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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:SIK3-CTNNBIP1

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SIK3-CTNNBIP1
	FusionPDB ID: 81864
	FusionGDB2.0 ID: 81864
		Hgene	Tgene
	Gene symbol	SIK3	CTNNBIP1
	Gene ID	23387	56998
	Gene name	SIK family kinase 3	catenin beta interacting protein 1
	Synonyms	L19\|QSK\|SEMDK\|SIK-3	ICAT
	Cytomap	11q23.3	1p36.22
	Type of gene	protein-coding	protein-coding
	Description	serine/threonine-protein kinase SIK3salt-inducible kinase 3serine/threonine-protein kinase QSK	beta-catenin-interacting protein 1beta-catenin-interacting protein ICATinhibitor of beta-catenin and Tcf-4
	Modification date	20200320	20200313
	UniProtAcc	.	Q9NSA3
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000375288, ENST00000434315, ENST00000292055, ENST00000375300, ENST00000446921, ENST00000542607, ENST00000488337,	ENST00000377256, ENST00000377258, ENST00000377263, ENST00000400904, ENST00000537447,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	17 X 12 X 10=2040	7 X 7 X 9=441
	# samples	23	13
	** MAII score	log2(23/2040*10)=-3.14886338591448 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(13/441*10)=-1.76226703252907 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: SIK3 [Title/Abstract] AND CTNNBIP1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SIK3(116968859)-CTNNBIP1(9910834), # samples:3
Anticipated loss of major functional domain due to fusion event.	SIK3-CTNNBIP1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. SIK3-CTNNBIP1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. SIK3-CTNNBIP1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. SIK3-CTNNBIP1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. SIK3-CTNNBIP1 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF. SIK3-CTNNBIP1 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	SIK3	GO:0006468	protein phosphorylation	14976552
Tgene	CTNNBIP1	GO:0032091	negative regulation of protein binding	12408825\|18287330

Fusion gene breakpoints across SIK3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across CTNNBIP1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Gene Sample Information

Fusion gene information from FusionGDB2.0.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	ACC	TCGA-OR-A5K5-01A	SIK3	chr11	116968859	-	CTNNBIP1	chr1	9910834	-
ChimerDB4	ACC	TCGA-OR-A5K5	SIK3	chr11	116968858	-	CTNNBIP1	chr1	9910834	-

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Fusion ORF Analysis

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000375300	SIK3	chr11	116968859	-	ENST00000400904	CTNNBIP1	chr1	9910834	-	947	279	31	372	113
ENST00000375300	SIK3	chr11	116968859	-	ENST00000377256	CTNNBIP1	chr1	9910834	-	397	279	31	372	113
ENST00000292055	SIK3	chr11	116968859	-	ENST00000400904	CTNNBIP1	chr1	9910834	-	803	135	194	451	85
ENST00000292055	SIK3	chr11	116968859	-	ENST00000377256	CTNNBIP1	chr1	9910834	-	253	135	140	0	47
ENST00000542607	SIK3	chr11	116968859	-	ENST00000400904	CTNNBIP1	chr1	9910834	-	803	135	194	451	85
ENST00000542607	SIK3	chr11	116968859	-	ENST00000377256	CTNNBIP1	chr1	9910834	-	253	135	140	0	47
ENST00000446921	SIK3	chr11	116968859	-	ENST00000400904	CTNNBIP1	chr1	9910834	-	963	295	47	388	113
ENST00000446921	SIK3	chr11	116968859	-	ENST00000377256	CTNNBIP1	chr1	9910834	-	413	295	47	388	113
ENST00000375300	SIK3	chr11	116968858	-	ENST00000400904	CTNNBIP1	chr1	9910834	-	947	279	31	372	113
ENST00000375300	SIK3	chr11	116968858	-	ENST00000377256	CTNNBIP1	chr1	9910834	-	397	279	31	372	113
ENST00000292055	SIK3	chr11	116968858	-	ENST00000400904	CTNNBIP1	chr1	9910834	-	803	135	194	451	85
ENST00000292055	SIK3	chr11	116968858	-	ENST00000377256	CTNNBIP1	chr1	9910834	-	253	135	140	0	47
ENST00000542607	SIK3	chr11	116968858	-	ENST00000400904	CTNNBIP1	chr1	9910834	-	803	135	194	451	85
ENST00000542607	SIK3	chr11	116968858	-	ENST00000377256	CTNNBIP1	chr1	9910834	-	253	135	140	0	47
ENST00000446921	SIK3	chr11	116968858	-	ENST00000400904	CTNNBIP1	chr1	9910834	-	963	295	47	388	113
ENST00000446921	SIK3	chr11	116968858	-	ENST00000377256	CTNNBIP1	chr1	9910834	-	413	295	47	388	113

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000375300	ENST00000400904	SIK3	chr11	116968859	-	CTNNBIP1	chr1	9910834	-	0.43157718	0.56842285
ENST00000375300	ENST00000377256	SIK3	chr11	116968859	-	CTNNBIP1	chr1	9910834	-	0.11090488	0.8890951
ENST00000292055	ENST00000400904	SIK3	chr11	116968859	-	CTNNBIP1	chr1	9910834	-	0.9228041	0.077195816
ENST00000292055	ENST00000377256	SIK3	chr11	116968859	-	CTNNBIP1	chr1	9910834	-	0.28915787	0.71084213
ENST00000542607	ENST00000400904	SIK3	chr11	116968859	-	CTNNBIP1	chr1	9910834	-	0.9228041	0.077195816
ENST00000542607	ENST00000377256	SIK3	chr11	116968859	-	CTNNBIP1	chr1	9910834	-	0.28915787	0.71084213
ENST00000446921	ENST00000400904	SIK3	chr11	116968859	-	CTNNBIP1	chr1	9910834	-	0.6376435	0.36235648
ENST00000446921	ENST00000377256	SIK3	chr11	116968859	-	CTNNBIP1	chr1	9910834	-	0.13549738	0.86450267
ENST00000375300	ENST00000400904	SIK3	chr11	116968858	-	CTNNBIP1	chr1	9910834	-	0.43157718	0.56842285
ENST00000375300	ENST00000377256	SIK3	chr11	116968858	-	CTNNBIP1	chr1	9910834	-	0.11090488	0.8890951
ENST00000292055	ENST00000400904	SIK3	chr11	116968858	-	CTNNBIP1	chr1	9910834	-	0.9228041	0.077195816
ENST00000292055	ENST00000377256	SIK3	chr11	116968858	-	CTNNBIP1	chr1	9910834	-	0.28915787	0.71084213
ENST00000542607	ENST00000400904	SIK3	chr11	116968858	-	CTNNBIP1	chr1	9910834	-	0.9228041	0.077195816
ENST00000542607	ENST00000377256	SIK3	chr11	116968858	-	CTNNBIP1	chr1	9910834	-	0.28915787	0.71084213
ENST00000446921	ENST00000400904	SIK3	chr11	116968858	-	CTNNBIP1	chr1	9910834	-	0.6376435	0.36235648
ENST00000446921	ENST00000377256	SIK3	chr11	116968858	-	CTNNBIP1	chr1	9910834	-	0.13549738	0.86450267

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>81864_81864_1_SIK3-CTNNBIP1_SIK3_chr11_116968858_ENST00000292055_CTNNBIP1_chr1_9910834_ENST00000377256_length(amino acids)=47AA_BP=

--------------------------------------------------------------

>81864_81864_2_SIK3-CTNNBIP1_SIK3_chr11_116968858_ENST00000292055_CTNNBIP1_chr1_9910834_ENST00000400904_length(amino acids)=85AA_BP=

--------------------------------------------------------------

>81864_81864_3_SIK3-CTNNBIP1_SIK3_chr11_116968858_ENST00000375300_CTNNBIP1_chr1_9910834_ENST00000377256_length(amino acids)=113AA_BP=82
MAGLPGPGLGEPGPRAACCLRPRRGPQPPPLPCPLRPASRVPQPRPPADPCPPVSATTRSTAPSARATSRWSSGPRTSSPRPRCRGRGDG

--------------------------------------------------------------

>81864_81864_4_SIK3-CTNNBIP1_SIK3_chr11_116968858_ENST00000375300_CTNNBIP1_chr1_9910834_ENST00000400904_length(amino acids)=113AA_BP=82
MAGLPGPGLGEPGPRAACCLRPRRGPQPPPLPCPLRPASRVPQPRPPADPCPPVSATTRSTAPSARATSRWSSGPRTSSPRPRCRGRGDG

--------------------------------------------------------------

>81864_81864_5_SIK3-CTNNBIP1_SIK3_chr11_116968858_ENST00000446921_CTNNBIP1_chr1_9910834_ENST00000377256_length(amino acids)=113AA_BP=82
MAGLPGPGLGEPGPRAACCLRPRRGPQPPPLPCPLRPASRVPQPRPPADPCPPVSATTRSTAPSARATSRWSSGPRTSSPRPRCRGRGDG

--------------------------------------------------------------

>81864_81864_6_SIK3-CTNNBIP1_SIK3_chr11_116968858_ENST00000446921_CTNNBIP1_chr1_9910834_ENST00000400904_length(amino acids)=113AA_BP=82
MAGLPGPGLGEPGPRAACCLRPRRGPQPPPLPCPLRPASRVPQPRPPADPCPPVSATTRSTAPSARATSRWSSGPRTSSPRPRCRGRGDG

--------------------------------------------------------------

>81864_81864_7_SIK3-CTNNBIP1_SIK3_chr11_116968858_ENST00000542607_CTNNBIP1_chr1_9910834_ENST00000377256_length(amino acids)=47AA_BP=

--------------------------------------------------------------

>81864_81864_8_SIK3-CTNNBIP1_SIK3_chr11_116968858_ENST00000542607_CTNNBIP1_chr1_9910834_ENST00000400904_length(amino acids)=85AA_BP=

--------------------------------------------------------------

>81864_81864_9_SIK3-CTNNBIP1_SIK3_chr11_116968859_ENST00000292055_CTNNBIP1_chr1_9910834_ENST00000377256_length(amino acids)=47AA_BP=

--------------------------------------------------------------

>81864_81864_10_SIK3-CTNNBIP1_SIK3_chr11_116968859_ENST00000292055_CTNNBIP1_chr1_9910834_ENST00000400904_length(amino acids)=85AA_BP=

--------------------------------------------------------------

>81864_81864_11_SIK3-CTNNBIP1_SIK3_chr11_116968859_ENST00000375300_CTNNBIP1_chr1_9910834_ENST00000377256_length(amino acids)=113AA_BP=82
MAGLPGPGLGEPGPRAACCLRPRRGPQPPPLPCPLRPASRVPQPRPPADPCPPVSATTRSTAPSARATSRWSSGPRTSSPRPRCRGRGDG

--------------------------------------------------------------

>81864_81864_12_SIK3-CTNNBIP1_SIK3_chr11_116968859_ENST00000375300_CTNNBIP1_chr1_9910834_ENST00000400904_length(amino acids)=113AA_BP=82
MAGLPGPGLGEPGPRAACCLRPRRGPQPPPLPCPLRPASRVPQPRPPADPCPPVSATTRSTAPSARATSRWSSGPRTSSPRPRCRGRGDG

--------------------------------------------------------------

>81864_81864_13_SIK3-CTNNBIP1_SIK3_chr11_116968859_ENST00000446921_CTNNBIP1_chr1_9910834_ENST00000377256_length(amino acids)=113AA_BP=82
MAGLPGPGLGEPGPRAACCLRPRRGPQPPPLPCPLRPASRVPQPRPPADPCPPVSATTRSTAPSARATSRWSSGPRTSSPRPRCRGRGDG

--------------------------------------------------------------

>81864_81864_14_SIK3-CTNNBIP1_SIK3_chr11_116968859_ENST00000446921_CTNNBIP1_chr1_9910834_ENST00000400904_length(amino acids)=113AA_BP=82
MAGLPGPGLGEPGPRAACCLRPRRGPQPPPLPCPLRPASRVPQPRPPADPCPPVSATTRSTAPSARATSRWSSGPRTSSPRPRCRGRGDG

--------------------------------------------------------------

>81864_81864_15_SIK3-CTNNBIP1_SIK3_chr11_116968859_ENST00000542607_CTNNBIP1_chr1_9910834_ENST00000377256_length(amino acids)=47AA_BP=

--------------------------------------------------------------

>81864_81864_16_SIK3-CTNNBIP1_SIK3_chr11_116968859_ENST00000542607_CTNNBIP1_chr1_9910834_ENST00000400904_length(amino acids)=85AA_BP=

--------------------------------------------------------------

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:116968859/chr1:9910834)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	CTNNBIP1 Q9NSA3
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.	FUNCTION: Prevents the interaction between CTNNB1 and TCF family members, and acts as negative regulator of the Wnt signaling pathway. {ECO:0000269\|PubMed:12408824}.

Retention 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.

- Retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

SIK3

chr11:116968858

chr1:9910834

ENST00000292055

2_54

33.0

1979.0

Compositional bias

Ala-rich

Hgene

SIK3

chr11:116968858

chr1:9910834

ENST00000292055

650_1016

33.0

1979.0

Compositional bias

Gln-rich

Hgene

SIK3

chr11:116968858

chr1:9910834

ENST00000375288

2_54

1314.0

Compositional bias

Ala-rich

Hgene

SIK3

chr11:116968858

chr1:9910834

ENST00000375288

650_1016

1314.0

Compositional bias

Gln-rich

Hgene

SIK3

chr11:116968859

chr1:9910834

ENST00000292055

2_54

33.0

1979.0

Compositional bias

Ala-rich

Hgene

SIK3

chr11:116968859

chr1:9910834

ENST00000292055

650_1016

33.0

1979.0

Compositional bias

Gln-rich

Hgene

SIK3

chr11:116968859

chr1:9910834

ENST00000375288

2_54

1314.0

Compositional bias

Ala-rich

Hgene

SIK3

chr11:116968859

chr1:9910834

ENST00000375288

650_1016

1314.0

Compositional bias

Gln-rich

Hgene

SIK3

chr11:116968858

chr1:9910834

ENST00000292055

344_384

33.0

1979.0

Domain

UBA

Hgene

SIK3

chr11:116968858

chr1:9910834

ENST00000292055

66_317

33.0

1979.0

Domain

Protein kinase

Hgene

SIK3

chr11:116968858

chr1:9910834

ENST00000375288

344_384

1314.0

Domain

UBA

Hgene

SIK3

chr11:116968858

chr1:9910834

ENST00000375288

66_317

1314.0

Domain

Protein kinase

Hgene

SIK3

chr11:116968859

chr1:9910834

ENST00000292055

344_384

33.0

1979.0

Domain

UBA

Hgene

SIK3

chr11:116968859

chr1:9910834

ENST00000292055

66_317

33.0

1979.0

Domain

Protein kinase

Hgene

SIK3

chr11:116968859

chr1:9910834

ENST00000375288

344_384

1314.0

Domain

UBA

Hgene

SIK3

chr11:116968859

chr1:9910834

ENST00000375288

66_317

1314.0

Domain

Protein kinase

Hgene

SIK3

chr11:116968858

chr1:9910834

ENST00000292055

72_80

33.0

1979.0

Nucleotide binding

ATP

Hgene

SIK3

chr11:116968858

chr1:9910834

ENST00000375288

72_80

1314.0

Nucleotide binding

ATP

Hgene

SIK3

chr11:116968859

chr1:9910834

ENST00000292055

72_80

33.0

1979.0

Nucleotide binding

ATP

Hgene

SIK3

chr11:116968859

chr1:9910834

ENST00000375288

72_80

1314.0

Nucleotide binding

ATP

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
SIK3
CTNNBIP1

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to SIK3-CTNNBIP1

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to SIK3-CTNNBIP1

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

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source