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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:CLIP1-MCEE (FusionGDB2 ID:HG6249TG84693)

Fusion Gene Summary for CLIP1-MCEE

check button Fusion gene summary
Fusion gene informationFusion gene name: CLIP1-MCEE
Fusion gene ID: hg6249tg84693
HgeneTgene
Gene symbol

CLIP1

MCEE

Gene ID

6249

84693

Gene nameCAP-Gly domain containing linker protein 1methylmalonyl-CoA epimerase
SynonymsCLIP|CLIP-170|CLIP170|CYLN1|RSNGLOD2
Cytomap('CLIP1')('MCEE')

12q24.31

2p13.3

Type of geneprotein-codingprotein-coding
DescriptionCAP-Gly domain-containing linker protein 1cytoplasmic linker protein 1cytoplasmic linker protein 170 alpha-2cytoplasmic linker protein CLIP-170restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)methylmalonyl-CoA epimerase, mitochondrialDL-methylmalonyl-CoA racemaseglyoxalase domain containing 2
Modification date2020031320200313
UniProtAcc

P30622

Q96PE7

Ensembl transtripts involved in fusion geneENST00000358808, ENST00000361654, 
ENST00000537178, ENST00000302528, 
ENST00000536634, ENST00000540338, 
ENST00000540539, ENST00000545889, 
Fusion gene scores* DoF score22 X 22 X 13=62924 X 4 X 2=32
# samples 314
** MAII scorelog2(31/6292*10)=-4.34317855014145
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CLIP1 [Title/Abstract] AND MCEE [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLIP1(122907067)-MCEE(71337252), # samples:2
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
TgeneMCEE

GO:0046491

L-methylmalonyl-CoA metabolic process

11481338



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
ChimerDB4PRADTCGA-EJ-7325CLIP1chr12

122907067

-MCEEchr2

71337252

-


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Fusion Gene ORF analysis for CLIP1-MCEE

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
5UTR-3CDSENST00000358808ENST00000244217CLIP1chr12

122907067

-MCEEchr2

71337252

-
5UTR-3CDSENST00000361654ENST00000244217CLIP1chr12

122907067

-MCEEchr2

71337252

-
5UTR-3CDSENST00000537178ENST00000244217CLIP1chr12

122907067

-MCEEchr2

71337252

-
5UTR-5UTRENST00000358808ENST00000462609CLIP1chr12

122907067

-MCEEchr2

71337252

-
5UTR-5UTRENST00000361654ENST00000462609CLIP1chr12

122907067

-MCEEchr2

71337252

-
5UTR-5UTRENST00000537178ENST00000462609CLIP1chr12

122907067

-MCEEchr2

71337252

-
intron-3CDSENST00000302528ENST00000244217CLIP1chr12

122907067

-MCEEchr2

71337252

-
intron-3CDSENST00000536634ENST00000244217CLIP1chr12

122907067

-MCEEchr2

71337252

-
intron-3CDSENST00000540338ENST00000244217CLIP1chr12

122907067

-MCEEchr2

71337252

-
intron-3CDSENST00000540539ENST00000244217CLIP1chr12

122907067

-MCEEchr2

71337252

-
intron-3CDSENST00000545889ENST00000244217CLIP1chr12

122907067

-MCEEchr2

71337252

-
intron-5UTRENST00000302528ENST00000462609CLIP1chr12

122907067

-MCEEchr2

71337252

-
intron-5UTRENST00000536634ENST00000462609CLIP1chr12

122907067

-MCEEchr2

71337252

-
intron-5UTRENST00000540338ENST00000462609CLIP1chr12

122907067

-MCEEchr2

71337252

-
intron-5UTRENST00000540539ENST00000462609CLIP1chr12

122907067

-MCEEchr2

71337252

-
intron-5UTRENST00000545889ENST00000462609CLIP1chr12

122907067

-MCEEchr2

71337252

-

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 CLIP1-MCEE


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 CLIP1-MCEE


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/:122907067/:71337252)
- 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
CLIP1

P30622

MCEE

Q96PE7

FUNCTION: Binds to the plus end of microtubules and regulates the dynamics of the microtubule cytoskeleton. Promotes microtubule growth and microtubule bundling. Links cytoplasmic vesicles to microtubules and thereby plays an important role in intracellular vesicle trafficking. Plays a role macropinocytosis and endosome trafficking. {ECO:0000269|PubMed:12433698, ECO:0000269|PubMed:17563362, ECO:0000269|PubMed:17889670}.FUNCTION: Methylmalonyl-CoA epimerase involved in propionyl-CoA metabolism. {ECO:0000269|PubMed:11481338}.

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 CLIP1-MCEE


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 CLIP1-MCEE


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 CLIP1-MCEE


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 CLIP1-MCEE


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC1855100Methylmalonyl-CoA Epimerase Deficiency3CTD_human;GENOMICS_ENGLAND;ORPHANET