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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:CDK12-LGALS9 (FusionGDB2 ID:15179)

Fusion Gene Summary for CDK12-LGALS9

check button Fusion gene summary
Fusion gene informationFusion gene name: CDK12-LGALS9
Fusion gene ID: 15179
HgeneTgene
Gene symbol

CDK12

LGALS9

Gene ID

51755

3965

Gene namecyclin dependent kinase 12galectin 9
SynonymsCRK7|CRKR|CRKRSHUAT|LGALS9A
Cytomap

17q12

17q11.2

Type of geneprotein-codingprotein-coding
Descriptioncyclin-dependent kinase 12CDC2-related protein kinase 7Cdc2-related kinase, arginine/serine-richcell division cycle 2-related protein kinase 7cell division protein kinase 12galectin-9ecalectingal-9lectin, galactoside-binding, soluble, 9tumor antigen HOM-HD-21urate transporter/channel protein
Modification date2020031320200315
UniProtAcc

Q9NYV4

Q3B8N2

Ensembl transtripts involved in fusion geneENST00000430627, ENST00000447079, 
ENST00000559545, 		ENST00000310394, 
ENST00000395473, ENST00000302228, 
ENST00000313648, ENST00000413914, 
ENST00000448970, 
Fusion gene scores* DoF score29 X 13 X 13=49018 X 8 X 5=320
# samples 319
** MAII scorelog2(31/4901*10)=-3.98273602613552
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/320*10)=-1.83007499855769
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CDK12 [Title/Abstract] AND LGALS9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDK12(37657692)-LGALS9(25965288), # samples:1
Anticipated loss of major functional domain due to fusion event.CDK12-LGALS9 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
CDK12-LGALS9 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
CDK12-LGALS9 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CDK12-LGALS9 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
HgeneCDK12

GO:0046777

protein autophosphorylation

11683387

TgeneLGALS9

GO:0006954

inflammatory response

23817958

TgeneLGALS9

GO:0007565

female pregnancy

23242525

TgeneLGALS9

GO:0010628

positive regulation of gene expression

16116184

TgeneLGALS9

GO:0010629

negative regulation of gene expression

23408620

TgeneLGALS9

GO:0032673

regulation of interleukin-4 production

16116184

TgeneLGALS9

GO:0032674

regulation of interleukin-5 production

16116184

TgeneLGALS9

GO:0032689

negative regulation of interferon-gamma production

23408620

TgeneLGALS9

GO:0032753

positive regulation of interleukin-4 production

20209097

TgeneLGALS9

GO:0032834

positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response

20209097

TgeneLGALS9

GO:0034134

toll-like receptor 2 signaling pathway

16116184

TgeneLGALS9

GO:0034142

toll-like receptor 4 signaling pathway

16116184

TgeneLGALS9

GO:0038066

p38MAPK cascade

16116184

TgeneLGALS9

GO:0045953

negative regulation of natural killer cell mediated cytotoxicity

23408620

TgeneLGALS9

GO:0046598

positive regulation of viral entry into host cell

21670307

TgeneLGALS9

GO:0050718

positive regulation of interleukin-1 beta secretion

20209097

TgeneLGALS9

GO:0060135

maternal process involved in female pregnancy

25578313

TgeneLGALS9

GO:0070241

positive regulation of activated T cell autonomous cell death

20209097

TgeneLGALS9

GO:0070371

ERK1 and ERK2 cascade

16116184

TgeneLGALS9

GO:0070555

response to interleukin-1

23817958

TgeneLGALS9

GO:0071346

cellular response to interferon-gamma

23817958

TgeneLGALS9

GO:0071636

positive regulation of transforming growth factor beta production

20209097

TgeneLGALS9

GO:1902715

positive regulation of interferon-gamma secretion

20209097

TgeneLGALS9

GO:1904469

positive regulation of tumor necrosis factor secretion

20209097

TgeneLGALS9

GO:2000562

negative regulation of CD4-positive, alpha-beta T cell proliferation

20209097

TgeneLGALS9

GO:2000563

positive regulation of CD4-positive, alpha-beta T cell proliferation

16116184

TgeneLGALS9

GO:2000667

positive regulation of interleukin-13 secretion

20209097

TgeneLGALS9

GO:2000670

positive regulation of dendritic cell apoptotic process

16116184

TgeneLGALS9

GO:2001181

positive regulation of interleukin-10 secretion

16116184|20209097

TgeneLGALS9

GO:2001190

positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell

16116184


check buttonFusion gene breakpoints across CDK12 (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 LGALS9 (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
ChimerDB4COADTCGA-AZ-6600CDK12chr17

37657692

+LGALS9chr17

25965288

+


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Fusion Gene ORF analysis for CDK12-LGALS9

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-shiftENST00000430627ENST00000310394CDK12chr17

37657692

+LGALS9chr17

25965288

+
Frame-shiftENST00000430627ENST00000395473CDK12chr17

37657692

+LGALS9chr17

25965288

+
Frame-shiftENST00000430627ENST00000302228CDK12chr17

37657692

+LGALS9chr17

25965288

+
Frame-shiftENST00000430627ENST00000313648CDK12chr17

37657692

+LGALS9chr17

25965288

+
5CDS-5UTRENST00000430627ENST00000413914CDK12chr17

37657692

+LGALS9chr17

25965288

+
5CDS-3UTRENST00000430627ENST00000448970CDK12chr17

37657692

+LGALS9chr17

25965288

+
Frame-shiftENST00000447079ENST00000310394CDK12chr17

37657692

+LGALS9chr17

25965288

+
Frame-shiftENST00000447079ENST00000395473CDK12chr17

37657692

+LGALS9chr17

25965288

+
Frame-shiftENST00000447079ENST00000302228CDK12chr17

37657692

+LGALS9chr17

25965288

+
Frame-shiftENST00000447079ENST00000313648CDK12chr17

37657692

+LGALS9chr17

25965288

+
5CDS-5UTRENST00000447079ENST00000413914CDK12chr17

37657692

+LGALS9chr17

25965288

+
5CDS-3UTRENST00000447079ENST00000448970CDK12chr17

37657692

+LGALS9chr17

25965288

+
intron-3CDSENST00000559545ENST00000310394CDK12chr17

37657692

+LGALS9chr17

25965288

+
intron-3CDSENST00000559545ENST00000395473CDK12chr17

37657692

+LGALS9chr17

25965288

+
intron-3CDSENST00000559545ENST00000302228CDK12chr17

37657692

+LGALS9chr17

25965288

+
intron-3CDSENST00000559545ENST00000313648CDK12chr17

37657692

+LGALS9chr17

25965288

+
intron-5UTRENST00000559545ENST00000413914CDK12chr17

37657692

+LGALS9chr17

25965288

+
intron-3UTRENST00000559545ENST00000448970CDK12chr17

37657692

+LGALS9chr17

25965288

+

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 CDK12-LGALS9


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)
CDK12chr1737657692+LGALS9chr1725965288+3.55E-070.99999964
CDK12chr1737657692+LGALS9chr1725965288+3.55E-070.99999964

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 CDK12-LGALS9


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
CDK12

Q9NYV4

LGALS9

Q3B8N2

FUNCTION: 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 transcription elongation. Regulates the expression of genes involved in DNA repair and is required for the maintenance of genomic stability. Preferentially phosphorylates 'Ser-5' in CTD repeats that are already phosphorylated at 'Ser-7', but can also phosphorylate 'Ser-2'. Required for RNA splicing, possibly by phosphorylating SRSF1/SF2. Involved in regulation of MAP kinase activity, possibly leading 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}.FUNCTION: Binds galactosides. {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 CDK12-LGALS9


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 CDK12-LGALS9


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 CDK12-LGALS9


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 CDK12-LGALS9


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCDK12C0033578Prostatic Neoplasms1CTD_human
HgeneCDK12C0376358Malignant neoplasm of prostate1CTD_human
TgeneLGALS9C0027697Nephritis1CTD_human