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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:CPSF6-CHMP1A (FusionGDB2 ID:19143)

Fusion Gene Summary for CPSF6-CHMP1A

check button Fusion gene summary
Fusion gene informationFusion gene name: CPSF6-CHMP1A
Fusion gene ID: 19143
HgeneTgene
Gene symbol

CPSF6

CHMP1A

Gene ID

11052

5119

Gene namecleavage and polyadenylation specific factor 6charged multivesicular body protein 1A
SynonymsCFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7CHMP1|PCH8|PCOLN3|PRSM1|VPS46-1|VPS46A
Cytomap

12q15

16q24.3

Type of geneprotein-codingprotein-coding
Descriptioncleavage and polyadenylation specificity factor subunit 6CPSF 68 kDa subunitcleavage and polyadenylation specific factor 6, 68kDacleavage and polyadenylation specificity factor 68 kDa subunitcleavage factor Im complex 68 kDa subunitpre-mRNA cleavage charged multivesicular body protein 1acharged multivesicular body protein 1/chromatin modifying protein 1chromatin modifying protein 1Aprocollagen (type III) N-endopeptidaseprotease, metallo, 1, 33kDvacuolar protein sorting-associated protein 46-1
Modification date2020031320200313
UniProtAcc

Q16630

Q9HD42

Ensembl transtripts involved in fusion geneENST00000266679, ENST00000435070, 
ENST00000456847, ENST00000551516, 
ENST00000550987, 		ENST00000253475, 
ENST00000397901, ENST00000535997, 
ENST00000550102, ENST00000547614, 
Fusion gene scores* DoF score69 X 12 X 19=1573245 X 11 X 21=10395
# samples 7148
** MAII scorelog2(71/15732*10)=-4.46973925655087
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(48/10395*10)=-4.43671154213721
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CPSF6 [Title/Abstract] AND CHMP1A [Title/Abstract] AND fusion [Title/Abstract]

The landscape and therapeutic relevance of cancer-associated transcript fusions (pmid: 25500544)
Most frequent breakpointCPSF6(69656342)-CHMP1A(89713739), # samples:12
Anticipated loss of major functional domain due to fusion event.CPSF6-CHMP1A seems lost the major protein functional domain in Hgene 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
HgeneCPSF6

GO:0006397

mRNA processing

14690600

HgeneCPSF6

GO:0051262

protein tetramerization

20695905

HgeneCPSF6

GO:0051290

protein heterotetramerization

23187700

HgeneCPSF6

GO:1990120

messenger ribonucleoprotein complex assembly

29276085

TgeneCHMP1A

GO:0007076

mitotic chromosome condensation

11559747

TgeneCHMP1A

GO:0016192

vesicle-mediated transport

11559748

TgeneCHMP1A

GO:0016458

gene silencing

11559747

TgeneCHMP1A

GO:0045892

negative regulation of transcription, DNA-templated

11559747


check buttonFusion gene breakpoints across CPSF6 (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 CHMP1A (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
ChimerDB4BLCATCGA-ZF-AA4VCPSF6chr12

69656342

+CHMP1Achr16

89713739

-
ChimerDB4BRCATCGA-A7-A5ZXCPSF6chr12

69656342

+CHMP1Achr16

89713739

-
ChimerDB4PCPGTCGA-PR-A5PH-01ACPSF6chr12

69656342

+CHMP1Achr16

89713739

-
ChimerDB4PRADTCGA-YL-A9WJCPSF6chr12

69656342

+CHMP1Achr16

89713739

-
ChimerDB4SARCTCGA-DX-A1L0-01ACPSF6chr12

69656342

+CHMP1Achr16

89713739

-
ChimerDB4SARCTCGA-DX-A48NCPSF6chr12

69656342

+CHMP1Achr16

89713739

-
ChimerDB4STADTCGA-FP-A4BFCPSF6chr12

69656342

+CHMP1Achr16

89713739

-
ChimerDB4TGCTTCGA-2G-AAGKCPSF6chr12

69656342

+CHMP1Achr16

89713739

-
ChimerDB4THCATCGA-ET-A2N4CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
ChimerDB4THYMTCGA-ZB-A96DCPSF6chr12

69656342

+CHMP1Achr16

89713739

-
ChimerDB4UCECTCGA-EY-A1GX-01ACPSF6chr12

69656342

+CHMP1Achr16

89713739

-
ChimerDB4UCECTCGA-EY-A1GXCPSF6chr12

69656342

+CHMP1Achr16

89713739

-


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Fusion Gene ORF analysis for CPSF6-CHMP1A

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
3UTR-3CDSENST00000266679ENST00000253475CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-3CDSENST00000266679ENST00000397901CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-3CDSENST00000266679ENST00000535997CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-3CDSENST00000266679ENST00000550102CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-3CDSENST00000435070ENST00000253475CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-3CDSENST00000435070ENST00000397901CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-3CDSENST00000435070ENST00000535997CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-3CDSENST00000435070ENST00000550102CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-3CDSENST00000456847ENST00000253475CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-3CDSENST00000456847ENST00000397901CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-3CDSENST00000456847ENST00000535997CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-3CDSENST00000456847ENST00000550102CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-5UTRENST00000266679ENST00000547614CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-5UTRENST00000435070ENST00000547614CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
3UTR-5UTRENST00000456847ENST00000547614CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
5CDS-5UTRENST00000551516ENST00000547614CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
Frame-shiftENST00000551516ENST00000253475CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
Frame-shiftENST00000551516ENST00000397901CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
Frame-shiftENST00000551516ENST00000535997CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
Frame-shiftENST00000551516ENST00000550102CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
intron-3CDSENST00000550987ENST00000253475CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
intron-3CDSENST00000550987ENST00000397901CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
intron-3CDSENST00000550987ENST00000535997CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
intron-3CDSENST00000550987ENST00000550102CPSF6chr12

69656342

+CHMP1Achr16

89713739

-
intron-5UTRENST00000550987ENST00000547614CPSF6chr12

69656342

+CHMP1Achr16

89713739

-

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 CPSF6-CHMP1A


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 CPSF6-CHMP1A


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/:69656342/:89713739)
- 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
CPSF6

Q16630

CHMP1A

Q9HD42

FUNCTION: Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs (PubMed:9659921, PubMed:8626397, PubMed:14690600, PubMed:29276085). CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals) (PubMed:9659921, PubMed:8626397, PubMed:14690600). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation (PubMed:23187700, PubMed:29276085). The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs (PubMed:20695905, PubMed:29276085). CPSF6 enhances NUDT21/CPSF5 binding to 5'-UGUA-3' elements localized upstream of pA signals and promotes RNA looping, and hence activates directly the mRNA 3'-processing machinery (PubMed:15169763, PubMed:29276085, PubMed:21295486). Plays a role in mRNA export (PubMed:19864460). {ECO:0000269|PubMed:14690600, ECO:0000269|PubMed:15169763, ECO:0000269|PubMed:19864460, ECO:0000269|PubMed:20695905, ECO:0000269|PubMed:21295486, ECO:0000269|PubMed:23187700, ECO:0000269|PubMed:29276085, ECO:0000269|PubMed:8626397, ECO:0000269|PubMed:9659921}.; FUNCTION: (Microbial infection) Binds HIV-1 capsid-nucleocapsid (HIV-1 CA-NC) complexes and might thereby promote the integration of the virus in the nucleus of dividing cells (in vitro). {ECO:0000269|PubMed:24130490}.FUNCTION: Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. Involved in cytokinesis. Involved in recruiting VPS4A and/or VPS4B to the midbody of dividing cells. May also be involved in chromosome condensation. Targets the Polycomb group (PcG) protein BMI1/PCGF4 to regions of condensed chromatin. May play a role in stable cell cycle progression and in PcG gene silencing. {ECO:0000269|PubMed:11559747, ECO:0000269|PubMed:11559748, ECO:0000269|PubMed:19129479, ECO:0000269|PubMed:23045692}.

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 CPSF6-CHMP1A


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 CPSF6-CHMP1A


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 CPSF6-CHMP1A


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 CPSF6-CHMP1A


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