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Center for Computational Systems Medicine
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Kinase Fusion Gene Summary

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Kinase Fusion Gene Sample Information

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Kinase Fusion ORF Analysis

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Kinase Fusion Amino Acid Sequences

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Multiple Sequence Alignment of All Fusion Protein Isoforms

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Kinase Fusion Protein Functional Features

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Kinase Fusion Protein Structures

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Comparison of Fusion Protein Isoforms

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Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB

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pLDDT Scores and Difference Analysis of pLDDT Scores Between the Active Sites (Best) and Non-Active Sites.

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Ramachandran Plot of Kinase Fusion Protein Structure

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Potential Active Site Information

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Virtual Screening Results

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Kinase-Substrate Information

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Related Drugs with This Kinase Fusion Protein

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Related Disease with This Kinase Fusion Protein

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Clinical Trials of the Found Drugs/Small Molecules

Kinase Fusion Gene:CDK7_SH3BGR

Kinase Fusion Protein Summary

check button Kinase Fusion gene summary
Kinase Fusion partner gene informationKinase Fusion gene name: CDK7_SH3BGR
KinaseFusionDB ID: KFG1196
FusionGDB2.0 ID: KFG1196
HgeneTgene
Gene symbol

CDK7

SH3BGR

Gene ID

1022

6451

Gene namecyclin dependent kinase 7SH3 domain binding glutamate rich protein like
SynonymsCAK|CAK1|CDKN7|HCAK|MO15|STK1|p39MO15HEL-S-115|SH3BGR
Cytomap

5q13.2

Xq21.1

Type of geneprotein-codingprotein-coding
Descriptioncyclin-dependent kinase 739 KDa protein kinaseCDK-activating kinase 1TFIIH basal transcription factor complex kinase subunitcell division protein kinase 7cyclin-dependent kinase 7 (MO15 homolog, Xenopus laevis, cdk-activating kinase)homolog of Xenopadapter SH3BGRLSH3 domain binding glutamic acid-rich protein likeSH3 domain-binding glutamic acid-rich-like proteinSH3 domain-binding glutamic acid-rich-like protein 1SH3-binding domain glutamic acid-rich protein likeepididymis secretory protein Li 1
Modification date2024041120240411
UniProtAcc

P50613

O75368

Ensembl transtripts involved in fusion geneENST idsENST00000513629, ENST00000256443, 
ENST00000514676, ENST00000502604, 
ENST00000380634, ENST00000380637, 
ENST00000333634, ENST00000380631, 
ENST00000458295, 
Context (manual curation of fusion genes in KinaseFusionDB)

PubMed: CDK7 [Title/Abstract] AND SH3BGR [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CDK7(68531280)-SH3BGR(40871749), # samples:3
check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCDK7

GO:0006367

transcription initiation at RNA polymerase II promoter

7533895|8692841

HgeneCDK7

GO:0045944

positive regulation of transcription by RNA polymerase II

9852112

HgeneCDK7

GO:2000045

regulation of G1/S transition of mitotic cell cycle

23622515


check buttonKinase Fusion gene breakpoints across CDK7 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonKinase Fusion gene breakpoints across SH3BGR (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Kinase Fusion Gene Sample Information

check buttonKinase Fusion gene information.
check button Kinase Fusion gene information from four resources (ChiTars 5.0, ChimerDB 4.0, COSMIC, and CCLE)
* 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.
SourceSampleHgeneHchrHbpTgeneTchrTbp
ChimerDB4TCGA-ZG-A9NI-01ACDK7chr5

68531280

SH3BGRchr21

40871749

ChimerDB4TCGA-ZG-A9NICDK7chr5

68531280

SH3BGRchr21

40871748



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Kinase Fusion ORF Analysis


check buttonKinase Fusion information from ORFfinder translation from full-length transcript sequence from KinaseFusionDB.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)		Seq length
(amino acids)

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Kinase Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from KinaseFusionDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>Henst_Tenst_Hgene_Hchr_Hbp_Tgene_Tchr_Tbp_length(fusion AA)_AAseq

Multiple Sequence Alignment of All Fusion Protein Isoforms



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Kinase Fusion Protein Functional Features


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/chr5:68531280/chr21:40871749)
- 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
CDK7

P50613

SH3BGR

O75368

FUNCTION: Serine/threonine kinase involved in cell cycle control and in RNA polymerase II-mediated RNA transcription. Cyclin-dependent kinases (CDKs) are activated by the binding to a cyclin and mediate the progression through the cell cycle. Each different complex controls a specific transition between 2 subsequent phases in the cell cycle. Required for both activation and complex formation of CDK1/cyclin-B during G2-M transition, and for activation of CDK2/cyclins during G1-S transition (but not complex formation). CDK7 is the catalytic subunit of the CDK-activating kinase (CAK) complex. Phosphorylates SPT5/SUPT5H, SF1/NR5A1, POLR2A, p53/TP53, CDK1, CDK2, CDK4, CDK6 and CDK11B/CDK11. CAK activates the cyclin-associated kinases CDK1, CDK2, CDK4 and CDK6 by threonine phosphorylation, thus regulating cell cycle progression. CAK complexed to the core-TFIIH basal transcription factor activates RNA polymerase II by serine phosphorylation of the repetitive C-terminal domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter and elongation of the transcripts (PubMed:9852112). Phosphorylation of POLR2A in complex with DNA promotes transcription initiation by triggering dissociation from DNA. Its expression and activity are constant throughout the cell cycle. Upon DNA damage, triggers p53/TP53 activation by phosphorylation, but is inactivated in turn by p53/TP53; this feedback loop may lead to an arrest of the cell cycle and of the transcription, helping in cell recovery, or to apoptosis. Required for DNA-bound peptides-mediated transcription and cellular growth inhibition. {ECO:0000269|PubMed:10024882, ECO:0000269|PubMed:11113184, ECO:0000269|PubMed:16327805, ECO:0000269|PubMed:17373709, ECO:0000269|PubMed:17386261, ECO:0000269|PubMed:17901130, ECO:0000269|PubMed:19015234, ECO:0000269|PubMed:19071173, ECO:0000269|PubMed:19136461, ECO:0000269|PubMed:19450536, ECO:0000269|PubMed:19667075, ECO:0000269|PubMed:20360007, ECO:0000269|PubMed:9372954, ECO:0000269|PubMed:9840937, ECO:0000269|PubMed:9852112}.FUNCTION: Appears to function as an adapter protein that bridges proteins together or proteins with mRNAs (PubMed:34331014). May function as a ubiquitin ligase-substrate adapter (PubMed:34331014, PubMed:34870550). Additionally, associates with translating cytoplasmic ribosomes and may promote the expression of specific mRNAs (PubMed:34331014, PubMed:34870550). {ECO:0000269|PubMed:34331014, ECO:0000269|PubMed:34870550}.

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.

check button - Retained domain in the 5'-partner of fusion protein (protein functional feature from UniProt).
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote


check button - Retained domain in the 3'-partner of fusion protein (protein functional feature from UniProt).
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote


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Kinase-Substrate Information of CDK7_SH3BGR


check button Phosphorylation target of the kinase
(phosphosite, 03-17-2024)
KinaseKinase UniProt AccKinase speciesSubstrateSubstrate UniProt AccSubstrate phosphorylated residuesSubstrate phosphorylated sites (+/-7AA)Domain
CDK7P50613humanCDK11BP21127T595GsPLKAytPVVVtLWPkinase
CDK7P50613humanRB1P06400S780strPPtLsPIPHIPrRb_C
CDK7P50613humanMCM2P49736S5___MAEssEsFtMAs
CDK7P50613humanPOU5F1Q01860S12LASDFAFsPPPGGGG
CDK7P50613humanCDK2P24941Y168HEVVtLWyRAPEILLPkinase
CDK7P50613humanESR1P03372S118LHPPPQLsPFLQPHGOest_recep
CDK7P50613humanCDK6Q00534T177YSFQMALtSVVVTLWPkinase
CDK7P50613humanOGFOD1Q8N543S256FEPPIPRsPHIPQDH
CDK7P50613humanTP53P04637S371AHssHLkskkGQsts
CDK7P50613humanSUPT5HO00267T784MyGsGsrtPMyGsQt
CDK7P50613humanMCM2P49736S41RtDALtssPGRDLPP
CDK7P50613humanCDK9P50750S175FGLARAFsLAkNSQPPkinase
CDK7P50613humanPOLR2AP24928S1616TPQSPSysPtsPsYSRNA_pol_Rpb1_R
CDK7P50613humanMED1Q15648T1457HsKsPAytPQNLDsE
CDK7P50613humanMCM2P49736S13EsFtMAssPAQRRRG
CDK7P50613humanRARAP10276S77EIVPsPPsPPPLPRI
CDK7P50613humanXRN2Q9H0D6T439FtPsGILtPHALGsRXRN_M
CDK7P50613humanTP53P04637S376LkskkGQstsRHkkL
CDK7P50613humanE2F1Q01094T433DCDFGDLtPLDF___
CDK7P50613humanSUPT5HO00267T775tPMyGsQtPMyGsGs
CDK7P50613humanSUPT5HO00267S782tPMyGsGsrtPMyGs
CDK7P50613humanCDK2P24941T160GVPVRtytHEVVtLWPkinase
CDK7P50613humanSUPT5HO00267S773GRtPMyGsQtPMyGs
CDK7P50613humanPOLR2AP24928S1621SysPtsPsYSPTSPSRNA_pol_Rpb1_R
CDK7P50613humanCDK4P11802T172YSYQMALtPVVVTLWPkinase
CDK7P50613humanTP53P04637S378skkGQstsRHkkLMF
CDK7P50613humanSMAD1Q15797S206SSStYPHsPTSSDPG
CDK7P50613humanCDK1P06493T161GIPIRVytHEVVTLWPkinase
CDK7P50613humanMCM2P49736S4____MAEssEsFtMA
CDK7P50613humanTP53P04637S392FktEGPDsD______
CDK7P50613humanPCGF6Q9BYE7S30LPPPPPVsPPALTPA
CDK7P50613humanTP53P04637S33LPENNVLsPLPsQAM
CDK7P50613humanPOLR2AP24928S1619SPSysPtsPsYSPTSRNA_pol_Rpb1_R
CDK7P50613humanMCM2P49736S108DVEELtAsQREAAERMCM2_N
CDK7P50613humanERCC3P19447S90HIFLEAFsPVYKYAQHelicase_C_3
CDK7P50613humanRARGP13631S79EMVPSsPsPPPPPRV
CDK7P50613humanCDK12Q9NYV4T893sEEsRPytNKVITLWPkinase
CDK7P50613humanRB1P06400S807PGGNIyIsPLksPykRb_C
CDK7P50613humanMCM2P49736S40RRtDALtssPGRDLP
CDK7P50613humanMCM2P49736T59EsEGLLGtEGPLEEEMCM2_N
CDK7P50613humanMCM2P49736S53LPPFEDEsEGLLGtEMCM2_N
CDK7P50613humanMCM2P49736S139RRGLLyDsDEEDEERMCM2_N
CDK7P50613humanE2F1Q01094S403PEEFISLsPPHEALD
CDK7P50613humanRB1P06400S811IyIsPLksPykIsEGRb_C
CDK7P50613humanRARGP13631S77SEEMVPSsPsPPPPP
CDK7P50613humanHSPA5P11021T69tPsyVAFtPEGERLIHSP70
CDK7P50613humanMCM2P49736S27GNDPLtssPGRssRR
CDK7P50613humanCDK2P24941S46tETEGVPsTAIREISPkinase
CDK7P50613humanCDK2P24941T165tytHEVVtLWyRAPEPkinase
CDK7P50613humanPOLR2AP24928S1878sPKysPtsPtysPttRNA_pol_Rpb1_R
CDK7P50613humanMCM2P49736S7_MAEssEsFtMAssP
CDK7P50613humanARP10275S516VSRVPYPsPTCVkSE
CDK7P50613humanNR5A1Q13285S203EYPEPYAsPPQPGLP


check button Biological Network Integration of This Kinase and Substrates
(GeneMANIA website)

check button Enriched GO biological processes of the phosphorylation target genes of the kinase
KinaseGOIDGO termP.adjust
CDK7IDDescription0.00e+00
CDK7GO:1902893regulation of miRNA transcription3.10e-07
CDK7GO:0061614miRNA transcription3.10e-07
CDK7GO:2000628regulation of miRNA metabolic process6.68e-07
CDK7GO:0140747regulation of ncRNA transcription7.56e-07
CDK7GO:0010586miRNA metabolic process1.26e-06
CDK7GO:0048144fibroblast proliferation1.26e-06
CDK7GO:0006367transcription initiation at RNA polymerase II promoter1.42e-06
CDK7GO:1901990regulation of mitotic cell cycle phase transition2.63e-06
CDK7GO:0098781ncRNA transcription3.56e-06
CDK7GO:0000082G1/S transition of mitotic cell cycle4.61e-06
CDK7GO:0006352DNA-templated transcription initiation6.12e-06
CDK7GO:0044843cell cycle G1/S phase transition7.71e-06
CDK7GO:1901987regulation of cell cycle phase transition1.05e-05
CDK7GO:0035265organ growth1.05e-05
CDK7GO:0048145regulation of fibroblast proliferation1.05e-05
CDK7GO:0044772mitotic cell cycle phase transition1.15e-05
CDK7GO:0009755hormone-mediated signaling pathway1.51e-05
CDK7GO:0006368transcription elongation by RNA polymerase II3.14e-05
CDK7GO:1902749regulation of cell cycle G2/M phase transition3.14e-05
CDK7GO:0030850prostate gland development3.90e-05
CDK7GO:0048146positive regulation of fibroblast proliferation4.71e-05
CDK7GO:0006354DNA-templated transcription elongation5.75e-05
CDK7GO:0032786positive regulation of DNA-templated transcriptio1.50e-06
CDK7GO:0001655urogenital system development1.02e-04
CDK7GO:0071391cellular response to estrogen stimulus1.06e-04
CDK7GO:0060444branching involved in mammary gland duct morphogenesis1.40e-04
CDK7GO:1902894negative regulation of miRNA transcription2.33e-04
CDK7GO:0034243regulation of transcription elongation by RNA polymerase II2.38e-04
CDK7GO:0060740prostate gland epithelium morphogenesis2.38e-04
CDK7GO:2000629negative regulation of miRNA metabolic process2.38e-04
CDK7GO:0030522intracellular receptor signaling pathway2.69e-04
CDK7GO:0060512prostate gland morphogenesis2.81e-04
CDK7GO:0060603mammary gland duct morphogenesis3.04e-04
CDK7GO:0045637regulation of myeloid cell differentiation3.36e-04
CDK7GO:0002064epithelial cell development3.36e-04
CDK7GO:0010389regulation of G2/M transition of mitotic cell cycle4.00e-04
CDK7GO:0032784regulation of DNA-templated transcription elongation4.04e-04
CDK7GO:0071353cellular response to interleukin-44.32e-04
CDK7GO:0045786negative regulation of cell cycle4.67e-04
CDK7GO:0002068glandular epithelial cell development4.67e-04
CDK7GO:0060218hematopoietic stem cell differentiation4.67e-04
CDK7GO:0070670response to interleukin-44.67e-04
CDK7GO:0065004protein-DNA complex assembly4.79e-04
CDK7GO:0048863stem cell differentiation5.27e-04
CDK7GO:0034502protein localization to chromosome5.48e-04
CDK7GO:0022612gland morphogenesis5.91e-04
CDK7GO:0006275regulation of DNA replication6.17e-04
CDK7GO:0048732gland development6.31e-04
CDK7GO:0000077DNA damage checkpoint signaling6.31e-04

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Related Drugs to CDK7_SH3BGR


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

check button Distribution of the number of studies mentioning CDK7-SH3BGR and kinase inhibitors the PubMed Abstract (04-01-2024)

Fusion gene - drug pair 1Fusion gene - drug pair 2PMIDPublication dateDOIStudy title

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Related Diseases to CDK7_SH3BGR


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Related diseases from the literature mentioned this fusion gene and drug.
(PubMed, 04-01-2024)
MeSH IDMeSH term

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


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Clinical Trials of the Found Drugs/Small Molecules


check button Statistics of the Clinical Trials of the Found Kinase Inibitors from clinicaltrials.gov (06-17-2024)

check button Clinical Trials from clinicaltrials.gov (06-17-2024)

Fusion GeneKinase InhibitorNCT IDStudy StatusPhasesDisease# EnrolmentDate