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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:GRIK2-CDKAL1 (FusionGDB2 ID:34658)

Fusion Gene Summary for GRIK2-CDKAL1

check button Fusion gene summary
Fusion gene informationFusion gene name: GRIK2-CDKAL1
Fusion gene ID: 34658
HgeneTgene
Gene symbol

GRIK2

CDKAL1

Gene ID

2901

54901

Gene nameglutamate ionotropic receptor kainate type subunit 5CDK5 regulatory subunit associated protein 1 like 1
SynonymsEAA2|GRIK2|GluK5|KA2-
Cytomap

19q13.2

6p22.3

Type of geneprotein-codingprotein-coding
Descriptionglutamate receptor ionotropic, kainate 5excitatory amino acid receptor 2glutamate receptor KA2threonylcarbamoyladenosine tRNA methylthiotransferasetRNA-t(6)A37 methylthiotransferase
Modification date2020031320200322
UniProtAcc

Q13002

Q5VV42

Ensembl transtripts involved in fusion geneENST00000413795, ENST00000369138, 
ENST00000421544, ENST00000358361, 
ENST00000318991, ENST00000369137, 
ENST00000369134, 		ENST00000274695, 
ENST00000378624, ENST00000378610, 
ENST00000476517, 
Fusion gene scores* DoF score9 X 4 X 6=21623 X 22 X 8=4048
# samples 1030
** MAII scorelog2(10/216*10)=-1.11103131238874
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(30/4048*10)=-3.75417488419843
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GRIK2 [Title/Abstract] AND CDKAL1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGRIK2(101847268)-CDKAL1(21065279), # samples:3
Anticipated loss of major functional domain due to fusion event.GRIK2-CDKAL1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
GRIK2-CDKAL1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* 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

check buttonFusion gene breakpoints across GRIK2 (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 CDKAL1 (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
ChimerDB4BRCATCGA-OL-A5DA-01AGRIK2chr6

101847268

+CDKAL1chr6

21065279

+
ChimerDB4BRCATCGA-OL-A5DA-01AGRIK2chr6

101847268

+CDKAL1chr6

21065279

+
ChimerDB4BRCATCGA-OL-A5DA-01AGRIK2chr6

101847268

-CDKAL1chr6

21065279

+


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Fusion Gene ORF analysis for GRIK2-CDKAL1

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
Frame-shiftENST00000413795ENST00000274695GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000413795ENST00000378624GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000413795ENST00000378610GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
5CDS-intronENST00000413795ENST00000476517GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000369138ENST00000274695GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000369138ENST00000378624GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000369138ENST00000378610GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
5CDS-intronENST00000369138ENST00000476517GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000421544ENST00000274695GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000421544ENST00000378624GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000421544ENST00000378610GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
5CDS-intronENST00000421544ENST00000476517GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000358361ENST00000274695GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000358361ENST00000378624GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000358361ENST00000378610GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
5CDS-intronENST00000358361ENST00000476517GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000318991ENST00000274695GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000318991ENST00000378624GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000318991ENST00000378610GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
5CDS-intronENST00000318991ENST00000476517GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000369137ENST00000274695GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000369137ENST00000378624GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
Frame-shiftENST00000369137ENST00000378610GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
5CDS-intronENST00000369137ENST00000476517GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
intron-3CDSENST00000369134ENST00000274695GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
intron-3CDSENST00000369134ENST00000378624GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
intron-3CDSENST00000369134ENST00000378610GRIK2chr6

101847268

+CDKAL1chr6

21065279

+
intron-intronENST00000369134ENST00000476517GRIK2chr6

101847268

+CDKAL1chr6

21065279

+

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 GRIK2-CDKAL1


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)
GRIK2chr6101847268+CDKAL1chr621065278+0.101437490.89856255
GRIK2chr6101847268+CDKAL1chr621065278+0.101437490.89856255

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 GRIK2-CDKAL1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
GRIK2

Q13002

CDKAL1

Q5VV42

FUNCTION: Ionotropic glutamate receptor. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L-glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist (PubMed:28180184). Modulates cell surface expression of NETO2 (By similarity). {ECO:0000250|UniProtKB:P39087, ECO:0000269|PubMed:28180184}.; FUNCTION: Independent of its ionotropic glutamate receptor activity, acts as a thermoreceptor conferring sensitivity to cold temperatures (PubMed:31474366). Functions in dorsal root ganglion neurons (By similarity). {ECO:0000250|UniProtKB:P39087, ECO:0000269|PubMed:31474366}.FUNCTION: Catalyzes the methylthiolation of N6-threonylcarbamoyladenosine (t(6)A), leading to the formation of 2-methylthio-N6-threonylcarbamoyladenosine (ms(2)t(6)A) at position 37 in tRNAs that read codons beginning with adenine. {ECO:0000250|UniProtKB:Q91WE6}.

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 GRIK2-CDKAL1


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 GRIK2-CDKAL1


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 GRIK2-CDKAL1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneGRIK2Q13002DB00849MethylphenobarbitalAntagonistSmall moleculeApproved
HgeneGRIK2Q13002DB00849MethylphenobarbitalAntagonistSmall moleculeApproved
HgeneGRIK2Q13002DB00237ButabarbitalAntagonistSmall moleculeApproved|Illicit
HgeneGRIK2Q13002DB00237ButabarbitalAntagonistSmall moleculeApproved|Illicit
HgeneGRIK2Q13002DB00241ButalbitalAntagonistSmall moleculeApproved|Illicit
HgeneGRIK2Q13002DB00241ButalbitalAntagonistSmall moleculeApproved|Illicit
HgeneGRIK2Q13002DB00306TalbutalAntagonistSmall moleculeApproved|Illicit
HgeneGRIK2Q13002DB00306TalbutalAntagonistSmall moleculeApproved|Illicit
HgeneGRIK2Q13002DB01351AmobarbitalAntagonistSmall moleculeApproved|Illicit
HgeneGRIK2Q13002DB01351AmobarbitalAntagonistSmall moleculeApproved|Illicit
HgeneGRIK2Q13002DB01353ButobarbitalAntagonistSmall moleculeApproved|Illicit
HgeneGRIK2Q13002DB01353ButobarbitalAntagonistSmall moleculeApproved|Illicit
HgeneGRIK2Q13002DB01174PhenobarbitalAntagonistSmall moleculeApproved|Investigational
HgeneGRIK2Q13002DB01174PhenobarbitalAntagonistSmall moleculeApproved|Investigational
HgeneGRIK2Q13002DB00312PentobarbitalAntagonistSmall moleculeApproved|Investigational|Vet_approved
HgeneGRIK2Q13002DB00312PentobarbitalAntagonistSmall moleculeApproved|Investigational|Vet_approved
HgeneGRIK2Q13002DB00142Glutamic acidSmall moleculeApproved|Nutraceutical
HgeneGRIK2Q13002DB00142Glutamic acidSmall moleculeApproved|Nutraceutical
HgeneGRIK2Q13002DB00418SecobarbitalAntagonistSmall moleculeApproved|Vet_approved
HgeneGRIK2Q13002DB00418SecobarbitalAntagonistSmall moleculeApproved|Vet_approved
HgeneGRIK2Q13002DB00599ThiopentalAntagonistSmall moleculeApproved|Vet_approved
HgeneGRIK2Q13002DB00599ThiopentalAntagonistSmall moleculeApproved|Vet_approved
HgeneGRIK2Q13002DB00794PrimidoneAntagonistSmall moleculeApproved|Vet_approved
HgeneGRIK2Q13002DB00794PrimidoneAntagonistSmall moleculeApproved|Vet_approved

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Related Diseases for GRIK2-CDKAL1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGRIK2C0005586Bipolar Disorder3CTD_human;PSYGENET
HgeneGRIK2C0004352Autistic Disorder2CTD_human
HgeneGRIK2C0005587Depression, Bipolar1CTD_human
HgeneGRIK2C0006142Malignant neoplasm of breast1CTD_human;UNIPROT
HgeneGRIK2C0007102Malignant tumor of colon1CTD_human
HgeneGRIK2C0007131Non-Small Cell Lung Carcinoma1CTD_human
HgeneGRIK2C0009375Colonic Neoplasms1CTD_human
HgeneGRIK2C0013146Drug abuse1CTD_human
HgeneGRIK2C0013170Drug habituation1CTD_human
HgeneGRIK2C0013222Drug Use Disorders1CTD_human
HgeneGRIK2C0014859Esophageal Neoplasms1CTD_human
HgeneGRIK2C0016722Frigidity1CTD_human
HgeneGRIK2C0017636Glioblastoma1CTD_human
HgeneGRIK2C0020594Hypoactive Sexual Desire Disorder1CTD_human
HgeneGRIK2C0023903Liver neoplasms1CTD_human
HgeneGRIK2C0024232Lymphatic Metastasis1CTD_human
HgeneGRIK2C0024713Manic Disorder1CTD_human
HgeneGRIK2C0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgeneGRIK2C0029261Orgasmic Disorder1CTD_human
HgeneGRIK2C0033953Psychosexual Disorders1CTD_human
HgeneGRIK2C0036341Schizophrenia1CTD_human
HgeneGRIK2C0036902Sexual Arousal Disorder1CTD_human
HgeneGRIK2C0038580Substance Dependence1CTD_human
HgeneGRIK2C0038586Substance Use Disorders1CTD_human
HgeneGRIK2C0236969Substance-Related Disorders1CTD_human
HgeneGRIK2C0334588Giant Cell Glioblastoma1CTD_human
HgeneGRIK2C0338831Manic1CTD_human
HgeneGRIK2C0345904Malignant neoplasm of liver1CTD_human
HgeneGRIK2C0525045Mood Disorders1PSYGENET
HgeneGRIK2C0546837Malignant neoplasm of esophagus1CTD_human
HgeneGRIK2C0678222Breast Carcinoma1CTD_human
HgeneGRIK2C0740858Substance abuse problem1CTD_human
HgeneGRIK2C0919267ovarian neoplasm1CTD_human
HgeneGRIK2C1140680Malignant neoplasm of ovary1CTD_human
HgeneGRIK2C1257931Mammary Neoplasms, Human1CTD_human
HgeneGRIK2C1458155Mammary Neoplasms1CTD_human
HgeneGRIK2C1510472Drug Dependence1CTD_human
HgeneGRIK2C1621958Glioblastoma Multiforme1CTD_human
HgeneGRIK2C1970198MENTAL RETARDATION, AUTOSOMAL RECESSIVE 61CTD_human;GENOMICS_ENGLAND
HgeneGRIK2C4316881Prescription Drug Abuse1CTD_human
HgeneGRIK2C4704874Mammary Carcinoma, Human1CTD_human
TgeneCDKAL1C0011860Diabetes Mellitus, Non-Insulin-Dependent3CTD_human
TgeneCDKAL1C0005910Body Weight2CTD_human
TgeneCDKAL1C0005612Birth Weight1CTD_human
TgeneCDKAL1C0263859Synovitis, Acne, Pustulosis, Hyperostosis, and Osteitis Syndrome1CTD_human