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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:MRPL48-CHKA (FusionGDB2 ID:55063)

Fusion Gene Summary for MRPL48-CHKA

check button Fusion gene summary
Fusion gene informationFusion gene name: MRPL48-CHKA
Fusion gene ID: 55063
HgeneTgene
Gene symbol

MRPL48

CHKA

Gene ID

51642

1119

Gene namemitochondrial ribosomal protein L48choline kinase alpha
SynonymsCGI-118|HSPC290|L48MT|MRP-L48CHK|CK|CKI|EK
Cytomap

11q13.4

11q13.2

Type of geneprotein-codingprotein-coding
Description39S ribosomal protein L48, mitochondrialmitochondrial large ribosomal subunit protein mL48choline kinase alphaCHETK-alphaethanolamine kinase
Modification date2020031320200313
UniProtAcc

Q96GC5

P35790

Ensembl transtripts involved in fusion geneENST00000310614, ENST00000542303, 
ENST00000411840, ENST00000535529, 
ENST00000314282, ENST00000398483, 
ENST00000265689, ENST00000356135, 
ENST00000533728, 
Fusion gene scores* DoF score16 X 9 X 9=129611 X 10 X 7=770
# samples 1913
** MAII scorelog2(19/1296*10)=-2.76999439455368
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/770*10)=-2.56634682255381
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MRPL48 [Title/Abstract] AND CHKA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMRPL48(73519395)-CHKA(67857347), # samples:2
MRPL48(73519395)-CHKA(67848924), # samples:2
Anticipated loss of major functional domain due to fusion event.MRPL48-CHKA seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
MRPL48-CHKA seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
MRPL48-CHKA 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
TgeneCHKA

GO:0006646

phosphatidylethanolamine biosynthetic process

19915674

TgeneCHKA

GO:0006656

phosphatidylcholine biosynthetic process

19915674


check buttonFusion gene breakpoints across MRPL48 (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 CHKA (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
ChimerDB4OVTCGA-10-0938-01AMRPL48chr11

73519395

+CHKAchr11

67848924

-
ChimerDB4OVTCGA-10-0938-01AMRPL48chr11

73519395

+CHKAchr11

67857347

-
ChimerDB4OVTCGA-10-0938MRPL48chr11

73519395

+CHKAchr11

67848924

-


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Fusion Gene ORF analysis for MRPL48-CHKA

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-intronENST00000310614ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67857347

-
5CDS-intronENST00000310614ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67857347

-
5CDS-intronENST00000310614ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67848924

-
5CDS-intronENST00000310614ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67857347

-
5CDS-intronENST00000310614ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67848924

-
5CDS-intronENST00000542303ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67857347

-
5CDS-intronENST00000542303ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67857347

-
5CDS-intronENST00000542303ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67848924

-
5CDS-intronENST00000542303ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67857347

-
5CDS-intronENST00000542303ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67848924

-
5UTR-3CDSENST00000411840ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67848924

-
5UTR-3CDSENST00000535529ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67848924

-
5UTR-intronENST00000411840ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67857347

-
5UTR-intronENST00000411840ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67857347

-
5UTR-intronENST00000411840ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67848924

-
5UTR-intronENST00000411840ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67857347

-
5UTR-intronENST00000411840ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67848924

-
5UTR-intronENST00000535529ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67857347

-
5UTR-intronENST00000535529ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67857347

-
5UTR-intronENST00000535529ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67848924

-
5UTR-intronENST00000535529ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67857347

-
5UTR-intronENST00000535529ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67848924

-
Frame-shiftENST00000310614ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67848924

-
Frame-shiftENST00000542303ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67848924

-
intron-3CDSENST00000314282ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67848924

-
intron-3CDSENST00000398483ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67848924

-
intron-intronENST00000314282ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67857347

-
intron-intronENST00000314282ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67857347

-
intron-intronENST00000314282ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67848924

-
intron-intronENST00000314282ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67857347

-
intron-intronENST00000314282ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67848924

-
intron-intronENST00000398483ENST00000265689MRPL48chr11

73519395

+CHKAchr11

67857347

-
intron-intronENST00000398483ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67857347

-
intron-intronENST00000398483ENST00000356135MRPL48chr11

73519395

+CHKAchr11

67848924

-
intron-intronENST00000398483ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67857347

-
intron-intronENST00000398483ENST00000533728MRPL48chr11

73519395

+CHKAchr11

67848924

-

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 MRPL48-CHKA


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 MRPL48-CHKA


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/:73519395/:67857347)
- 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
MRPL48

Q96GC5

CHKA

P35790

FUNCTION: Has a key role in phospholipid biosynthesis and may contribute to tumor cell growth. Catalyzes the first step in phosphatidylcholine biosynthesis. Contributes to phosphatidylethanolamine biosynthesis. Phosphorylates choline and ethanolamine. Has higher activity with choline. {ECO:0000269|PubMed:19915674}.

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 MRPL48-CHKA


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 MRPL48-CHKA


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 MRPL48-CHKA


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 MRPL48-CHKA


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