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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:CNOT4-CALD1 (FusionGDB2 ID:17770)

Fusion Gene Summary for CNOT4-CALD1

check button Fusion gene summary
Fusion gene informationFusion gene name: CNOT4-CALD1
Fusion gene ID: 17770
HgeneTgene
Gene symbol

CNOT4

CALD1

Gene ID

4850

800

Gene nameCCR4-NOT transcription complex subunit 4caldesmon 1
SynonymsCLONE243|NOT4|NOT4HCDM|H-CAD|HCAD|L-CAD|LCAD|NAG22
Cytomap

7q33

7q33

Type of geneprotein-codingprotein-coding
DescriptionCCR4-NOT transcription complex subunit 4CCR4-associated factor 4E3 ubiquitin-protein ligase CNOT4NOT4 (negative regulator of transcription 4, yeast) homologRING-type E3 ubiquitin transferase CNOT4potential transcriptional repressor NOT4Hpcaldesmontestis secretory sperm-binding protein Li 227n
Modification date2020031320200313
UniProtAcc

O95628

Q05682

Ensembl transtripts involved in fusion geneENST00000315544, ENST00000356162, 
ENST00000361528, ENST00000423368, 
ENST00000428680, ENST00000451834, 
ENST00000541284, ENST00000414802, 
ENST00000473470, 		ENST00000361388, 
ENST00000361675, ENST00000361901, 
ENST00000393118, ENST00000417172, 
ENST00000422748, ENST00000424922, 
ENST00000495522, ENST00000543443, 
ENST00000466704, 
Fusion gene scores* DoF score7 X 3 X 5=10517 X 22 X 5=1870
# samples 623
** MAII scorelog2(6/105*10)=-0.807354922057604
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(23/1870*10)=-3.02333250383062
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CNOT4 [Title/Abstract] AND CALD1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCNOT4(135194637)-CALD1(134613505), # 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
HgeneCNOT4

GO:0006511

ubiquitin-dependent protein catabolic process

26575292

HgeneCNOT4

GO:0045652

regulation of megakaryocyte differentiation

26575292

HgeneCNOT4

GO:0051865

protein autoubiquitination

15001359


check buttonFusion gene breakpoints across CNOT4 (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 CALD1 (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
ChimerDB4PAADTCGA-HZ-A9TJ-06ACNOT4chr7

135194637

-CALD1chr7

134613505

+
ChimerDB4PAADTCGA-HZ-A9TJCNOT4chr7

135194637

-CALD1chr7

134613505

+


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Fusion Gene ORF analysis for CNOT4-CALD1

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-3CDSENST00000315544ENST00000361388CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000315544ENST00000361675CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000315544ENST00000361901CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000315544ENST00000393118CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000315544ENST00000417172CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000315544ENST00000422748CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000315544ENST00000424922CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000315544ENST00000495522CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000315544ENST00000543443CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000356162ENST00000361388CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000356162ENST00000361675CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000356162ENST00000361901CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000356162ENST00000393118CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000356162ENST00000417172CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000356162ENST00000422748CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000356162ENST00000424922CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000356162ENST00000495522CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000356162ENST00000543443CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000361528ENST00000361388CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000361528ENST00000361675CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000361528ENST00000361901CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000361528ENST00000393118CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000361528ENST00000417172CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000361528ENST00000422748CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000361528ENST00000424922CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000361528ENST00000495522CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000361528ENST00000543443CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000423368ENST00000361388CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000423368ENST00000361675CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000423368ENST00000361901CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000423368ENST00000393118CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000423368ENST00000417172CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000423368ENST00000422748CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000423368ENST00000424922CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000423368ENST00000495522CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000423368ENST00000543443CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000428680ENST00000361388CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000428680ENST00000361675CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000428680ENST00000361901CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000428680ENST00000393118CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000428680ENST00000417172CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000428680ENST00000422748CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000428680ENST00000424922CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000428680ENST00000495522CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000428680ENST00000543443CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000451834ENST00000361388CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000451834ENST00000361675CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000451834ENST00000361901CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000451834ENST00000393118CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000451834ENST00000417172CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000451834ENST00000422748CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000451834ENST00000424922CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000451834ENST00000495522CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000451834ENST00000543443CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000541284ENST00000361388CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000541284ENST00000361675CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000541284ENST00000361901CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000541284ENST00000393118CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000541284ENST00000417172CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000541284ENST00000422748CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000541284ENST00000424922CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000541284ENST00000495522CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-3CDSENST00000541284ENST00000543443CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-intronENST00000315544ENST00000466704CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-intronENST00000356162ENST00000466704CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-intronENST00000361528ENST00000466704CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-intronENST00000423368ENST00000466704CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-intronENST00000428680ENST00000466704CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-intronENST00000451834ENST00000466704CNOT4chr7

135194637

-CALD1chr7

134613505

+
5UTR-intronENST00000541284ENST00000466704CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000414802ENST00000361388CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000414802ENST00000361675CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000414802ENST00000361901CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000414802ENST00000393118CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000414802ENST00000417172CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000414802ENST00000422748CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000414802ENST00000424922CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000414802ENST00000495522CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000414802ENST00000543443CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000473470ENST00000361388CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000473470ENST00000361675CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000473470ENST00000361901CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000473470ENST00000393118CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000473470ENST00000417172CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000473470ENST00000422748CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000473470ENST00000424922CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000473470ENST00000495522CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-3CDSENST00000473470ENST00000543443CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-intronENST00000414802ENST00000466704CNOT4chr7

135194637

-CALD1chr7

134613505

+
intron-intronENST00000473470ENST00000466704CNOT4chr7

135194637

-CALD1chr7

134613505

+

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 CNOT4-CALD1


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)
CNOT4chr7135194636-CALD1chr7134613504+2.19E-081
CNOT4chr7135194636-CALD1chr7134613504+2.19E-081
CNOT4chr7135194636-CALD1chr7134613504+2.19E-081
CNOT4chr7135194636-CALD1chr7134613504+2.19E-081

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.
genomic feature of top 1%

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Fusion Protein Features for CNOT4-CALD1


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/:135194637/:134613505)
- 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
CNOT4

O95628

CALD1

Q05682

FUNCTION: Has E3 ubiquitin ligase activity, promoting ubiquitination and degradation of target proteins (PubMed:11823428, PubMed:22159038, PubMed:26575292). Involved in activation of the JAK/STAT pathway (PubMed:11823428, PubMed:22159038). Catalyzes ubiquitination of methylated RBM15 (PubMed:26575292). Plays a role in quality control of translation of mitochondrial outer membrane-localized mRNA (PubMed:29861391). As part of the PINK1-regulated signaling, upon mitochondria damage, ubiquitinates ABCE1 and thereby recruits autophagy receptors to the mitochondrial outer membrane to initiate mitophagy (PubMed:29861391). {ECO:0000269|PubMed:11823428, ECO:0000269|PubMed:22159038, ECO:0000269|PubMed:26575292, ECO:0000269|PubMed:29861391}.FUNCTION: Actin- and myosin-binding protein implicated in the regulation of actomyosin interactions in smooth muscle and nonmuscle cells (could act as a bridge between myosin and actin filaments). Stimulates actin binding of tropomyosin which increases the stabilization of actin filament structure. In muscle tissues, inhibits the actomyosin ATPase by binding to F-actin. This inhibition is attenuated by calcium-calmodulin and is potentiated by tropomyosin. Interacts with actin, myosin, two molecules of tropomyosin and with calmodulin. Also plays an essential role during cellular mitosis and receptor capping. Involved in Schwann cell migration during peripheral nerve regeneration (By similarity). {ECO:0000250, ECO:0000269|PubMed:8227296}.

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 CNOT4-CALD1


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 CNOT4-CALD1


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 CNOT4-CALD1


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 CNOT4-CALD1


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