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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:RAD9A-KDM2A (FusionGDB2 ID:71349)

Fusion Gene Summary for RAD9A-KDM2A

check button Fusion gene summary
Fusion gene informationFusion gene name: RAD9A-KDM2A
Fusion gene ID: 71349
HgeneTgene
Gene symbol

RAD9A

KDM2A

Gene ID

5883

22992

Gene nameRAD9 checkpoint clamp component Alysine demethylase 2A
SynonymsRAD9CXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINA
Cytomap

11q13.2

11q13.2

Type of geneprotein-codingprotein-coding
Descriptioncell cycle checkpoint control protein RAD9ADNA repair exonuclease rad9 homolog ARAD9 homolog AhRAD9lysine-specific demethylase 2ACXXC-type zinc finger protein 8F-box and leucine-rich repeat protein 11F-box/LRR-repeat protein 11[Histone-H3]-lysine-36 demethylase 1AjmjC domain-containing histone demethylation protein 1Ajumonji C domain-containing h
Modification date2020032220200320
UniProtAcc.

Q9Y2K7

Ensembl transtripts involved in fusion geneENST00000307980, ENST00000535644, 
ENST00000398645, ENST00000529006, 
ENST00000526258, ENST00000308783, 
ENST00000530342, 
Fusion gene scores* DoF score8 X 50 X 13=520028 X 27 X 8=6048
# samples 4832
** MAII scorelog2(48/5200*10)=-3.4374053123073
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(32/6048*10)=-4.24031432933371
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RAD9A [Title/Abstract] AND KDM2A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRAD9A(67161261)-KDM2A(67024955), # 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
HgeneRAD9A

GO:0006974

cellular response to DNA damage stimulus

9872989

HgeneRAD9A

GO:0071479

cellular response to ionizing radiation

21659603


check buttonFusion gene breakpoints across RAD9A (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 KDM2A (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
ChimerDB4BRCATCGA-C8-A12Q-01ARAD9Achr11

67161261

+KDM2Achr11

67024955

+
ChimerDB4UCSTCGA-N5-A4RT-01ARAD9Achr11

67088804

+KDM2Achr11

66947550

+
ChimerDB4BRCATCGA-C8-A12Q-01ARAD9Achr11

67161261

+KDM2Achr11

67024955

+


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Fusion Gene ORF analysis for RAD9A-KDM2A

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
5CDS-3UTRENST00000307980ENST00000398645RAD9Achr11

67161261

+KDM2Achr11

67024955

+
5CDS-3UTRENST00000307980ENST00000529006RAD9Achr11

67161261

+KDM2Achr11

67024955

+
5CDS-3UTRENST00000307980ENST00000526258RAD9Achr11

67161261

+KDM2Achr11

67024955

+
5CDS-intronENST00000307980ENST00000308783RAD9Achr11

67161261

+KDM2Achr11

67024955

+
5CDS-intronENST00000307980ENST00000530342RAD9Achr11

67161261

+KDM2Achr11

67024955

+
intron-3UTRENST00000535644ENST00000398645RAD9Achr11

67161261

+KDM2Achr11

67024955

+
intron-3UTRENST00000535644ENST00000529006RAD9Achr11

67161261

+KDM2Achr11

67024955

+
intron-3UTRENST00000535644ENST00000526258RAD9Achr11

67161261

+KDM2Achr11

67024955

+
intron-intronENST00000535644ENST00000308783RAD9Achr11

67161261

+KDM2Achr11

67024955

+
intron-intronENST00000535644ENST00000530342RAD9Achr11

67161261

+KDM2Achr11

67024955

+
intron-3CDSENST00000307980ENST00000398645RAD9Achr11

67088804

+KDM2Achr11

66947550

+
intron-3CDSENST00000307980ENST00000529006RAD9Achr11

67088804

+KDM2Achr11

66947550

+
intron-intronENST00000307980ENST00000526258RAD9Achr11

67088804

+KDM2Achr11

66947550

+
intron-intronENST00000307980ENST00000308783RAD9Achr11

67088804

+KDM2Achr11

66947550

+
intron-intronENST00000307980ENST00000530342RAD9Achr11

67088804

+KDM2Achr11

66947550

+
intron-3CDSENST00000535644ENST00000398645RAD9Achr11

67088804

+KDM2Achr11

66947550

+
intron-3CDSENST00000535644ENST00000529006RAD9Achr11

67088804

+KDM2Achr11

66947550

+
intron-intronENST00000535644ENST00000526258RAD9Achr11

67088804

+KDM2Achr11

66947550

+
intron-intronENST00000535644ENST00000308783RAD9Achr11

67088804

+KDM2Achr11

66947550

+
intron-intronENST00000535644ENST00000530342RAD9Achr11

67088804

+KDM2Achr11

66947550

+

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 RAD9A-KDM2A


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)

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 RAD9A-KDM2A


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
.KDM2A

Q9Y2K7

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Histone demethylase that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. May also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis. Regulates circadian gene expression by repressing the transcriptional activator activity of CLOCK-ARNTL/BMAL1 heterodimer and RORA in a catalytically-independent manner (PubMed:26037310). {ECO:0000269|PubMed:16362057, ECO:0000269|PubMed:19001877, ECO:0000269|PubMed:26037310, ECO:0000269|PubMed:28262558}.

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 RAD9A-KDM2A


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 RAD9A-KDM2A


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 RAD9A-KDM2A


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 RAD9A-KDM2A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRAD9AC0085183Neoplasms, Second Primary1CTD_human
HgeneRAD9AC0086696Neoplasms, Therapy-Associated1CTD_human
HgeneRAD9AC0877578Treatment related secondary malignancy1CTD_human
TgeneKDM2AC0009402Colorectal Carcinoma1CTD_human
TgeneKDM2AC0009404Colorectal Neoplasms1CTD_human
TgeneKDM2AC2931456Prostate cancer, familial1CTD_human
TgeneKDM2AC4722327PROSTATE CANCER, HEREDITARY, 11CTD_human