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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 5568

FusionGeneSummary for CASC3_CDK12

check button Fusion gene summary
Fusion gene informationFusion gene name: CASC3_CDK12
Fusion gene ID: 5568
HgeneTgene
Gene symbol

CASC3

CDK12

Gene ID

22794

51755

Gene nameCASC3, exon junction complex subunitcyclin dependent kinase 12
SynonymsBTZ|MLN51CRK7|CRKR|CRKRS
Cytomap

17q21.1

17q12

Type of geneprotein-codingprotein-coding
Descriptionprotein CASC3MLN 51barentszcancer susceptibility 3cancer susceptibility candidate 3cancer susceptibility candidate gene 3 proteinmetastatic lymph node 51metastatic lymph node gene 51 proteinprotein barentszcyclin-dependent kinase 12CDC2-related protein kinase 7Cdc2-related kinase, arginine/serine-richcell division cycle 2-related protein kinase 7cell division protein kinase 12
Modification date2018052320180523
UniProtAcc

O15234

Q9NYV4

Ensembl transtripts involved in fusion geneENST00000264645, ENST00000430627, 
ENST00000447079, ENST00000559545, 
Fusion gene scores* DoF score15 X 7 X 8=84027 X 15 X 12=4860
# samples 1731
** MAII scorelog2(17/840*10)=-2.30485458152842
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(31/4860*10)=-3.97061619321891
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CASC3 [Title/Abstract] AND CDK12 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationKinase involved fusion gene, inframe and retained kinase domain.
* 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
TgeneCDK12

GO:0046777

protein autophosphorylation

11683387


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVSTADTCGA-BR-4366-01ACASC3chr17

38297860

+CDK12chr17

37686884

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
In-frameENST00000264645ENST00000430627CASC3chr17

38297860

+CDK12chr17

37686884

+
Frame-shiftENST00000264645ENST00000447079CASC3chr17

38297860

+CDK12chr17

37686884

+
5CDS-intronENST00000264645ENST00000559545CASC3chr17

38297860

+CDK12chr17

37686884

+

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FusionProtFeatures for CASC3_CDK12


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CASC3

O15234

CDK12

Q9NYV4

Core component of the splicing-dependent multiproteinexon junction complex (EJC) deposited at splice junctions onmRNAs. The EJC is a dynamic structure consisting of core proteinsand several peripheral nuclear and cytoplasmic associated factorsthat join the complex only transiently either during EJC assemblyor during subsequent mRNA metabolism. The EJC marks the positionof the exon-exon junction in the mature mRNA for the geneexpression machinery and the core components remain bound tospliced mRNAs throughout all stages of mRNA metabolism therebyinfluencing downstream processes including nuclear mRNA export,subcellular mRNA localization, translation efficiency andnonsense-mediated mRNA decay (NMD). Stimulates the ATPase and RNA-helicase activities of EIF4A3. Plays a role in the stress responseby participating in cytoplasmic stress granules assembly and byfavoring cell recovery following stress. Component of thedendritic ribonucleoprotein particles (RNPs) in hippocampalneurons. May play a role in mRNA transport. Binds spliced mRNA insequence-independent manner, 20-24 nucleotides upstream of mRNAexon-exon junctions. Binds poly(G) and poly(U) RNA homopolymer.{ECO:0000269|PubMed:17375189, ECO:0000269|PubMed:17652158}. Cyclin-dependent kinase that phosphorylates the C-terminal domain (CTD) of the large subunit of RNA polymerase II(POLR2A), thereby acting as a key regulator of transcriptionelongation. Regulates the expression of genes involved in DNArepair and is required for the maintenance of genomic stability.Preferentially phosphorylates 'Ser-5' in CTD repeats that arealready phosphorylated at 'Ser-7', but can also phosphorylate'Ser-2'. Required for RNA splicing, possibly by phosphorylatingSRSF1/SF2. Involved in regulation of MAP kinase activity, possiblyleading to affect the response to estrogen inhibitors.{ECO:0000269|PubMed:11683387, ECO:0000269|PubMed:19651820,ECO:0000269|PubMed:20952539, ECO:0000269|PubMed:22012619,ECO:0000269|PubMed:24662513}.

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
HgeneCASC3chr17:38297860chr17:37686884ENST00000264645+31441_46991130Compositional biasNote=Poly-Gly
TgeneCDK12chr17:38297860chr17:37686884ENST00000430627+12141266_128012531482Compositional biasNote=Poly-Pro
TgeneCDK12chr17:38297860chr17:37686884ENST00000447079+0141266_1280-111491Compositional biasNote=Poly-Pro
TgeneCDK12chr17:38297860chr17:37686884ENST00000447079+014407_413-111491Compositional biasNote=Poly-Ala
TgeneCDK12chr17:38297860chr17:37686884ENST00000447079+014535_540-111491Compositional biasNote=Poly-Pro
TgeneCDK12chr17:38297860chr17:37686884ENST00000447079+014727_1020-111491DomainProtein kinase
TgeneCDK12chr17:38297860chr17:37686884ENST00000447079+014733_741-111491Nucleotide bindingNote=ATP
TgeneCDK12chr17:38297860chr17:37686884ENST00000447079+014814_819-111491Nucleotide bindingNote=ATP

- In-frame and not-retained protein feature among the 13 regional features.
>>>>>>>>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCASC3chr17:38297860chr17:37686884ENST00000264645+31495_131991130Coiled coilOntology_term=ECO:0000255
HgeneCASC3chr17:38297860chr17:37686884ENST00000264645+314392_395991130Compositional biasNote=Poly-Pro
HgeneCASC3chr17:38297860chr17:37686884ENST00000264645+314425_428991130Compositional biasNote=Poly-Pro
HgeneCASC3chr17:38297860chr17:37686884ENST00000264645+314643_648991130Compositional biasNote=Poly-Pro
HgeneCASC3chr17:38297860chr17:37686884ENST00000264645+314692_695991130Compositional biasNote=Poly-Pro
HgeneCASC3chr17:38297860chr17:37686884ENST00000264645+314204_210991130MotifNuclear localization signal 1
HgeneCASC3chr17:38297860chr17:37686884ENST00000264645+314254_262991130MotifNuclear localization signal 2
HgeneCASC3chr17:38297860chr17:37686884ENST00000264645+314462_466991130MotifNote=Nuclear export signal
HgeneCASC3chr17:38297860chr17:37686884ENST00000264645+314137_283991130RegionNote=Sufficient to form the EJC
HgeneCASC3chr17:38297860chr17:37686884ENST00000264645+314377_703991130RegionNote=Necessary for localization in cytoplasmic stress granules
TgeneCDK12chr17:38297860chr17:37686884ENST00000430627+1214407_41312531482Compositional biasNote=Poly-Ala
TgeneCDK12chr17:38297860chr17:37686884ENST00000430627+1214535_54012531482Compositional biasNote=Poly-Pro
TgeneCDK12chr17:38297860chr17:37686884ENST00000430627+1214727_102012531482DomainProtein kinase
TgeneCDK12chr17:38297860chr17:37686884ENST00000430627+1214733_74112531482Nucleotide bindingNote=ATP
TgeneCDK12chr17:38297860chr17:37686884ENST00000430627+1214814_81912531482Nucleotide bindingNote=ATP


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FusionGeneSequence for CASC3_CDK12


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_CASC3_ENST00000264645_chr17_38297860_+_CDK12_ENST00000430627_chr17_37686884_+_327aa
MADRRRQRASQDTEDEESGASGSDSGGSPLRGGGSCSGSAGGGGSGSLPSQRGGRTGALHLRRVESGGAKSAEESECESEDGIEGDAVLS
DYESAEDSERRGPLSPPDLHRRHLHPLWLKAIFPAPPRSXTQPXQPPCCNFYPSLKQSLLATCHMSTRPXDQWSTPPDPVQTGLMETLMG
LKQGSVPLTLMNETLVQPXQNPWSRPWXRTGPSQALXATLGSPAVTRAQGQCSFQGTRTSVLPGSPXRYTRWSGNHSXRLREAAILWYMQ


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_CASC3_ENST00000264645_chr17_38297860_+_CDK12_ENST00000430627_chr17_37686884_+_983nt
ATGGCGGACCGGCGGCGGCAGCGCGCTTCGCAAGACACCGAGGACGAGGAATCTGGTGCTTCGGGCTCCGACAGCGGCGGCTCCCCGTTG
CGGGGAGGCGGGAGCTGCAGCGGTAGCGCCGGAGGCGGCGGCAGCGGCTCTCTGCCTTCACAGCGCGGAGGCCGAACCGGGGCCCTTCAT
CTGCGGCGGGTGGAGAGCGGGGGCGCCAAGAGTGCTGAGGAGTCGGAGTGTGAGAGTGAAGATGGCATTGAAGGTGATGCTGTTCTCTCG
GATTATGAAAGTGCAGAAGACTCGGAAAGAAGAGGCCCCCTGAGCCCCCCGGACCTCCACCGCCGCCACCTCCACCCCCTCTGGTTGAAG
GCGATCTTTCCAGCGCCCCCCAGGAGTTGAACCCAGCCGTGACAGCCGCCTTGCTGCAACTTTTATCCCAGCCTGAAGCAGAGCCTCCTG
GCCACCTGCCACATGAGCACCAGGCCTTGAGACCAATGGAGTACTCCACCCGACCCCGTCCAAACAGGACTTATGGAAACACTGATGGGC
CTGAAACAGGGTTCAGTGCCATTGACACTGATGAACGAAACTCTGGTCCAGCCTTGACAGAATCCTTGGTCCAGACCCTGGTGAAGAACA
GGACCTTCTCAGGCTCTCTGAGCCACCTTGGGGAGTCCAGCAGTTACCAGGGCACAGGGTCAGTGCAGTTTCCAGGGGACCAGGACCTCC
GTTTTGCCAGGGTCCCCTTAGCGTTACACCCGGTGGTCGGGCAACCATTCCTGAAGGCTGAGGGAAGCAGCAATTCTGTGGTACATGCAG
AGACCAAATTGCAAAACTATGGGGAGCTGGGGCCAGGAACCACTGGGGCCAGCAGCTCAGGAGCAGGCCTTCACTGGGGGGGCCCAACTC


* Fusion transcript sequences (Full-length transcript).
>In-frame_CASC3_ENST00000264645_chr17_38297860_+_CDK12_ENST00000430627_chr17_37686884_+_2370nt
CACACACACACACACACACACACACACCCCAACACACACACACACACCCCAACACACACACACACACACACACACACACACACACACACA
CACACACACACACACACAGCGGGATGGCCGAGCGCCGCACGCGTAGCACGCCGGGACTAGCTATCCAGCCTCCCAGCAGCCTCTGCGACG
GGCGCGGTGCGTAAGTACCTCGCCGGTGGTGGCCGTTCTCCGTAAGATGGCGGACCGGCGGCGGCAGCGCGCTTCGCAAGACACCGAGGA
CGAGGAATCTGGTGCTTCGGGCTCCGACAGCGGCGGCTCCCCGTTGCGGGGAGGCGGGAGCTGCAGCGGTAGCGCCGGAGGCGGCGGCAG
CGGCTCTCTGCCTTCACAGCGCGGAGGCCGAACCGGGGCCCTTCATCTGCGGCGGGTGGAGAGCGGGGGCGCCAAGAGTGCTGAGGAGTC
GGAGTGTGAGAGTGAAGATGGCATTGAAGGTGATGCTGTTCTCTCGGATTATGAAAGTGCAGAAGACTCGGAAAGAAGAGGCCCCCTGAG
CCCCCCGGACCTCCACCGCCGCCACCTCCACCCCCTCTGGTTGAAGGCGATCTTTCCAGCGCCCCCCAGGAGTTGAACCCAGCCGTGACA
GCCGCCTTGCTGCAACTTTTATCCCAGCCTGAAGCAGAGCCTCCTGGCCACCTGCCACATGAGCACCAGGCCTTGAGACCAATGGAGTAC
TCCACCCGACCCCGTCCAAACAGGACTTATGGAAACACTGATGGGCCTGAAACAGGGTTCAGTGCCATTGACACTGATGAACGAAACTCT
GGTCCAGCCTTGACAGAATCCTTGGTCCAGACCCTGGTGAAGAACAGGACCTTCTCAGGCTCTCTGAGCCACCTTGGGGAGTCCAGCAGT
TACCAGGGCACAGGGTCAGTGCAGTTTCCAGGGGACCAGGACCTCCGTTTTGCCAGGGTCCCCTTAGCGTTACACCCGGTGGTCGGGCAA
CCATTCCTGAAGGCTGAGGGAAGCAGCAATTCTGTGGTACATGCAGAGACCAAATTGCAAAACTATGGGGAGCTGGGGCCAGGAACCACT
GGGGCCAGCAGCTCAGGAGCAGGCCTTCACTGGGGGGGCCCAACTCAGTCTTCTGCTTATGGAAAACTCTATCGGGGGCCTACAAGAGTC
CCACCAAGAGGGGGAAGAGGGAGAGGAGTTCCTTACTAACCCAGAGACTTCAGTGTCCTGAAAGATTCCTTTCCTATCCATCCTTCCATC
CAGTTCTCTGAATCTTTAATGAAATCATTTGCCAGAGCGAGGTAATCATCTGCATTTGGCTACTGCAAAGCTGTCCGTTGTATTCCTTGC
TCACTTGCTACTAGCAGGCGACTTACGAAATAATGATGTTGGCACCAGTTCCCCCTGGATGGGCTATAGCCAGAACATTTACTTCAACTC
TACCTTAGTAGATACAAGTAGAGAATATGGAGAGGATCATTACATTGAAAAGTAAATGTTTTATTAGTTCATTGCCTGCACTTACTGATC
GGAAGAGAGAAAGAACAGTTTCAGTATTGAGATGGCTCAGGAGAGGCTCTTTGATTTTTAAAGTTTTGGGGTGGGGGATTGTGTGTGGTT
TCTTTCTTTTGAATTTTAATTTAGGTGTTTTGGGTTTTTTTCCTTTAAAGAGAATAGTGTTCACAAAATTTGAGCTGCTCTTTGGCTTTT
GCTATAAGGGAAACAGAGTGGCCTGGCTGATTTGAATAAATGTTTCTTTCCTCTCCACCATCTCACATTTTGCTTTTAAGTGAACACTTT
TTCCCCATTGAGCATCTTGAACATACTTTTTTTCCAAATAAATTACTCATCCTTAAAGTTTACTCCACTTTGACAAAAGATACGCCCTTC
TCCCTGCACATAAAGCAGGTTGTAGAACGTGGCATTCTTGGGCAAGTAGGTAGACTTTACCCAGTCTCTTTCCTTTTTTGCTGATGTGTG
CTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCTCGCTTGCTCGCTCTCGCTGTTTCTCTCTCT
TTGAGGCATTTGTTTGGAAAAAATCGTTGAGATGCCCAAGAACCTGGGATAATTCTTTACTTTTTTTGAAATAAAGGAAAGGAAATTCAG
ACTCTTACATTGTTCTCTGTAACTCTTCAATTCTAAAATGTTTTGTTTTTTAAACCATGTTCTGATGGGGAAGTTGATTTGTAAGTGTGG
ACAGCTTGGACATTGCTGCTGAGCTGTGGTTAGAGATGATGCCTCCATTCCTAGAGGGCTAATAACAGCATTTAGCATATTGTTTACACA


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FusionGenePPI for CASC3_CDK12


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
CASC3ELAVL1, CAND1, EIF4A3, MAGOH, CDK6, GRB2, NXF1, BMI1, VTI1B, TRA2A, PRR11, LUC7L, LUC7L2, SNIP1, UPF3B, AKT1, APC, CASP8, CDKN2A, ESR2, FGFR4, NBN, PHB, PTPN1, PTPRJ, EWSR1, XPO1, LLGL2, RBM8A, MED12, CHST15, KDM1B, UPF3A, WIBG, PNN, ELAVL2, GSPT2, U2AF2, CDX1, APOBEC3D, C11orf57, CLK2, PRDM5, CELF5, RBM3CDK12MGMT, SRRM2, RBM39, ELAVL1, MYC, PRPF4, CDK13, CCNK, TRIM24, IPPK, VPS51, ZNF606, TCEB3, BARD1, PAXIP1, PRPF40A, EWSR1, CDK20, CDK9, PIN1, RPL14, ACAA1, MAP4K4, SCAF4, SUPT16H, SRPK2, CLK1, BCLAF1, RNPS1, SNW1, PCGF1, CDX1, RPL37A, RRS1, ZNF2, FGF8, RPS14, WEE1, LASP1


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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RelatedDrugs for CASC3_CDK12


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for CASC3_CDK12


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