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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:CNOT1-HERPUD1 (FusionGDB2 ID:17713)

Fusion Gene Summary for CNOT1-HERPUD1

check button Fusion gene summary
Fusion gene informationFusion gene name: CNOT1-HERPUD1
Fusion gene ID: 17713
HgeneTgene
Gene symbol

CNOT1

HERPUD1

Gene ID

23019

9709

Gene nameCCR4-NOT transcription complex subunit 1homocysteine inducible ER protein with ubiquitin like domain 1
SynonymsAD-005|CDC39|HPE12|NOT1|NOT1HHERP|Mif1|SUP
Cytomap

16q21

16q13

Type of geneprotein-codingprotein-coding
DescriptionCCR4-NOT transcription complex subunit 1CCR4-associated factor 1NOT1 (negative regulator of transcription 1, yeast) homologadrenal gland protein AD-005negative regulator of transcription subunit 1 homologhomocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 proteinMMS-induciblehomocysteine-inducible endoplasmic reticulum stress-inducible ubiquitin-like domain member 1 proteinhomocysteine-inducible, endoplasmic reticulum
Modification date2020032220200313
UniProtAcc

A5YKK6

Q15011

Ensembl transtripts involved in fusion geneENST00000317147, ENST00000441024, 
ENST00000569240, ENST00000245138, 
ENST00000569732, 		ENST00000300302, 
ENST00000344114, ENST00000379792, 
ENST00000439977, ENST00000570273, 
Fusion gene scores* DoF score19 X 17 X 11=35534 X 4 X 2=32
# samples 214
** MAII scorelog2(21/3553*10)=-4.0805764556651
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: CNOT1 [Title/Abstract] AND HERPUD1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCNOT1(58663632)-HERPUD1(56977894), # 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
HgeneCNOT1

GO:0000122

negative regulation of transcription by RNA polymerase II

16778766

HgeneCNOT1

GO:0010606

positive regulation of cytoplasmic mRNA processing body assembly

21976065

HgeneCNOT1

GO:0017148

negative regulation of translation

24736845

HgeneCNOT1

GO:0033147

negative regulation of intracellular estrogen receptor signaling pathway

16778766

HgeneCNOT1

GO:0035195

gene silencing by miRNA

23172285|24768540

HgeneCNOT1

GO:0048387

negative regulation of retinoic acid receptor signaling pathway

16778766

HgeneCNOT1

GO:0060213

positive regulation of nuclear-transcribed mRNA poly(A) tail shortening

23644599

TgeneHERPUD1

GO:0032469

endoplasmic reticulum calcium ion homeostasis

15102845|22045699

TgeneHERPUD1

GO:1902236

negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway

15102845

TgeneHERPUD1

GO:1903071

positive regulation of ER-associated ubiquitin-dependent protein catabolic process

22045699


check buttonFusion gene breakpoints across CNOT1 (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 HERPUD1 (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
ChimerDB4OVTCGA-13-0885-01ACNOT1chr16

58663632

-HERPUD1chr16

56977894

+


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Fusion Gene ORF analysis for CNOT1-HERPUD1

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-intronENST00000317147ENST00000300302CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000317147ENST00000344114CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000317147ENST00000379792CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000317147ENST00000439977CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000317147ENST00000570273CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000441024ENST00000300302CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000441024ENST00000344114CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000441024ENST00000379792CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000441024ENST00000439977CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000441024ENST00000570273CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000569240ENST00000300302CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000569240ENST00000344114CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000569240ENST00000379792CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000569240ENST00000439977CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
5UTR-intronENST00000569240ENST00000570273CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
intron-intronENST00000245138ENST00000300302CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
intron-intronENST00000245138ENST00000344114CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
intron-intronENST00000245138ENST00000379792CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
intron-intronENST00000245138ENST00000439977CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
intron-intronENST00000245138ENST00000570273CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
intron-intronENST00000569732ENST00000300302CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
intron-intronENST00000569732ENST00000344114CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
intron-intronENST00000569732ENST00000379792CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
intron-intronENST00000569732ENST00000439977CNOT1chr16

58663632

-HERPUD1chr16

56977894

+
intron-intronENST00000569732ENST00000570273CNOT1chr16

58663632

-HERPUD1chr16

56977894

+

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 CNOT1-HERPUD1


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 CNOT1-HERPUD1


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/:58663632/:56977894)
- 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
CNOT1

A5YKK6

HERPUD1

Q15011

FUNCTION: Scaffolding component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Its scaffolding function implies its interaction with the catalytic complex module and diverse RNA-binding proteins mediating the complex recruitment to selected mRNA 3'UTRs. Involved in degradation of AU-rich element (ARE)-containing mRNAs probably via association with ZFP36. Mediates the recruitment of the CCR4-NOT complex to miRNA targets and to the RISC complex via association with TNRC6A, TNRC6B or TNRC6C. Acts as a transcriptional repressor. Represses the ligand-dependent transcriptional activation by nuclear receptors. Involved in the maintenance of embryonic stem (ES) cell identity. {ECO:0000269|PubMed:10637334, ECO:0000269|PubMed:16778766, ECO:0000269|PubMed:21278420, ECO:0000269|PubMed:21976065, ECO:0000269|PubMed:21984185, ECO:0000269|PubMed:22367759, ECO:0000269|PubMed:23644599, ECO:0000269|PubMed:27558897, ECO:0000269|PubMed:32354837}.FUNCTION: Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins (PubMed:16289116, PubMed:28827405). Could enhance presenilin-mediated amyloid-beta protein 40 generation. Binds to ubiquilins and this interaction is required for efficient degradation of CD3D via the ERAD pathway (PubMed:18307982). {ECO:0000269|PubMed:16289116, ECO:0000269|PubMed:18307982, ECO:0000269|PubMed:28827405}.

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 CNOT1-HERPUD1


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 CNOT1-HERPUD1


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 CNOT1-HERPUD1


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 CNOT1-HERPUD1


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