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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:CALM3-CHRNA4 (FusionGDB2 ID:HG808TG1137)

Fusion Gene Summary for CALM3-CHRNA4

check button Fusion gene summary
Fusion gene informationFusion gene name: CALM3-CHRNA4
Fusion gene ID: hg808tg1137
HgeneTgene
Gene symbol

CALM3

CHRNA4

Gene ID

808

1137

Gene namecalmodulin 3cholinergic receptor nicotinic alpha 4 subunit
SynonymsCALM|CAM1|CAM2|CAMB|CPVT6|CaM|CaMIII|HEL-S-72|LQT16|PHKD|PHKD3BFNC|EBN|EBN1|NACHR|NACHRA4|NACRA4
Cytomap('CALM3')('CHRNA4')

19q13.32

20q13.33

Type of geneprotein-codingprotein-coding
Descriptioncalmodulin-3Calmodulin-1Calmodulin-2epididymis secretory protein Li 72phosphorylase kinase subunit deltaprepro-calmodulin 3neuronal acetylcholine receptor subunit alpha-4cholinergic receptor, nicotinic alpha 4cholinergic receptor, nicotinic, alpha 4 (neuronal)cholinergic receptor, nicotinic, alpha polypeptide 4neuronal nicotinic acetylcholine receptor alpha-4 subunit
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000477244, ENST00000291295, 
ENST00000597743, ENST00000594523, 
ENST00000598871, ENST00000391918, 
ENST00000596362, ENST00000599839, 
Fusion gene scores* DoF score11 X 9 X 7=6931 X 1 X 1=1
# samples 131
** MAII scorelog2(13/693*10)=-2.41434372910876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: CALM3 [Title/Abstract] AND CHRNA4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCALM3(47104694)-CHRNA4(61975738), # 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
HgeneCALM3

GO:0010880

regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum

20226167

HgeneCALM3

GO:0032516

positive regulation of phosphoprotein phosphatase activity

8631777

HgeneCALM3

GO:0035307

positive regulation of protein dephosphorylation

8631777

HgeneCALM3

GO:0051343

positive regulation of cyclic-nucleotide phosphodiesterase activity

8631777

HgeneCALM3

GO:0051592

response to calcium ion

7607248

HgeneCALM3

GO:0060316

positive regulation of ryanodine-sensitive calcium-release channel activity

20226167

TgeneCHRNA4

GO:0001666

response to hypoxia

12189247

TgeneCHRNA4

GO:0007165

signal transduction

8906617

TgeneCHRNA4

GO:0035094

response to nicotine

12189247



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
ChimerDB4SKCMTCGA-FS-A1ZD-06ACALM3chr19

47104694

+CHRNA4chr20

61975738

-


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Fusion Gene ORF analysis for CALM3-CHRNA4

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-3UTRENST00000477244ENST00000370263CALM3chr19

47104694

+CHRNA4chr20

61975738

-
3UTR-5UTRENST00000477244ENST00000463705CALM3chr19

47104694

+CHRNA4chr20

61975738

-
5CDS-3UTRENST00000291295ENST00000370263CALM3chr19

47104694

+CHRNA4chr20

61975738

-
5CDS-3UTRENST00000597743ENST00000370263CALM3chr19

47104694

+CHRNA4chr20

61975738

-
5CDS-5UTRENST00000291295ENST00000463705CALM3chr19

47104694

+CHRNA4chr20

61975738

-
5CDS-5UTRENST00000597743ENST00000463705CALM3chr19

47104694

+CHRNA4chr20

61975738

-
5UTR-3UTRENST00000594523ENST00000370263CALM3chr19

47104694

+CHRNA4chr20

61975738

-
5UTR-3UTRENST00000598871ENST00000370263CALM3chr19

47104694

+CHRNA4chr20

61975738

-
5UTR-5UTRENST00000594523ENST00000463705CALM3chr19

47104694

+CHRNA4chr20

61975738

-
5UTR-5UTRENST00000598871ENST00000463705CALM3chr19

47104694

+CHRNA4chr20

61975738

-
intron-3UTRENST00000391918ENST00000370263CALM3chr19

47104694

+CHRNA4chr20

61975738

-
intron-3UTRENST00000596362ENST00000370263CALM3chr19

47104694

+CHRNA4chr20

61975738

-
intron-3UTRENST00000599839ENST00000370263CALM3chr19

47104694

+CHRNA4chr20

61975738

-
intron-5UTRENST00000391918ENST00000463705CALM3chr19

47104694

+CHRNA4chr20

61975738

-
intron-5UTRENST00000596362ENST00000463705CALM3chr19

47104694

+CHRNA4chr20

61975738

-
intron-5UTRENST00000599839ENST00000463705CALM3chr19

47104694

+CHRNA4chr20

61975738

-

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 CALM3-CHRNA4


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)


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Fusion Protein Features for CALM3-CHRNA4


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/:47104694/:61975738)
- 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
..
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: 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}.

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 CALM3-CHRNA4


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 CALM3-CHRNA4


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 CALM3-CHRNA4


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 CALM3-CHRNA4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0001973Alcoholic Intoxication, Chronic4PSYGENET
TgeneC0036341Schizophrenia4PSYGENET
TgeneC1838049Epilepsy, Nocturnal Frontal Lobe, Type 14CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0011570Mental Depression3PSYGENET
TgeneC0011581Depressive disorder3PSYGENET
TgeneC0085541Epilepsy, Frontal Lobe3CTD_human
TgeneC0344315Depressed mood3PSYGENET
TgeneC0393671Frontal Epilepsy, Benign, Childhood3CTD_human
TgeneC0393683Epilepsy, Supplementary Motor3CTD_human
TgeneC0393684Epilepsy, Cingulate3CTD_human
TgeneC0393688Epilepsy, Opercular3CTD_human
TgeneC0751642Epilepsy, Anterior Fronto-Polar3CTD_human
TgeneC0751643Epilepsy, Orbito-Frontal3CTD_human
TgeneC0022333Jacksonian Seizure2CTD_human
TgeneC0036572Seizures2CTD_human
TgeneC0149958Complex partial seizures2CTD_human
TgeneC0234533Generalized seizures2CTD_human
TgeneC0234535Clonic Seizures2CTD_human
TgeneC0270824Visual seizure2CTD_human
TgeneC0270844Tonic Seizures2CTD_human
TgeneC0270846Epileptic drop attack2CTD_human
TgeneC0422850Seizures, Somatosensory2CTD_human
TgeneC0422852Seizures, Auditory2CTD_human
TgeneC0422853Olfactory seizure2CTD_human
TgeneC0422854Gustatory seizure2CTD_human
TgeneC0422855Vertiginous seizure2CTD_human
TgeneC0494475Tonic - clonic seizures2CTD_human
TgeneC0751056Non-epileptic convulsion2CTD_human
TgeneC0751110Single Seizure2CTD_human
TgeneC0751123Atonic Absence Seizures2CTD_human
TgeneC0751494Convulsive Seizures2CTD_human
TgeneC0751495Seizures, Focal2CTD_human
TgeneC0751496Seizures, Sensory2CTD_human
TgeneC3495874Nonepileptic Seizures2CTD_human
TgeneC4048158Convulsions2CTD_human
TgeneC4316903Absence Seizures2CTD_human
TgeneC4317109Epileptic Seizures2CTD_human
TgeneC4317123Myoclonic Seizures2CTD_human
TgeneC4505436Generalized Absence Seizures2CTD_human
TgeneC0004352Autistic Disorder1CTD_human
TgeneC0008073Developmental Disabilities1CTD_human
TgeneC0009171Cocaine Abuse1PSYGENET
TgeneC0013421Dystonia1CTD_human
TgeneC0021368Inflammation1CTD_human
TgeneC0027765nervous system disorder1CTD_human
TgeneC0041671Attention Deficit Disorder1CTD_human
TgeneC0085996Child Development Deviations1CTD_human
TgeneC0085997Child Development Disorders, Specific1CTD_human
TgeneC0393588Dystonia, Paroxysmal1CTD_human
TgeneC0393610Dystonia, Diurnal1CTD_human
TgeneC0751093Dystonia, Limb1CTD_human
TgeneC0751508Long Sleeper Syndrome1CTD_human
TgeneC0751509Short Sleeper Syndrome1CTD_human
TgeneC0751510Sleep-Related Neurogenic Tachypnea1CTD_human
TgeneC0751511Subwakefullness Syndrome1CTD_human
TgeneC0851578Sleep Disorders1CTD_human
TgeneC1263846Attention deficit hyperactivity disorder1CTD_human
TgeneC1321905Minimal Brain Dysfunction1CTD_human
TgeneC1861063TOBACCO ADDICTION, SUSCEPTIBILITY TO (finding)1CTD_human;GENOMICS_ENGLAND
TgeneC3696898Autosomal Dominant Nocturnal Frontal Lobe Epilepsy1ORPHANET
TgeneC4042891Sleep Wake Disorders1CTD_human