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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:RPL13-MAPKAPK3 (FusionGDB2 ID:75915)

Fusion Gene Summary for RPL13-MAPKAPK3

check button Fusion gene summary
Fusion gene informationFusion gene name: RPL13-MAPKAPK3
Fusion gene ID: 75915
HgeneTgene
Gene symbol

RPL13

MAPKAPK3

Gene ID

28998

7867

Gene namemitochondrial ribosomal protein L13MAPK activated protein kinase 3
SynonymsL13|L13A|L13mt|RPL13|RPML133PK|MAPKAP-K3|MAPKAP3|MAPKAPK-3|MDPT3|MK-3|MK3
Cytomap

8q24.12

3p21.2

Type of geneprotein-codingprotein-coding
Description39S ribosomal protein L13, mitochondrialMRP-L13mitochondrial large ribosomal subunit protein uL13mMAP kinase-activated protein kinase 3MAPKAP kinase 3chromosome 3p kinasemitogen-activated protein kinase-activated protein kinase 3
Modification date2020031320200327
UniProtAcc.

Q16644

Ensembl transtripts involved in fusion geneENST00000311528, ENST00000393099, 
ENST00000452368, ENST00000567815, 
ENST00000357955, ENST00000497283, 
ENST00000446044, 
Fusion gene scores* DoF score19 X 18 X 4=13682 X 2 X 2=8
# samples 202
** MAII scorelog2(20/1368*10)=-2.77399632511117
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: RPL13 [Title/Abstract] AND MAPKAPK3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRPL13(89629431)-MAPKAPK3(50683209), # samples:1
Anticipated loss of major functional domain due to fusion event.RPL13-MAPKAPK3 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
RPL13-MAPKAPK3 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
RPL13-MAPKAPK3 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
RPL13-MAPKAPK3 seems lost the major protein functional domain in Tgene partner, which is a kinase 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
TgeneMAPKAPK3

GO:0018105

peptidyl-serine phosphorylation

15850461

TgeneMAPKAPK3

GO:0034097

response to cytokine

8774846


check buttonFusion gene breakpoints across RPL13 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across MAPKAPK3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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/AAA524181RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-


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Fusion Gene ORF analysis for RPL13-MAPKAPK3

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-intronENST00000311528ENST00000357955RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-
5CDS-intronENST00000311528ENST00000497283RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-
5CDS-intronENST00000393099ENST00000357955RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-
5CDS-intronENST00000393099ENST00000497283RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-
5CDS-intronENST00000452368ENST00000357955RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-
5CDS-intronENST00000452368ENST00000497283RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-
5CDS-intronENST00000567815ENST00000357955RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-
5CDS-intronENST00000567815ENST00000497283RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-
Frame-shiftENST00000311528ENST00000446044RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-
Frame-shiftENST00000393099ENST00000446044RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-
Frame-shiftENST00000567815ENST00000446044RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-
In-frameENST00000452368ENST00000446044RPL13chr16

89629431

-MAPKAPK3chr3

50683209

-

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)
ENST00000452368RPL13chr1689629431-ENST00000446044MAPKAPK3chr350683209-3010131512421766174

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
ENST00000452368ENST00000446044RPL13chr1689629431-MAPKAPK3chr350683209-0.0112417780.9887582

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Fusion Genomic Features for RPL13-MAPKAPK3


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.
genomic feature

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 RPL13-MAPKAPK3


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/chr16:89629431/chr3:50683209)
- 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
.MAPKAPK3

Q16644

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: Stress-activated serine/threonine-protein kinase involved in cytokines production, endocytosis, cell migration, chromatin remodeling and transcriptional regulation. Following stress, it is phosphorylated and activated by MAP kinase p38-alpha/MAPK14, leading to phosphorylation of substrates. Phosphorylates serine in the peptide sequence, Hyd-X-R-X(2)-S, where Hyd is a large hydrophobic residue. MAPKAPK2 and MAPKAPK3, share the same function and substrate specificity, but MAPKAPK3 kinase activity and level in protein expression are lower compared to MAPKAPK2. Phosphorylates HSP27/HSPB1, KRT18, KRT20, RCSD1, RPS6KA3, TAB3 and TTP/ZFP36. Mediates phosphorylation of HSP27/HSPB1 in response to stress, leading to dissociate HSP27/HSPB1 from large small heat-shock protein (sHsps) oligomers and impair their chaperone activities and ability to protect against oxidative stress effectively. Involved in inflammatory response by regulating tumor necrosis factor (TNF) and IL6 production post-transcriptionally: acts by phosphorylating AU-rich elements (AREs)-binding proteins, such as TTP/ZFP36, leading to regulate the stability and translation of TNF and IL6 mRNAs. Phosphorylation of TTP/ZFP36, a major post-transcriptional regulator of TNF, promotes its binding to 14-3-3 proteins and reduces its ARE mRNA affinity leading to inhibition of dependent degradation of ARE-containing transcript. Involved in toll-like receptor signaling pathway (TLR) in dendritic cells: required for acute TLR-induced macropinocytosis by phosphorylating and activating RPS6KA3. Also acts as a modulator of Polycomb-mediated repression. {ECO:0000269|PubMed:10383393, ECO:0000269|PubMed:15563468, ECO:0000269|PubMed:18021073, ECO:0000269|PubMed:20599781, ECO:0000269|PubMed:8626550, ECO:0000269|PubMed:8774846}.

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
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST0000035795501144_3040383.0DomainProtein kinase
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST0000044604401344_3040383.0DomainProtein kinase
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST00000357955011335_3440383.0MotifNuclear export signal (NES)
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST00000357955011350_3530383.0MotifBipartite nuclear localization signal 1
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST00000357955011364_3680383.0MotifBipartite nuclear localization signal 2
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST00000446044013335_3440383.0MotifNuclear export signal (NES)
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST00000446044013350_3530383.0MotifBipartite nuclear localization signal 1
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST00000446044013364_3680383.0MotifBipartite nuclear localization signal 2
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST0000035795501150_580383.0Nucleotide bindingATP
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST0000044604401350_580383.0Nucleotide bindingATP
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST00000357955011307_3430383.0RegionAutoinhibitory helix
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST00000357955011345_3690383.0Regionp38 MAPK-binding site
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST00000446044013307_3430383.0RegionAutoinhibitory helix
TgeneMAPKAPK3chr16:89629431chr3:50683209ENST00000446044013345_3690383.0Regionp38 MAPK-binding site

- 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 RPL13-MAPKAPK3


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.
>75915_75915_1_RPL13-MAPKAPK3_RPL13_chr16_89629431_ENST00000452368_MAPKAPK3_chr3_50683209_ENST00000446044_length(transcript)=3010nt_BP=1315nt
TTTCCGCTCGGCTGTTTTCCTGCGCAGGAGCCGCAGGGCCGTAGGCAGCCATGGCGCCCAGCCGGAATGGCATGGTCTTGAAGCCCCACT
TCCACAAGGACTGGCAGCGGCGCGTGGCCACGTGGTTCAACCAGCCGGCCCGTAAGATCCGCAGACGTAAGGCCCGGCAAGCCAAGGCGC
GCCGCATCGCCCCGCGCCCCGCGTCGGGTCCCATCCGGCCCATCGTGCGCTGCCCCACGGTTCGGTACCACACGAAGGTGCGCGCCGGCC
GCGGCTTCAGCCTGGAGGAGCTCAGGGTGGCCGGCATTCACAAGAAGGGAGACAGTTCTGCTGAAGAACTGAAACTGGCCACCCAGCTGA
CCGGACCGGTCATGCCCGTCCGGAACTGTTGAAAAGAAAAAATAAAGCCCTCCTGGGGACTTGGAATCAGTCGGCAGTCATGCTGGGTCT
CCACGTGGTGTGTTTCGTGGGAACAACTGGGCCTGGGATGGGGCTTCACTGCTGTGACTTCCTCCTGCCAGGGGATTTGGGGCTTTCTTG
AAAGACAGTCCAAGCCCTGGATAATGCTTTACTTTCTGTGTTGAAGCACTGTTGGTTGTTTGGTTAGTGACTGATGTAAAACGGTTTTCT
TGTGGGGAGGTTACAGAGGCTGACTTCAGAGTGGACTTGTGTTTTTTCTTTTTAAAGAGGCAAGGTTGGGCTGGTGCTCACAGCTGTAAT
CCCAGCACTTTGAGGTTGGCTGGGAGTTCAAGACCAGCCTGGCCAACATGTCAGAACTACTAAAAATAAAGAAATCAGCCATGCTTGGTG
CTGCACACTTGTAGTTGCAGCTCCTGGGAGGCAGAGGTGAGGGATCACTTAACCCAGGAGGCAGAGGCTGCACTGAGCCAGGATCACGCC
ACTGCACTCTAGCCTGGGCAACAGTGAGACTGTCTCAAAAAAAAAAAAAGAGACAGGGTCTTCGGCACCCAGGCTGGAGTACAGTGCCAC
AATCATGGCTCACTGCAGTCTTGAACTCATGGCCTCAAGCAGTCCTCCCTCAGCCTCCCAAGTAGAGGGGTTTATAGGCACGAGACCCTG
CACCCAACCTAGAGTTGCCTTTTTTAAGCAAAGCAGTTTCTAGTTAATGTAGCATCTTGGACTTTGGGGCGTCATTCTTAAGCTTGTTGT
GCCCGGTAACCATGGTCCTCTTGCTCTGATTAACCCTTCCTTCAATGGGCTTCTTCACCCAGACACCAAGGTATGAGATGGCCCTGCCAA
GTGTCGGCCTCTCCTGTTAAACAAAAACATTCTAAAGCCATTGTTCTTGCTTCATACATCCTCCTTTGTGGCTTCCCACCCTTCTACTCC
AACACGGGCCAGGCCATCTCCCCGGGGATGAAGAGGAGGATTCGCCTGGGCCAGTACGGCTTCCCCAATCCTGAGTGGTCAGAAGTCTCT
GAGGATGCCAAGCAGCTGATCCGCCTCCTGTTGAAGACAGACCCCACAGAGAGGCTGACCATCACTCAGTTCATGAACCACCCCTGGATC
AACCAATCGATGGTAGTGCCACAGACCCCACTCCACACGGCCCGAGTGCTGCAGGAGGACAAAGACCACTGGGACGAAGTCAAGGAGGAG
ATGACCAGTGCCTTGGCCACTATGCGGGTAGACTACGACCAGGTGAAGATCAAGGACCTGAAGACCTCTAACAACCGGCTCCTCAACAAG
AGGAGAAAAAAGCAGGCAGGCAGCTCCTCTGCCTCACAGGGCTGCAACAACCAGTAGCTCATGGGGCCTTGGAGGAGCCTGGCCTCTCAG
CCTGCATAACAGACTGAAATGTGCTCAGGCCCTGGCCAGGAGGGCCCAGGGTCATTCTTTTAACAAAAGGATTATTTTGTTGTGTTTTAA
TTTGTCACTCGGAACTTCAGGATGGAGGACCCTGACCCTAAACCTCCTTCAGATCTCTGGCCCAGGCTCAAGCCCTAGAGATGGGCAGGG
CCTAGGGGCTGGGAGCTGCCTGCTGCCATAGCAGCACCTTTAGCTAGGTTGGCCCGAGTGAGGCCTCTGTGCTGTCCTGCCCTGGTGCAT
GGCCTTAGCTTTCTAGGCCACTGGGAGTTGTGGCTGGGCTTCCCATCTTCCACAGAGACATCTCCCTGTGGGATGGGCAGATGGGCCTGG
CCTTGAGAAAGGCATTGGCCATTGGTTGCCATGGTGACCAGGGACCACGTTGCTGCCTGTGAATGCTGAGTGAGCGAGTAAGGGAGGAGG
GGCGATTGAGGGTTCACCTCTGCCTTGGGGAGGCTGATTTCTCACACACTGGCTGGCCCTCTCATTCTCACTCCTCCTTGGGCCCTGAGG
CTGCTGGATCCGGTCTGCCTGCCTCCCTGTGCAGTCCAGCCCTGCCTTGCTGCAGCCCCAGCCCAGATGGCACTCAGCGCTCTCCCCTGA
GGGAGTCCCTGGGCCTAGCCATCCCCTCACTATTCCCGACCCAAAGGGTGACTTTTCATCTGAACTTAAGGTGGGAGATATTTTTAACTT
TTTTCCACTTTGGAAAATGTCACTGTGACAAAAGCCAGCATACTTTCCCTGCACCCATCTGCTCACCAGATCTCAGGCAGGAAAGCCCCT
CTCTGTTGAAGTCAGGGGCTATCTTTTGGTATACTTGTGTGAAAGTGGCTGGTTGGGAGCAGAGCTAAGTGGCTTCCCATTAACCTGAGG
TCTCTTTCTTTACTCTGGGTCAGACCTGAGGTTGGGGAAGGCGACTGAGCCATGCTCAGAATGTCTGGTCCTGGCTTGGGCCTGAGTAGG
GCAGAGAGGGCCTTTCCTGGCTGATCAGAGCTTACCAGCCCCACCCCACCATGGTAGCCTTAGGGTGCTGAGTGCCTGATACTGCCTGAC
AAGTGCCTGACACGCAGCCTAGTTCCTTCCTGGCCCCTCTCTCACTGGCTGGGAAACCCTAGACCATGTCAGATAGGACAACACTGCTGG

>75915_75915_1_RPL13-MAPKAPK3_RPL13_chr16_89629431_ENST00000452368_MAPKAPK3_chr3_50683209_ENST00000446044_length(amino acids)=174AA_BP=
MRWPCQVSASPVKQKHSKAIVLASYILLCGFPPFYSNTGQAISPGMKRRIRLGQYGFPNPEWSEVSEDAKQLIRLLLKTDPTERLTITQF

--------------------------------------------------------------

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Fusion Gene PPI Analysis for RPL13-MAPKAPK3


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 RPL13-MAPKAPK3


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 RPL13-MAPKAPK3


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