN1AP38936DB01169Arsenic trioxideSmall moleculeApproved|Investigational
HgeneCDKN1AP38936DB01169Arsenic trioxideSmall moleculeApproved|Investigational

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Related Diseases for CDKN1A-CD9


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCDKN1AC0007138Carcinoma, Transitional Cell2CTD_human
HgeneCDKN1AC0021841Intestinal Neoplasms2CTD_human
HgeneCDKN1AC0024121Lung Neoplasms2CTD_human
HgeneCDKN1AC0033578Prostatic Neoplasms2CTD_human
HgeneCDKN1AC0242379Malignant neoplasm of lung2CTD_human
HgeneCDKN1AC0346627Intestinal Cancer2CTD_human
HgeneCDKN1AC0376358Malignant neoplasm of prostate2CTD_human
HgeneCDKN1AC0004238Atrial Fibrillation1CTD_human
HgeneCDKN1AC0005684Malignant neoplasm of urinary bladder1CTD_human
HgeneCDKN1AC0005695Bladder Neoplasm1CTD_human
HgeneCDKN1AC0007102Malignant tumor of colon1CTD_human
HgeneCDKN1AC0009375Colonic Neoplasms1CTD_human
HgeneCDKN1AC0011881Diabetic Nephropathy1CTD_human
HgeneCDKN1AC0017667Nodular glomerulosclerosis1CTD_human
HgeneCDKN1AC0019693HIV Infections1CTD_human
HgeneCDKN1AC0020564Hypertrophy1CTD_human
HgeneCDKN1AC0022658Kidney Diseases1CTD_human
HgeneCDKN1AC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneCDKN1AC0024623Malignant neoplasm of stomach1CTD_human
HgeneCDKN1AC0025267Multiple Endocrine Neoplasia Type 11ORPHANET
HgeneCDKN1AC0030354Papilloma1CTD_human
HgeneCDKN1AC0035126Reperfusion Injury1CTD_human
HgeneCDKN1AC0038356Stomach Neoplasms1CTD_human
HgeneCDKN1AC0205874Papilloma, Squamous Cell1CTD_human
HgeneCDKN1AC0205875Papillomatosis1CTD_human
HgeneCDKN1AC0235480Paroxysmal atrial fibrillation1CTD_human
HgeneCDKN1AC0238288Muscular Dystrophy, Facioscapulohumeral1CTD_human
HgeneCDKN1AC0279626Squamous cell carcinoma of esophagus1CTD_human
HgeneCDKN1AC0345967Malignant mesothelioma1CTD_human
HgeneCDKN1AC1708349Hereditary Diffuse Gastric Cancer1CTD_human
HgeneCDKN1AC2585653Persistent atrial fibrillation1CTD_human
HgeneCDKN1AC3468561familial atrial fibrillation1CTD_human
HgeneCDKN1AC4505456HIV Coinfection1CTD_human
TgeneCD9C0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneCD9C0009402Colorectal Carcinoma1CTD_human
TgeneCD9C0009404Colorectal Neoplasms1CTD_human
TgeneCD9C0017636Glioblastoma1CTD_human
TgeneCD9C0023467Leukemia, Myelocytic, Acute1CTD_human
TgeneCD9C0023890Liver Cirrhosis1CTD_human
TgeneCD9C0026998Acute Myeloid Leukemia, M11CTD_human
TgeneCD9C0027654Embryonal Neoplasm1CTD_human
TgeneCD9C0027658Neoplasms, Germ Cell and Embryonal1CTD_human
TgeneCD9C0027746Nerve Degeneration1CTD_human
TgeneCD9C0033578Prostatic Neoplasms1CTD_human
TgeneCD9C0205851Germ cell tumor1CTD_human
TgeneCD9C0205852Neoplasms, Embryonal and Mixed1CTD_human
TgeneCD9C0239946Fibrosis, Liver1CTD_human
TgeneCD9C0334588Giant Cell Glioblastoma1CTD_human
TgeneCD9C0376358Malignant neoplasm of prostate1CTD_human
TgeneCD9C0740345Germ Cell Cancer1CTD_human
TgeneCD9C0751364Cancer, Embryonal1CTD_human
TgeneCD9C0751365Cancer, Embryonal and Mixed1CTD_human
TgeneCD9C1621958Glioblastoma Multiforme1CTD_human
TgeneCD9C1879321Acute Myeloid Leukemia (AML-M2)1CTD_human