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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:CERKL-GABRA1 (FusionGDB2 ID:HG375298TG2554)

Fusion Gene Summary for CERKL-GABRA1

check button Fusion gene summary
Fusion gene informationFusion gene name: CERKL-GABRA1
Fusion gene ID: hg375298tg2554
HgeneTgene
Gene symbol

CERKL

GABRA1

Gene ID

375298

2554

Gene nameceramide kinase likegamma-aminobutyric acid type A receptor subunit alpha1
SynonymsRP26ECA4|EIEE19|EJM|EJM5
Cytomap('CERKL')('GABRA1')

2q31.3

5q34

Type of geneprotein-codingprotein-coding
Descriptionceramide kinase-like proteingamma-aminobutyric acid receptor subunit alpha-1GABA(A) receptor subunit alpha-1GABA(A) receptor, alpha 1gamma-aminobutyric acid (GABA) A receptor, alpha 1gamma-aminobutyric acid type A receptor alpha1 subunit
Modification date2020031320200322
UniProtAcc

Q49MI3

.
Ensembl transtripts involved in fusion geneENST00000339098, ENST00000374969, 
ENST00000374970, ENST00000409440, 
ENST00000410087, ENST00000479558, 
Fusion gene scores* DoF score3 X 3 X 1=92 X 3 X 2=12
# samples 33
** MAII scorelog2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CERKL [Title/Abstract] AND GABRA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCERKL(182450237)-GABRA1(161293247), # 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
TgeneGABRA1

GO:1902476

chloride transmembrane transport

9039914

TgeneGABRA1

GO:1904862

inhibitory synapse assembly

23909897|25489750



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
ChiTaRS5.0N/AFN086754CERKLchr2

182450237

+GABRA1chr5

161293247

+


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Fusion Gene ORF analysis for CERKL-GABRA1

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
intron-intronENST00000339098ENST00000023897CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000339098ENST00000393943CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000339098ENST00000420560CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000339098ENST00000428797CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000339098ENST00000437025CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000339098ENST00000444819CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374969ENST00000023897CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374969ENST00000393943CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374969ENST00000420560CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374969ENST00000428797CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374969ENST00000437025CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374969ENST00000444819CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374970ENST00000023897CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374970ENST00000393943CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374970ENST00000420560CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374970ENST00000428797CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374970ENST00000437025CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000374970ENST00000444819CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000409440ENST00000023897CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000409440ENST00000393943CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000409440ENST00000420560CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000409440ENST00000428797CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000409440ENST00000437025CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000409440ENST00000444819CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000410087ENST00000023897CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000410087ENST00000393943CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000410087ENST00000420560CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000410087ENST00000428797CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000410087ENST00000437025CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000410087ENST00000444819CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000479558ENST00000023897CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000479558ENST00000393943CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000479558ENST00000420560CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000479558ENST00000428797CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000479558ENST00000437025CERKLchr2

182450237

+GABRA1chr5

161293247

+
intron-intronENST00000479558ENST00000444819CERKLchr2

182450237

+GABRA1chr5

161293247

+

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 CERKL-GABRA1


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 CERKL-GABRA1


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/:182450237/:161293247)
- 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
CERKL

Q49MI3

.
FUNCTION: Has no detectable ceramide-kinase activity. Overexpression of CERKL protects cells from apoptosis in oxidative stress conditions. {ECO:0000269|PubMed:15708351, ECO:0000269|PubMed:19158957}.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 CERKL-GABRA1


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 CERKL-GABRA1


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 CERKL-GABRA1


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 CERKL-GABRA1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCERKLC1842127Retinitis Pigmentosa 262CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC4013473EPILEPSY, IDIOPATHIC GENERALIZED, SUSCEPTIBILITY TO, 135GENOMICS_ENGLAND;UNIPROT
TgeneC0036341Schizophrenia4PSYGENET
TgeneC0525045Mood Disorders4PSYGENET
TgeneC0001973Alcoholic Intoxication, Chronic3PSYGENET
TgeneC0270853Juvenile Myoclonic Epilepsy2CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC3810400EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 192CTD_human;UNIPROT
TgeneC0001969Alcoholic Intoxication1PSYGENET
TgeneC0004134Ataxia1CTD_human
TgeneC0004352Autistic Disorder1CTD_human
TgeneC0005586Bipolar Disorder1PSYGENET
TgeneC0010093Corpus Luteum Cyst1CTD_human
TgeneC0019147Hepatic Coma1CTD_human
TgeneC0019151Hepatic Encephalopathy1CTD_human
TgeneC0029927Ovarian Cysts1CTD_human
TgeneC0085762Alcohol abuse1PSYGENET
TgeneC0240991Ataxia, Sensory1CTD_human
TgeneC0270736Essential Tremor1CTD_human
TgeneC0278161Ataxia, Motor1CTD_human
TgeneC0393615Familial Tremor1CTD_human
TgeneC0427190Ataxia, Truncal1CTD_human
TgeneC0520966Abnormal coordination1CTD_human
TgeneC0543888Epileptic encephalopathy1GENOMICS_ENGLAND
TgeneC0750937Ataxia, Appendicular1CTD_human
TgeneC0750940Tremor, Rubral1CTD_human
TgeneC0751122Infantile Severe Myoclonic Epilepsy1ORPHANET
TgeneC0751197Fulminant Hepatic Failure with Cerebral Edema1CTD_human
TgeneC0751198Hepatic Stupor1CTD_human
TgeneC1838604EPILEPSY, CHILDHOOD ABSENCE, 11ORPHANET
TgeneC1862939AMYOTROPHIC LATERAL SCLEROSIS 11CTD_human
TgeneC1862941Amyotrophic Lateral Sclerosis, Sporadic1CTD_human
TgeneC4551993Amyotrophic Lateral Sclerosis, Familial1CTD_human