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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:MKRN1-DENND2A (FusionGDB2 ID:54113)

Fusion Gene Summary for MKRN1-DENND2A

check button Fusion gene summary
Fusion gene informationFusion gene name: MKRN1-DENND2A
Fusion gene ID: 54113
HgeneTgene
Gene symbol

MKRN1

DENND2A

Gene ID

23608

27147

Gene namemakorin ring finger protein 1DENN domain containing 2A
SynonymsRNF61FAM31D|KIAA1277
Cytomap

7q34

7q34

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase makorin-1RING finger protein 61RING-type E3 ubiquitin transferase makorin-1DENN domain-containing protein 2ADENN/MADD domain containing 2A
Modification date2020031320200313
UniProtAcc

Q9UHC7

Q9ULE3

Ensembl transtripts involved in fusion geneENST00000255977, ENST00000437223, 
ENST00000474576, ENST00000481705, 
ENST00000443720, ENST00000480552, 
ENST00000492720, ENST00000275884, 
ENST00000496613, ENST00000537639, 
Fusion gene scores* DoF score10 X 11 X 9=9909 X 7 X 8=504
# samples 1511
** MAII scorelog2(15/990*10)=-2.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/504*10)=-2.19592020997526
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MKRN1 [Title/Abstract] AND DENND2A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMKRN1(140171683)-DENND2A(140246739), # samples:3
MKRN1(140156452)-DENND2A(140219518), # samples:3
Anticipated loss of major functional domain due to fusion event.MKRN1-DENND2A seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
MKRN1-DENND2A seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneMKRN1

GO:0000209

protein polyubiquitination

19536131


check buttonFusion gene breakpoints across MKRN1 (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 DENND2A (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
ChimerDB4BLCATCGA-DK-A6B2-01AMKRN1chr7

140171683

-DENND2Achr7

140246739

-
ChimerDB4LGGTCGA-HT-A5RA-01AMKRN1chr7

140156452

-DENND2Achr7

140219518

-
ChimerDB4LGGTCGA-HT-A5RAMKRN1chr7

140156452

-DENND2Achr7

140219518

-


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Fusion Gene ORF analysis for MKRN1-DENND2A

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-intronENST00000255977ENST00000492720MKRN1chr7

140156452

-DENND2Achr7

140219518

-
5CDS-intronENST00000437223ENST00000492720MKRN1chr7

140156452

-DENND2Achr7

140219518

-
5CDS-intronENST00000474576ENST00000492720MKRN1chr7

140156452

-DENND2Achr7

140219518

-
5UTR-3CDSENST00000437223ENST00000275884MKRN1chr7

140171683

-DENND2Achr7

140246739

-
5UTR-3CDSENST00000437223ENST00000492720MKRN1chr7

140171683

-DENND2Achr7

140246739

-
5UTR-3CDSENST00000437223ENST00000496613MKRN1chr7

140171683

-DENND2Achr7

140246739

-
5UTR-3CDSENST00000437223ENST00000537639MKRN1chr7

140171683

-DENND2Achr7

140246739

-
5UTR-3CDSENST00000481705ENST00000275884MKRN1chr7

140171683

-DENND2Achr7

140246739

-
5UTR-3CDSENST00000481705ENST00000492720MKRN1chr7

140171683

-DENND2Achr7

140246739

-
5UTR-3CDSENST00000481705ENST00000496613MKRN1chr7

140171683

-DENND2Achr7

140246739

-
5UTR-3CDSENST00000481705ENST00000537639MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000255977ENST00000275884MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000255977ENST00000275884MKRN1chr7

140156452

-DENND2Achr7

140219518

-
Frame-shiftENST00000255977ENST00000492720MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000255977ENST00000496613MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000255977ENST00000496613MKRN1chr7

140156452

-DENND2Achr7

140219518

-
Frame-shiftENST00000255977ENST00000537639MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000255977ENST00000537639MKRN1chr7

140156452

-DENND2Achr7

140219518

-
Frame-shiftENST00000437223ENST00000275884MKRN1chr7

140156452

-DENND2Achr7

140219518

-
Frame-shiftENST00000437223ENST00000496613MKRN1chr7

140156452

-DENND2Achr7

140219518

-
Frame-shiftENST00000437223ENST00000537639MKRN1chr7

140156452

-DENND2Achr7

140219518

-
Frame-shiftENST00000443720ENST00000275884MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000443720ENST00000492720MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000443720ENST00000496613MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000443720ENST00000537639MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000474576ENST00000275884MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000474576ENST00000275884MKRN1chr7

140156452

-DENND2Achr7

140219518

-
Frame-shiftENST00000474576ENST00000492720MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000474576ENST00000496613MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000474576ENST00000496613MKRN1chr7

140156452

-DENND2Achr7

140219518

-
Frame-shiftENST00000474576ENST00000537639MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000474576ENST00000537639MKRN1chr7

140156452

-DENND2Achr7

140219518

-
Frame-shiftENST00000480552ENST00000275884MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000480552ENST00000492720MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000480552ENST00000496613MKRN1chr7

140171683

-DENND2Achr7

140246739

-
Frame-shiftENST00000480552ENST00000537639MKRN1chr7

140171683

-DENND2Achr7

140246739

-
intron-3CDSENST00000443720ENST00000275884MKRN1chr7

140156452

-DENND2Achr7

140219518

-
intron-3CDSENST00000443720ENST00000496613MKRN1chr7

140156452

-DENND2Achr7

140219518

-
intron-3CDSENST00000443720ENST00000537639MKRN1chr7

140156452

-DENND2Achr7

140219518

-
intron-3CDSENST00000480552ENST00000275884MKRN1chr7

140156452

-DENND2Achr7

140219518

-
intron-3CDSENST00000480552ENST00000496613MKRN1chr7

140156452

-DENND2Achr7

140219518

-
intron-3CDSENST00000480552ENST00000537639MKRN1chr7

140156452

-DENND2Achr7

140219518

-
intron-3CDSENST00000481705ENST00000275884MKRN1chr7

140156452

-DENND2Achr7

140219518

-
intron-3CDSENST00000481705ENST00000496613MKRN1chr7

140156452

-DENND2Achr7

140219518

-
intron-3CDSENST00000481705ENST00000537639MKRN1chr7

140156452

-DENND2Achr7

140219518

-
intron-intronENST00000443720ENST00000492720MKRN1chr7

140156452

-DENND2Achr7

140219518

-
intron-intronENST00000480552ENST00000492720MKRN1chr7

140156452

-DENND2Achr7

140219518

-
intron-intronENST00000481705ENST00000492720MKRN1chr7

140156452

-DENND2Achr7

140219518

-

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 MKRN1-DENND2A


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 MKRN1-DENND2A


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/:140171683/:140246739)
- 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
MKRN1

Q9UHC7

DENND2A

Q9ULE3

FUNCTION: E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. These substrates include FILIP1, p53/TP53, CDKN1A and TERT. Keeps cells alive by suppressing p53/TP53 under normal conditions, but stimulates apoptosis by repressing CDKN1A under stress conditions. Acts as a negative regulator of telomerase. Has negative and positive effects on RNA polymerase II-dependent transcription. {ECO:0000269|PubMed:16785614, ECO:0000269|PubMed:19536131}.FUNCTION: Guanine nucleotide exchange factor (GEF) which may activate RAB9A and RAB9B. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. May play a role in late endosomes back to trans-Golgi network/TGN transport. {ECO:0000269|PubMed:20937701}.

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 MKRN1-DENND2A


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 MKRN1-DENND2A


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 MKRN1-DENND2A


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 MKRN1-DENND2A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource