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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:CSTB-KRT13 (FusionGDB2 ID:19993)

Fusion Gene Summary for CSTB-KRT13

Fusion gene summary

Fusion gene information	Fusion gene name: CSTB-KRT13
	Fusion gene ID: 19993
		Hgene	Tgene
	Gene symbol	CSTB	KRT13
	Gene ID	1476	3860
	Gene name	cystatin B	keratin 13
	Synonyms	CPI-B\|CST6\|EPM1\|EPM1A\|PME\|STFB\|ULD	CK13\|K13\|WSN2
	Cytomap	21q22.3	17q21.2
	Type of gene	protein-coding	protein-coding
	Description	cystatin-Bcystatin B (stefin B)epididymis secretory sperm binding proteinliver thiol proteinase inhibitor	keratin, type I cytoskeletal 13CK-13cytokeratin 13keratin 13, type I
	Modification date	20200313	20200313
	UniProtAcc	P04080	P13646
	Ensembl transtripts involved in fusion gene	ENST00000291568,	ENST00000587118, ENST00000246635, ENST00000336861, ENST00000587544,
Fusion gene scores	* DoF score	10 X 9 X 5=450	19 X 33 X 6=3762
	# samples	9	24
	** MAII score	log2(9/450*10)=-2.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(24/3762*10)=-3.97039353791468 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: CSTB [Title/Abstract] AND KRT13 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	CSTB(45193941)-KRT13(39658788), # samples:1 CSTB(45196085)-KRT13(39659350), # samples:1
Anticipated loss of major functional domain due to fusion event.

* 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	CSTB	GO:0010466	negative regulation of peptidase activity	6203523
Hgene	CSTB	GO:0045861	negative regulation of proteolysis	3488317
Tgene	KRT13	GO:0007010	cytoskeleton organization	21371075

Fusion gene breakpoints across CSTB (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 KRT13 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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	Non-Cancer	TCGA-IN-8462-11A	CSTB	chr21	45193941	-	KRT13	chr17	39658788	-
ChimerDB4	Non-Cancer	TCGA-IN-8462-11A	CSTB	chr21	45196085	-	KRT13	chr17	39659350	-

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Fusion Gene ORF analysis for CSTB-KRT13

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5CDS-intron	ENST00000291568	ENST00000587118	CSTB	chr21	45196085	-	KRT13	chr17	39659350	-
In-frame	ENST00000291568	ENST00000246635	CSTB	chr21	45196085	-	KRT13	chr17	39659350	-
In-frame	ENST00000291568	ENST00000336861	CSTB	chr21	45196085	-	KRT13	chr17	39659350	-
In-frame	ENST00000291568	ENST00000587544	CSTB	chr21	45196085	-	KRT13	chr17	39659350	-
intron-3CDS	ENST00000291568	ENST00000246635	CSTB	chr21	45193941	-	KRT13	chr17	39658788	-
intron-3CDS	ENST00000291568	ENST00000336861	CSTB	chr21	45193941	-	KRT13	chr17	39658788	-
intron-3CDS	ENST00000291568	ENST00000587544	CSTB	chr21	45193941	-	KRT13	chr17	39658788	-
intron-intron	ENST00000291568	ENST00000587118	CSTB	chr21	45193941	-	KRT13	chr17	39658788	-

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)
ENST00000291568	CSTB	chr21	45196085	-	ENST00000336861	KRT13	chr17	39659350	-	1133	242	760	2	253
ENST00000291568	CSTB	chr21	45196085	-	ENST00000246635	KRT13	chr17	39659350	-	1159	242	11	883	290
ENST00000291568	CSTB	chr21	45196085	-	ENST00000587544	KRT13	chr17	39659350	-	900	242	11	754	247

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
ENST00000291568	ENST00000336861	CSTB	chr21	45196085	-	KRT13	chr17	39659350	-	0.003298661	0.9967013
ENST00000291568	ENST00000246635	CSTB	chr21	45196085	-	KRT13	chr17	39659350	-	0.005426645	0.9945734
ENST00000291568	ENST00000587544	CSTB	chr21	45196085	-	KRT13	chr17	39659350	-	0.001200028	0.9987999

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Fusion Genomic Features for CSTB-KRT13

FusionAI 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.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution 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.

Distribution 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 CSTB-KRT13

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr21:45193941/chr17:39658788)
- 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
CSTB P04080	KRT13 P13646
FUNCTION: This is an intracellular thiol proteinase inhibitor. Tightly binding reversible inhibitor of cathepsins L, H and B.

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.

- In-frame and 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

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000246635

251_273

245

459.0

Region

Note=Linker 12

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000246635

274_412

245

459.0

Region

Note=Coil 2

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000246635

413_458

245

459.0

Region

Note=Tail

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000336861

251_273

245

421.0

Region

Note=Linker 12

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000336861

274_412

245

421.0

Region

Note=Coil 2

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000336861

413_458

245

421.0

Region

Note=Tail

- In-frame and 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

CSTB

chr21:45196085

chr17:39659350

ENST00000291568

46_50

99.0

Motif

Note=Secondary area of contact

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000246635

13_102

245

459.0

Compositional bias

Note=Gly-rich

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000336861

13_102

245

421.0

Compositional bias

Note=Gly-rich

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000246635

104_416

245

459.0

Domain

IF rod

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000336861

104_416

245

421.0

Domain

IF rod

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000246635

104_139

245

459.0

Region

Note=Coil 1A

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000246635

140_158

245

459.0

Region

Note=Linker 1

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000246635

159_250

245

459.0

Region

Note=Coil 1B

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000246635

1_103

245

459.0

Region

Note=Head

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000336861

104_139

245

421.0

Region

Note=Coil 1A

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000336861

140_158

245

421.0

Region

Note=Linker 1

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000336861

159_250

245

421.0

Region

Note=Coil 1B

Tgene

KRT13

chr21:45196085

chr17:39659350

ENST00000336861

1_103

245

421.0

Region

Note=Head

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Fusion Gene Sequence for CSTB-KRT13

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.

>19993_19993_1_CSTB-KRT13_CSTB_chr21_45196085_ENST00000291568_KRT13_chr17_39659350_ENST00000246635_length(transcript)=1159nt_BP=242nt
CGCGTCCCTTCTTGCGGGGCCACCGCGACCCCGCAGGGGACTCCGAAGCCAAAGTGCCTCCTCCCCGCCCCTTGGTTCCGCCCGCGCGTC
ACGTGACCCCAGCGCCTACTTGGGCTGAGGAGCCGCCGCGTCCCCTCGCCGAGTCCCCTCGCCAGATTCCCTCCGTCGCCGCCAAGATGA
TGTGCGGGGCGCCCTCCGCCACGCAGCCGGCCACCGCCGAGACCCAGCACATCGCCGACCAGGAGATGAAGGAATTTAGCAACCAGGTGG
TCGGCCAGGTCAACGTGGAGATGGATGCCACCCCAGGCATTGACCTGACCCGCGTGCTGGCAGAGATGAGGGAGCAGTACGAGGCCATGG
CAGAGAGGAACCGCCGGGATGCTGAGGAATGGTTCCACACCAAGAGTGCAGAGCTGAACAAGGAGGTGTCTACCAACACTGCCATGATTC
AGACCAGCAAGACAGAGATCACGGAGCTCAGGCGCACGCTCCAAGGCCTGGAGATTGAGCTGCAGTCCCAGCTGAGCATGAAAGCGGGGC
TGGAGAACACGGTGGCAGAGACGGAGTGCCGCTATGCCCTGCAGCTGCAGCAGATCCAGGGACTCATCAGCAGCATCGAGGCCCAGCTGA
GCGAGCTCCGCAGTGAGATGGAGTGCCAGAACCAAGAGTACAAGATGCTGCTGGACATCAAGACACGTCTGGAGCAGGAGATCGCCACCT
ACCGCAGCCTGCTCGAGGGCCAGGACGCCAAGATGATTGGTTTCCCTTCCTCAGCAGGAAGCGTCAGCCCCCGTAGCACCTCTGTTACCA
CGACTTCTAGTGCCTCTGTTACCACCACCTCTAATGCCTCTGGTCGCCGCACTTCTGATGTCCGTAGGCCTTAAATCTGCCTGGCGTCCC
CTCCCTCTGTCTTCAGCACCCAGAGGAGGAGAGAGCCGGCAGTTCCCTGCAGGAGAGAGGAGGGGCTGCTGGACCCAAGGCTCAGTCCCT
CTGCTCTCAGGACCCCCTGTCCTGACTCTCTCCTGATGGTGGGCCCTCTGTGCTCTTCTCTTCCGGTCGGATCTCTCTCCTCTCTGACCT

>19993_19993_1_CSTB-KRT13_CSTB_chr21_45196085_ENST00000291568_KRT13_chr17_39659350_ENST00000246635_length(amino acids)=290AA_BP=146
MRGHRDPAGDSEAKVPPPRPLVPPARHVTPAPTWAEEPPRPLAESPRQIPSVAAKMMCGAPSATQPATAETQHIADQEMKEFSNQVVGQV
NVEMDATPGIDLTRVLAEMREQYEAMAERNRRDAEEWFHTKSAELNKEVSTNTAMIQTSKTEITELRRTLQGLEIELQSQLSMKAGLENT
VAETECRYALQLQQIQGLISSIEAQLSELRSEMECQNQEYKMLLDIKTRLEQEIATYRSLLEGQDAKMIGFPSSAGSVSPRSTSVTTTSS

--------------------------------------------------------------
>19993_19993_2_CSTB-KRT13_CSTB_chr21_45196085_ENST00000291568_KRT13_chr17_39659350_ENST00000336861_length(transcript)=1133nt_BP=242nt
CGCGTCCCTTCTTGCGGGGCCACCGCGACCCCGCAGGGGACTCCGAAGCCAAAGTGCCTCCTCCCCGCCCCTTGGTTCCGCCCGCGCGTC
ACGTGACCCCAGCGCCTACTTGGGCTGAGGAGCCGCCGCGTCCCCTCGCCGAGTCCCCTCGCCAGATTCCCTCCGTCGCCGCCAAGATGA
TGTGCGGGGCGCCCTCCGCCACGCAGCCGGCCACCGCCGAGACCCAGCACATCGCCGACCAGGAGATGAAGGAATTTAGCAACCAGGTGG
TCGGCCAGGTCAACGTGGAGATGGATGCCACCCCAGGCATTGACCTGACCCGCGTGCTGGCAGAGATGAGGGAGCAGTACGAGGCCATGG
CAGAGAGGAACCGCCGGGATGCTGAGGAATGGTTCCACACCAAGAGTGCAGAGCTGAACAAGGAGGTGTCTACCAACACTGCCATGATTC
AGACCAGCAAGACAGAGATCACGGAGCTCAGGCGCACGCTCCAAGGCCTGGAGATTGAGCTGCAGTCCCAGCTGAGCATGAAAGCGGGGC
TGGAGAACACGGTGGCAGAGACGGAGTGCCGCTATGCCCTGCAGCTGCAGCAGATCCAGGGACTCATCAGCAGCATCGAGGCCCAGCTGA
GCGAGCTCCGCAGTGAGATGGAGTGCCAGAACCAAGAGTACAAGATGCTGCTGGACATCAAGACACGTCTGGAGCAGGAGATCGCCACCT
ACCGCAGCCTGCTCGAGGGCCAGGACGCCAAGAAGCGTCAGCCCCCGTAGCACCTCTGTTACCACGACTTCTAGTGCCTCTGTTACCACC
ACCTCTAATGCCTCTGGTCGCCGCACTTCTGATGTCCGTAGGCCTTAAATCTGCCTGGCGTCCCCTCCCTCTGTCTTCAGCACCCAGAGG
AGGAGAGAGCCGGCAGTTCCCTGCAGGAGAGAGGAGGGGCTGCTGGACCCAAGGCTCAGTCCCTCTGCTCTCAGGACCCCCTGTCCTGAC
TCTCTCCTGATGGTGGGCCCTCTGTGCTCTTCTCTTCCGGTCGGATCTCTCTCCTCTCTGACCTGGATACGCTTTGGTTTCTCAACTTCT

>19993_19993_2_CSTB-KRT13_CSTB_chr21_45196085_ENST00000291568_KRT13_chr17_39659350_ENST00000336861_length(amino acids)=253AA_BP=3
MTLLGVLALEQAAVGGDLLLQTCLDVQQHLVLLVLALHLTAELAQLGLDAADESLDLLQLQGIAALRLCHRVLQPRFHAQLGLQLNLQAL
ERAPELRDLCLAGLNHGSVGRHLLVQLCTLGVEPFLSIPAVPLCHGLVLLPHLCQHAGQVNAWGGIHLHVDLADHLVAKFLHLLVGDVLG

--------------------------------------------------------------
>19993_19993_3_CSTB-KRT13_CSTB_chr21_45196085_ENST00000291568_KRT13_chr17_39659350_ENST00000587544_length(transcript)=900nt_BP=242nt
CGCGTCCCTTCTTGCGGGGCCACCGCGACCCCGCAGGGGACTCCGAAGCCAAAGTGCCTCCTCCCCGCCCCTTGGTTCCGCCCGCGCGTC
ACGTGACCCCAGCGCCTACTTGGGCTGAGGAGCCGCCGCGTCCCCTCGCCGAGTCCCCTCGCCAGATTCCCTCCGTCGCCGCCAAGATGA
TGTGCGGGGCGCCCTCCGCCACGCAGCCGGCCACCGCCGAGACCCAGCACATCGCCGACCAGGAGATGAAGGAATTTAGCAACCAGGTGG
TCGGCCAGGTCAACGTGGAGATGGATGCCACCCCAGGCATTGACCTGACCCGCGTGCTGGCAGAGATGAGGGAGCAGTACGAGGCCATGG
CAGAGAGGAACCGCCGGGATGCTGAGGAATGGTTCCACACCAAGAGTGCAGAGCTGAACAAGGAGGTGTCTACCAACACTGCCATGATTC
AGACCAGCAAGACAGAGATCACGGAGCTCAGGCGCACGCTCCAAGGCCTGGAGATTGAGCTGCAGTCCCAGCTGAGCATGAAAGCGGGGC
TGGAGAACACGGTGGCAGAGACGGAGTGCCGCTATGCCCTGCAGCTGCAGCAGATCCAGGGACTCATCAGCAGCATCGAGGCCCAGCTGA
GCGAGCTCCGCAGTGAGATGGAGTGCCAGAACCAAGAGTACAAGATGCTGCTGGACATCAAGACACGTCTGGAGCAGGAGATCGCCACCT
ACCGCAGCCTGCTCGAGGGCCAGGACGCCAAGTAGGTCCTCTCCAGCCTCTTTCTTAGGATAGTGACTGCAGGACCCGTGGGTGTCAGAG
CAGGCAGGGCCTTAGAGATCCACCCCCTCATGTCAGAGAGGAGACCCCTCACTGTCTGACTTTACGGGGACATTTCCTTGGTAGGCTGCA

>19993_19993_3_CSTB-KRT13_CSTB_chr21_45196085_ENST00000291568_KRT13_chr17_39659350_ENST00000587544_length(amino acids)=247AA_BP=146
MRGHRDPAGDSEAKVPPPRPLVPPARHVTPAPTWAEEPPRPLAESPRQIPSVAAKMMCGAPSATQPATAETQHIADQEMKEFSNQVVGQV
NVEMDATPGIDLTRVLAEMREQYEAMAERNRRDAEEWFHTKSAELNKEVSTNTAMIQTSKTEITELRRTLQGLEIELQSQLSMKAGLENT

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

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Fusion Gene PPI Analysis for CSTB-KRT13

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 (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for CSTB-KRT13

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for CSTB-KRT13

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source