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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:MRPL21-CPT1A (FusionGDB2 ID:HG219927TG1374)

Fusion Gene Summary for MRPL21-CPT1A

check button Fusion gene summary
Fusion gene informationFusion gene name: MRPL21-CPT1A
Fusion gene ID: hg219927tg1374
HgeneTgene
Gene symbol

MRPL21

CPT1A

Gene ID

219927

1374

Gene namemitochondrial ribosomal protein L21carnitine palmitoyltransferase 1A
SynonymsL21mt|MRP-L21CPT1|CPT1-L|L-CPT1
Cytomap('MRPL21')('CPT1A')

11q13.3

11q13.3

Type of geneprotein-codingprotein-coding
Description39S ribosomal protein L21, mitochondrialmitochondrial large ribosomal subunit protein bL21mcarnitine O-palmitoyltransferase 1, liver isoformCPT ICPTI-Lcarnitine O-palmitoyltransferase I, liver isoformcarnitine palmitoyltransferase 1A (liver)carnitine palmitoyltransferase I, liver
Modification date2020031320200315
UniProtAcc

Q7Z2W9

.
Ensembl transtripts involved in fusion geneENST00000362034, ENST00000450904, 
ENST00000567045, 
ENST00000362034, 
ENST00000450904, ENST00000567045, 
Fusion gene scores* DoF score12 X 14 X 10=168012 X 9 X 8=864
# samples 1715
** MAII scorelog2(17/1680*10)=-3.30485458152842
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(15/864*10)=-2.52606881166759
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MRPL21 [Title/Abstract] AND CPT1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMRPL21(68660357)-CPT1A(68582955), # samples:3
Anticipated loss of major functional domain due to fusion event.MRPL21-CPT1A seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
MRPL21-CPT1A seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
MRPL21-CPT1A 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
TgeneCPT1A

GO:0001676

long-chain fatty acid metabolic process

11350182

TgeneCPT1A

GO:0009437

carnitine metabolic process

11350182



check button Fusion gene information
* 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-XF-AAMZ-01AMRPL21chr11

68660358

-CPT1Achr11

68527806

-
ChimerDB4LGGTCGA-DU-5871MRPL21chr11

68660357

-CPT1Achr11

68582955

-
ChimerDB4LGGTCGA-FG-6691MRPL21chr11

68660357

-CPT1Achr11

68582955

-
ChimerDB4LGGTCGA-HW-8320MRPL21chr11

68660357

-CPT1Achr11

68582955

-


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Fusion Gene ORF analysis for MRPL21-CPT1A

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-5UTRENST00000362034ENST00000265641MRPL21chr11

68660357

-CPT1Achr11

68582955

-
5CDS-5UTRENST00000362034ENST00000376618MRPL21chr11

68660357

-CPT1Achr11

68582955

-
5CDS-5UTRENST00000362034ENST00000539743MRPL21chr11

68660357

-CPT1Achr11

68582955

-
5CDS-5UTRENST00000362034ENST00000540367MRPL21chr11

68660357

-CPT1Achr11

68582955

-
5CDS-5UTRENST00000450904ENST00000265641MRPL21chr11

68660357

-CPT1Achr11

68582955

-
5CDS-5UTRENST00000450904ENST00000376618MRPL21chr11

68660357

-CPT1Achr11

68582955

-
5CDS-5UTRENST00000450904ENST00000539743MRPL21chr11

68660357

-CPT1Achr11

68582955

-
5CDS-5UTRENST00000450904ENST00000540367MRPL21chr11

68660357

-CPT1Achr11

68582955

-
5CDS-intronENST00000362034ENST00000537756MRPL21chr11

68660358

-CPT1Achr11

68527806

-
5CDS-intronENST00000362034ENST00000537756MRPL21chr11

68660357

-CPT1Achr11

68582955

-
5CDS-intronENST00000362034ENST00000538994MRPL21chr11

68660358

-CPT1Achr11

68527806

-
5CDS-intronENST00000362034ENST00000538994MRPL21chr11

68660357

-CPT1Achr11

68582955

-
5CDS-intronENST00000450904ENST00000537756MRPL21chr11

68660358

-CPT1Achr11

68527806

-
5CDS-intronENST00000450904ENST00000537756MRPL21chr11

68660357

-CPT1Achr11

68582955

-
5CDS-intronENST00000450904ENST00000538994MRPL21chr11

68660358

-CPT1Achr11

68527806

-
5CDS-intronENST00000450904ENST00000538994MRPL21chr11

68660357

-CPT1Achr11

68582955

-
Frame-shiftENST00000362034ENST00000265641MRPL21chr11

68660358

-CPT1Achr11

68527806

-
Frame-shiftENST00000362034ENST00000376618MRPL21chr11

68660358

-CPT1Achr11

68527806

-
Frame-shiftENST00000362034ENST00000539743MRPL21chr11

68660358

-CPT1Achr11

68527806

-
Frame-shiftENST00000362034ENST00000540367MRPL21chr11

68660358

-CPT1Achr11

68527806

-
Frame-shiftENST00000450904ENST00000265641MRPL21chr11

68660358

-CPT1Achr11

68527806

-
Frame-shiftENST00000450904ENST00000376618MRPL21chr11

68660358

-CPT1Achr11

68527806

-
Frame-shiftENST00000450904ENST00000539743MRPL21chr11

68660358

-CPT1Achr11

68527806

-
Frame-shiftENST00000450904ENST00000540367MRPL21chr11

68660358

-CPT1Achr11

68527806

-
intron-3CDSENST00000567045ENST00000265641MRPL21chr11

68660358

-CPT1Achr11

68527806

-
intron-3CDSENST00000567045ENST00000376618MRPL21chr11

68660358

-CPT1Achr11

68527806

-
intron-3CDSENST00000567045ENST00000539743MRPL21chr11

68660358

-CPT1Achr11

68527806

-
intron-3CDSENST00000567045ENST00000540367MRPL21chr11

68660358

-CPT1Achr11

68527806

-
intron-5UTRENST00000567045ENST00000265641MRPL21chr11

68660357

-CPT1Achr11

68582955

-
intron-5UTRENST00000567045ENST00000376618MRPL21chr11

68660357

-CPT1Achr11

68582955

-
intron-5UTRENST00000567045ENST00000539743MRPL21chr11

68660357

-CPT1Achr11

68582955

-
intron-5UTRENST00000567045ENST00000540367MRPL21chr11

68660357

-CPT1Achr11

68582955

-
intron-intronENST00000567045ENST00000537756MRPL21chr11

68660358

-CPT1Achr11

68527806

-
intron-intronENST00000567045ENST00000537756MRPL21chr11

68660357

-CPT1Achr11

68582955

-
intron-intronENST00000567045ENST00000538994MRPL21chr11

68660358

-CPT1Achr11

68527806

-
intron-intronENST00000567045ENST00000538994MRPL21chr11

68660357

-CPT1Achr11

68582955

-

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 MRPL21-CPT1A


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 MRPL21-CPT1A


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/:68660357/:68582955)
- 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
MRPL21

Q7Z2W9

.
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}.

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 MRPL21-CPT1A


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 MRPL21-CPT1A


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 MRPL21-CPT1A


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 MRPL21-CPT1A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC1829703Carnitine palmitoyl transferase 1A deficiency13CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0002152Alloxan Diabetes1CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0011849Diabetes Mellitus1CTD_human
TgeneC0011853Diabetes Mellitus, Experimental1CTD_human
TgeneC0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
TgeneC0022661Kidney Failure, Chronic1CTD_human
TgeneC0038433Streptozotocin Diabetes1CTD_human
TgeneC0400966Non-alcoholic Fatty Liver Disease1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC3241937Nonalcoholic Steatohepatitis1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human