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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:CPSF3L-MYL6 (FusionGDB2 ID:HG54973TG4637)

Fusion Gene Summary for CPSF3L-MYL6

check button Fusion gene summary
Fusion gene informationFusion gene name: CPSF3L-MYL6
Fusion gene ID: hg54973tg4637
HgeneTgene
Gene symbol

CPSF3L

MYL6

Gene ID

54973

4637

Gene nameintegrator complex subunit 11myosin light chain 6
SynonymsCPSF3L|CPSF73L|INT11|RC-68|RC68ESMLC|LC17|LC17-GI|LC17-NM|LC17A|LC17B|MLC-3|MLC1SM|MLC3NM|MLC3SM
Cytomap('CPSF3L')('MYL6')

1p36.33

12q13.2

Type of geneprotein-codingprotein-coding
Descriptionintegrator complex subunit 11CPSF3-like proteincleavage and polyadenylation specific factor 3-likecleavage and polyadenylation-specific factor 3-like proteinprotein related to CPSF subunits of 68 kDarelated to CPSF subunits 68 kDamyosin light polypeptide 617 kDa myosin light chainmyosin light chain A3myosin light chain alkali 3myosin, light chain 6, alkali, smooth muscle and non-musclemyosin, light polypeptide 6, alkali, smooth muscle and non-muscle
Modification date2020031320200313
UniProtAcc.

P60660

Ensembl transtripts involved in fusion geneENST00000435064, ENST00000450926, 
ENST00000540437, ENST00000545578, 
ENST00000411962, ENST00000419704, 
ENST00000421495, ENST00000462432, 
Fusion gene scores* DoF score8 X 8 X 6=38417 X 20 X 7=2380
# samples 1020
** MAII scorelog2(10/384*10)=-1.94110631094643
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(20/2380*10)=-3.57288966842058
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CPSF3L [Title/Abstract] AND MYL6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCPSF3L(1255835)-MYL6(56555170), # 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
HgeneCPSF3L

GO:0016180

snRNA processing

16239144



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
ChimerDB4Non-Cancer257NCPSF3Lchr1

1255835

-MYL6chr12

56555170

+


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Fusion Gene ORF analysis for CPSF3L-MYL6

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-3UTRENST00000435064ENST00000293422CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000435064ENST00000348108CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000435064ENST00000548400CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000435064ENST00000548580CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000435064ENST00000549017CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000435064ENST00000549566CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000435064ENST00000550697CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000450926ENST00000293422CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000450926ENST00000348108CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000450926ENST00000548400CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000450926ENST00000548580CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000450926ENST00000549017CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000450926ENST00000549566CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000450926ENST00000550697CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000540437ENST00000293422CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000540437ENST00000348108CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000540437ENST00000548400CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000540437ENST00000548580CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000540437ENST00000549017CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000540437ENST00000549566CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000540437ENST00000550697CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000545578ENST00000293422CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000545578ENST00000348108CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000545578ENST00000548400CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000545578ENST00000548580CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000545578ENST00000549017CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000545578ENST00000549566CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-3UTRENST00000545578ENST00000550697CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000435064ENST00000536128CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000435064ENST00000547408CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000435064ENST00000547649CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000435064ENST00000548293CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000435064ENST00000551589CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000435064ENST00000551954CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000450926ENST00000536128CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000450926ENST00000547408CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000450926ENST00000547649CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000450926ENST00000548293CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000450926ENST00000551589CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000450926ENST00000551954CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000540437ENST00000536128CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000540437ENST00000547408CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000540437ENST00000547649CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000540437ENST00000548293CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000540437ENST00000551589CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000540437ENST00000551954CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000545578ENST00000536128CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000545578ENST00000547408CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000545578ENST00000547649CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000545578ENST00000548293CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000545578ENST00000551589CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
5CDS-intronENST00000545578ENST00000551954CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000411962ENST00000293422CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000411962ENST00000348108CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000411962ENST00000548400CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000411962ENST00000548580CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000411962ENST00000549017CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000411962ENST00000549566CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000411962ENST00000550697CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000419704ENST00000293422CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000419704ENST00000348108CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000419704ENST00000548400CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000419704ENST00000548580CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000419704ENST00000549017CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000419704ENST00000549566CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000419704ENST00000550697CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000421495ENST00000293422CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000421495ENST00000348108CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000421495ENST00000548400CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000421495ENST00000548580CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000421495ENST00000549017CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000421495ENST00000549566CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000421495ENST00000550697CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000462432ENST00000293422CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000462432ENST00000348108CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000462432ENST00000548400CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000462432ENST00000548580CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000462432ENST00000549017CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000462432ENST00000549566CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-3UTRENST00000462432ENST00000550697CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000411962ENST00000536128CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000411962ENST00000547408CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000411962ENST00000547649CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000411962ENST00000548293CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000411962ENST00000551589CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000411962ENST00000551954CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000419704ENST00000536128CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000419704ENST00000547408CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000419704ENST00000547649CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000419704ENST00000548293CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000419704ENST00000551589CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000419704ENST00000551954CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000421495ENST00000536128CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000421495ENST00000547408CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000421495ENST00000547649CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000421495ENST00000548293CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000421495ENST00000551589CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000421495ENST00000551954CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000462432ENST00000536128CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000462432ENST00000547408CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000462432ENST00000547649CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000462432ENST00000548293CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000462432ENST00000551589CPSF3Lchr1

1255835

-MYL6chr12

56555170

+
intron-intronENST00000462432ENST00000551954CPSF3Lchr1

1255835

-MYL6chr12

56555170

+

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 CPSF3L-MYL6


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)
CPSF3Lchr11255835-MYL6chr1256555170+0.0620432570.93795675
CPSF3Lchr11255835-MYL6chr1256555170+0.0620432570.93795675


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.
genomic feature of top 1%

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Fusion Protein Features for CPSF3L-MYL6


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/:1255835/:56555170)
- 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
.MYL6

P60660

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: Regulatory light chain of myosin. Does not bind calcium.

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 CPSF3L-MYL6


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 CPSF3L-MYL6


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 CPSF3L-MYL6


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 CPSF3L-MYL6


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