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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-GMCL1 (FusionGDB2 ID:19157)

Fusion Gene Summary for CPSF6-GMCL1

check button Fusion gene summary
Fusion gene informationFusion gene name: CPSF6-GMCL1
Fusion gene ID: 19157
HgeneTgene
Gene symbol

CPSF6

GMCL1

Gene ID

11052

64395

Gene namecleavage and polyadenylation specific factor 6germ cell-less 1, spermatogenesis associated
SynonymsCFIM|CFIM68|CFIM72|HPBRII-4|HPBRII-7BTBD13|GCL|GCL1|SPATA29
Cytomap

12q15

2p13.3

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 germ cell-less protein-like 1germ cell-less homolog 1germ cell-less, spermatogenesis associated 1spermatogenesis associated 29
Modification date2020031320200327
UniProtAcc

Q16630

Q96IK5

Ensembl transtripts involved in fusion geneENST00000266679, ENST00000435070, 
ENST00000456847, ENST00000551516, 
ENST00000550987, 		ENST00000282570, 
ENST00000468386, 
Fusion gene scores* DoF score69 X 12 X 19=157325 X 5 X 2=50
# samples 715
** MAII scorelog2(71/15732*10)=-4.46973925655087
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/50*10)=0
Context

PubMed: CPSF6 [Title/Abstract] AND GMCL1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCPSF6(69656342)-GMCL1(70106041), # 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
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


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.
all structure

check buttonFusion gene breakpoints across GMCL1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4STADTCGA-CG-5717-01ACPSF6chr12

69656342

+GMCL1chr2

70106041

+


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Fusion Gene ORF analysis for CPSF6-GMCL1

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-3CDSENST00000266679ENST00000282570CPSF6chr12

69656342

+GMCL1chr2

70106041

+
3UTR-3CDSENST00000435070ENST00000282570CPSF6chr12

69656342

+GMCL1chr2

70106041

+
3UTR-3CDSENST00000456847ENST00000282570CPSF6chr12

69656342

+GMCL1chr2

70106041

+
3UTR-intronENST00000266679ENST00000468386CPSF6chr12

69656342

+GMCL1chr2

70106041

+
3UTR-intronENST00000435070ENST00000468386CPSF6chr12

69656342

+GMCL1chr2

70106041

+
3UTR-intronENST00000456847ENST00000468386CPSF6chr12

69656342

+GMCL1chr2

70106041

+
5CDS-intronENST00000551516ENST00000468386CPSF6chr12

69656342

+GMCL1chr2

70106041

+
In-frameENST00000551516ENST00000282570CPSF6chr12

69656342

+GMCL1chr2

70106041

+
intron-3CDSENST00000550987ENST00000282570CPSF6chr12

69656342

+GMCL1chr2

70106041

+
intron-intronENST00000550987ENST00000468386CPSF6chr12

69656342

+GMCL1chr2

70106041

+

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)
ENST00000551516CPSF6chr1269656342+ENST00000282570GMCL1chr270106041+26601723132104

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
ENST00000551516ENST00000282570CPSF6chr1269656342+GMCL1chr270106041+0.29108420.7089158

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Fusion Genomic Features for CPSF6-GMCL1


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)
CPSF6chr1269656342+GMCL1chr270106040+2.44E-091
CPSF6chr1269656342+GMCL1chr270106040+2.44E-091

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.
genomic feature

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 CPSF6-GMCL1


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/chr12:69656342/chr2:70106041)
- 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

GMCL1

Q96IK5

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: Possible function in spermatogenesis. Enhances the degradation of MDM2 and increases the amount of p53 probably by modulating the nucleocytoplasmic transport (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
HgeneCPSF6chr12:69656342chr2:70106041ENST00000266679+1011208_398590701.3333333333334Compositional biasNote=Pro-rich
HgeneCPSF6chr12:69656342chr2:70106041ENST00000266679+1011490_551590701.3333333333334Compositional biasNote=Arg-rich
HgeneCPSF6chr12:69656342chr2:70106041ENST00000435070+910208_3985532111.0Compositional biasNote=Pro-rich
HgeneCPSF6chr12:69656342chr2:70106041ENST00000435070+910490_5515532111.0Compositional biasNote=Arg-rich
HgeneCPSF6chr12:69656342chr2:70106041ENST00000266679+1011202_206590701.3333333333334MotifGAR
HgeneCPSF6chr12:69656342chr2:70106041ENST00000435070+910202_2065532111.0MotifGAR
HgeneCPSF6chr12:69656342chr2:70106041ENST00000266679+1011358_551590701.3333333333334Region(Microbial infection) Binds to HIV-1 capsid protein p24 (CA)
HgeneCPSF6chr12:69656342chr2:70106041ENST00000266679+1011404_551590701.3333333333334RegionSufficient for nuclear speckle localization
HgeneCPSF6chr12:69656342chr2:70106041ENST00000266679+1011405_551590701.3333333333334RegionNecessary for RNA-binding
HgeneCPSF6chr12:69656342chr2:70106041ENST00000266679+1011510_551590701.3333333333334RegionSufficient for nuclear targeting
HgeneCPSF6chr12:69656342chr2:70106041ENST00000266679+101181_161590701.3333333333334RegionNecessary for nuclear paraspeckles localization
HgeneCPSF6chr12:69656342chr2:70106041ENST00000435070+910358_5515532111.0Region(Microbial infection) Binds to HIV-1 capsid protein p24 (CA)
HgeneCPSF6chr12:69656342chr2:70106041ENST00000435070+910404_5515532111.0RegionSufficient for nuclear speckle localization
HgeneCPSF6chr12:69656342chr2:70106041ENST00000435070+910405_5515532111.0RegionNecessary for RNA-binding
HgeneCPSF6chr12:69656342chr2:70106041ENST00000435070+910510_5515532111.0RegionSufficient for nuclear targeting
HgeneCPSF6chr12:69656342chr2:70106041ENST00000435070+91081_1615532111.0RegionNecessary for nuclear paraspeckles localization

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneGMCL1chr12:69656342chr2:70106041ENST000002825701214108_178484516.0DomainBTB
TgeneGMCL1chr12:69656342chr2:70106041ENST00000282570121449_55484516.0MotifNuclear localization signal
TgeneGMCL1chr12:69656342chr2:70106041ENST00000282570121485_91484516.0MotifNuclear localization signal


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Fusion Gene Sequence for CPSF6-GMCL1


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.
>19157_19157_1_CPSF6-GMCL1_CPSF6_chr12_69656342_ENST00000551516_GMCL1_chr2_70106041_ENST00000282570_length(transcript)=2660nt_BP=172nt
GGAAGATGGCGGACGGCGTGGACCACATAGACATTTACGCGGATGTCGGCGAAGAGTTCAACCAGGAAGCTGAATATGAGAGAGAAGCAG
AGAACGAGAGAGGCACCGGGATCGTGACCGAGACCGTGACCGAGAGCGTGACCGAGAGCGCGAATATCGTCATCGTTAGAAGGAACAAGT
GGTGATGAACTTGGACAGCAGGCTTCTGATCTTCCCTTTATATATCTGCTGTAACTTCTTGTATATATCACCAGAAAAAAAGAATTGAAA
ATAATCGTCACCCAGAAAATCCAGAAAACTGAAGATTTCATCAGTTGGAAACAGTAGCACTTTGAAAACTTTTTAGGCCAGCTTTAATTT
AATGGCCCTACTGATATTCACATCGAAGGTGACTAACAATGACAAAGGCCTTATGAACTGTACAGACAATACAGAAGATTATTCTTATCC
TCATTGCATTTCTATGCATATGCGTAAGAACATTTTAAAGCCAAGAAAATATCTGTCAAACCATTTCTGTTAGAACGATGTCAATTCATG
CTTTTAATTTAGCATCAATAGAAAATTGCTGTAGGTAAATCTCACATTTATCTGCAACAAAATATAGATTTAATTTTTAGCTTAAACTTT
GTTTCTACCTTATGTTAGTGGACCTCAGTTATCCATCTGTAAATTTCTTTTTATTTGGCTAAAATAATCTAAAAGAATAATTTGGTTGGC
CAATTAGAAATGCCTTTTTCAGTTGGTGTATTGAAAGCTTTCCTTTAACATTTTCACCTGCTCATTGTGATTCCTCCTTTTAGTCTAATA
TCTTTCCAGGTCATACTTGTTTTTAATCATTAAATATTTTCTTCCTGGTTTTGGAGACTAAGCTGATAAACTTTTTTTAAAACTTAAGCA
TTGTCATTGCTATTTTTTTTAATTTGACTTTCCTAGGAGTTTAAGAACAGTGAAAGTTAGCTTTGCACCTTCAAATGATCTTGAATGAGG
GAAAAATCAGTTTGATTCCAAGGATATTTCTTGCCTTACATGGTCTTTTCTTTGACAGTCTGTACACCTTTATTATTAGGTTTTGAATTA
TTTATGTACCAGATATTATAGTTTTAAACATTTTAATATTCTCTGATCTTTAGAATTATTTATGTTCAAATTTTAGTTGGGAACTTTGTT
TCCTACTTAAGCTCAGGACTTTTTACCCTCTGAATTGAGTGCCTTTGAGTGACACATGCTAATAGAAATTTCATAGTAAATGTAAATAAG
GTCAGAGGATGTAATATGGAGCCTGATGATGAAGCATTAATGTAAAAATGGAACTTATTTTTGTCAAAAATGAGATGTACACTTGTCATG
ATTTATGTATGTTGACCTTTTGTGTTTATTACTGTTTTGAAAATAGCCATGTTCATTTTCTTTCCAGTTAGAGTAAGTACTTCTGTGGTT
AATGTATATTTTTATTATGGTTTTTAAAATGGGAATCATTTTTATGTATCTGTGCAAATAATAAATGCCCATTTGGAAAAAGAGTAAGCT
CTTACATAAAATGGACCAAAAAATCCCCCTTAATTGAAACCAAAATTTTTTCTTTCTAGTTAGGTTTTTTTCCCAACTCCTTTTAACTTT
TGGAATTTATTAATAATTTTTTTCTTTTTTAATGATATGCCCATAGGTTCATAAATTGCTTTTGTTCTTTTAAAATTCATCCATTTGGTT
TAACTTAAAGGAACCTTTTAAATGCCTCACCCTTGACCCTCAGAGCTGGAATTTAAATGTTTCTAATACAGTGATTTGGCTGTTATCAAG
AGGTTACATTTCAGCTGGGTGTCAGCCAGGTGTGGTGGCTCACACTTGTAAGCCCAGCACTTTGGGAGGCCGAGGCAGGCAGATCATCTG
AGGTCAGGAGTTTAAGATCAGCCATGACCAACATGGTGAAACCCCATCTCTATTAAATACACAAAATAAAAATTAGCCAGGCATGGTGGC
ACACGCCTGTCATCTCAGCTACTCAGGAGGCTGAGGCAGGAGAATCACTTGAACCCAGGAGGCAGAGGTTGCAGTGAGTGGAGATTGCGC
CATTGCACTCCAACCTAGGCGACAGAGTGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAGAGGCTACTGTACTTATTTTTATATTTG
ACTACATTAGGTCTTTTTCACGGGAAGCTGTTGTTTTCTTTCCGTCTCATTACTGTATAAGAGTTTCCTTACCCTTTATGTATTGAAAAA
TATATAAATTCCAAACTTAAATTATTTGGATAATTAAGTTTTTGCAGATCTTGGAAGTAAAGATAATGTTTTGATCATATTAATGAATAA
AGTTAACTGTTTCATTTCACTTACATAAGTTAACTGGCCAAATTGGATTTATATGTGGTTTCATCCATTGGTTCTGTCCTGGCCAAGTTG
CTTATGTCATCCATAGACAGGATAATTCTTTCTTCAATCACAAGTAGGTTAATGTTCTTATTTGAGAAGTTGATAATTGTCAGGTAGTAA
TTCACACTGGTAGTAAAGATGTGCTTTTGTTTTCTTACCAAATATTTTTATGTGTTTCCAGAGTTCTTTTCAATAGAAATATTTTCAATA

>19157_19157_1_CPSF6-GMCL1_CPSF6_chr12_69656342_ENST00000551516_GMCL1_chr2_70106041_ENST00000282570_length(amino acids)=104AA_BP=1
MMKSSVFWIFWVTIIFNSFFLVIYTRSYSRYIKGRSEACCPSSSPLVPSNDDDIRALGHALGHGLGHDPGASLVLCFSLIFSFLVELFAD

--------------------------------------------------------------

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Fusion Gene PPI Analysis for CPSF6-GMCL1


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-GMCL1


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-GMCL1


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