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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:MRPL4-DNMT3A (FusionGDB2 ID:HG51073TG1788)

Fusion Gene Summary for MRPL4-DNMT3A

check button Fusion gene summary
Fusion gene informationFusion gene name: MRPL4-DNMT3A
Fusion gene ID: hg51073tg1788
HgeneTgene
Gene symbol

MRPL4

DNMT3A

Gene ID

51073

1788

Gene namemitochondrial ribosomal protein L4DNA methyltransferase 3 alpha
SynonymsCGI-28|L4mtDNMT3A2|HESJAS|M.HsaIIIA|TBRS
Cytomap('MRPL4')('DNMT3A')

19p13.2

2p23.3

Type of geneprotein-codingprotein-coding
Description39S ribosomal protein L4, mitochondrialMRP-L4mitochondrial large ribosomal subunit protein uL4mDNA (cytosine-5)-methyltransferase 3ADNA (cytosine-5-)-methyltransferase 3 alphaDNA MTase HsaIIIADNA cytosine methyltransferase 3A2
Modification date2020031320200322
UniProtAcc.

Q9Y6K1

Ensembl transtripts involved in fusion geneENST00000393733, ENST00000253099, 
ENST00000307422, ENST00000588502, 
ENST00000590669, 
Fusion gene scores* DoF score6 X 7 X 2=844 X 4 X 3=48
# samples 74
** MAII scorelog2(7/84*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MRPL4 [Title/Abstract] AND DNMT3A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMRPL4(10370361)-DNMT3A(25493422), # samples:1
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
TgeneDNMT3A

GO:0006306

DNA methylation

12138111|19786833|23042785



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
ChiTaRS5.0N/ACA454864MRPL4chr19

10370361

+DNMT3Achr2

25493422

+


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Fusion Gene ORF analysis for MRPL4-DNMT3A

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-intronENST00000393733ENST00000264709MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
3UTR-intronENST00000393733ENST00000321117MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
3UTR-intronENST00000393733ENST00000380746MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
3UTR-intronENST00000393733ENST00000402667MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
3UTR-intronENST00000393733ENST00000406659MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
3UTR-intronENST00000393733ENST00000474887MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000253099ENST00000264709MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000253099ENST00000321117MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000253099ENST00000380746MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000253099ENST00000402667MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000253099ENST00000406659MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000253099ENST00000474887MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000307422ENST00000264709MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000307422ENST00000321117MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000307422ENST00000380746MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000307422ENST00000402667MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000307422ENST00000406659MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
5CDS-intronENST00000307422ENST00000474887MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000588502ENST00000264709MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000588502ENST00000321117MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000588502ENST00000380746MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000588502ENST00000402667MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000588502ENST00000406659MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000588502ENST00000474887MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000590669ENST00000264709MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000590669ENST00000321117MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000590669ENST00000380746MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000590669ENST00000402667MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000590669ENST00000406659MRPL4chr19

10370361

+DNMT3Achr2

25493422

+
intron-intronENST00000590669ENST00000474887MRPL4chr19

10370361

+DNMT3Achr2

25493422

+

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 MRPL4-DNMT3A


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)


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Fusion Protein Features for MRPL4-DNMT3A


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/:10370361/:25493422)
- 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
.DNMT3A

Q9Y6K1

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: Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. It modifies DNA in a non-processive manner and also methylates non-CpG sites. May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. Plays a role in paternal and maternal imprinting. Required for methylation of most imprinted loci in germ cells. Acts as a transcriptional corepressor for ZBTB18. Recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. Can actively repress transcription through the recruitment of HDAC activity. {ECO:0000269|PubMed:16357870, ECO:0000269|PubMed:30478443}.

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 MRPL4-DNMT3A


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 MRPL4-DNMT3A


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 MRPL4-DNMT3A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneDNMT3AQ9Y6K1DB01262DecitabineInhibitorSmall moleculeApproved|Investigational
TgeneDNMT3AQ9Y6K1DB00721ProcaineInhibitorSmall moleculeApproved|Investigational|Vet_approved

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Related Diseases for MRPL4-DNMT3A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC4014545Tatton Brown Rahman syndrome4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0018273Growth Disorders2CTD_human
TgeneC0079774Peripheral T-Cell Lymphoma2CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0010346Crohn Disease1CTD_human
TgeneC0013336Dwarfism1CTD_human
TgeneC0020796Profound Mental Retardation1CTD_human
TgeneC0020981Angioimmunoblastic Lymphadenopathy1CTD_human
TgeneC0023465Acute monocytic leukemia1CTD_human
TgeneC0023487Acute Promyelocytic Leukemia1CTD_human
TgeneC0024121Lung Neoplasms1CTD_human
TgeneC0025363Mental Retardation, Psychosocial1CTD_human
TgeneC0025958Microcephaly1CTD_human
TgeneC0027643Neoplasm Recurrence, Local1CTD_human
TgeneC0036920Sezary Syndrome1CTD_human
TgeneC0079773Lymphoma, T-Cell, Cutaneous1CTD_human
TgeneC0156147Crohn's disease of large bowel1CTD_human
TgeneC0242379Malignant neoplasm of lung1CTD_human
TgeneC0265202Seckel syndrome1GENOMICS_ENGLAND
TgeneC0267380Crohn's disease of the ileum1CTD_human
TgeneC0282631Facies1CTD_human
TgeneC0349639Juvenile Myelomonocytic Leukemia1CTD_human
TgeneC0376407Granulomatous Slack Skin1CTD_human
TgeneC0376634Craniofacial Abnormalities1CTD_human
TgeneC0678202Regional enteritis1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC0917816Mental deficiency1CTD_human
TgeneC0949272IIeocolitis1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1510586Autism Spectrum Disorders1CTD_human
TgeneC1956147Microlissencephaly1CTD_human
TgeneC2931852Clear-cell metastatic renal cell carcinoma1CTD_human
TgeneC3496069cocaine use1PSYGENET
TgeneC3714756Intellectual Disability1CTD_human
TgeneC3853041Severe Congenital Microcephaly1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human