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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:CTSB-UBAP2L

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CTSB-UBAP2L
	FusionPDB ID: 20480
	FusionGDB2.0 ID: 20480
		Hgene	Tgene
	Gene symbol	CTSB	UBAP2L
	Gene ID	1508	9898
	Gene name	cathepsin B	ubiquitin associated protein 2 like
	Synonyms	APPS\|CPSB\|RECEUP	NICE-4\|NICE4
	Cytomap	8p23.1	1q21.3
	Type of gene	protein-coding	protein-coding
	Description	cathepsin BAPP secretaseamyloid precursor protein secretasecathepsin B1cysteine proteaseepididymis secretory sperm binding protein	ubiquitin-associated protein 2-likeprotein NICE-4
	Modification date	20200313	20200313
	UniProtAcc	P07858	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000345125, ENST00000353047, ENST00000415599, ENST00000434271, ENST00000453527, ENST00000530640, ENST00000531089, ENST00000533455, ENST00000534510, ENST00000525076,	ENST00000484819, ENST00000271877, ENST00000343815, ENST00000361546, ENST00000428931,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	24 X 19 X 10=4560	17 X 15 X 7=1785
	# samples	25	18
	** MAII score	log2(25/4560*10)=-4.18903382439002 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(18/1785*10)=-3.30985526258679 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: CTSB [Title/Abstract] AND UBAP2L [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CTSB(11710837)-UBAP2L(154234067), # samples:1
Anticipated loss of major functional domain due to fusion event.	CTSB-UBAP2L 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. CTSB-UBAP2L 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. CTSB-UBAP2L seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. CTSB-UBAP2L seems lost the major protein functional domain in Tgene partner, which is a essential gene 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	CTSB	GO:0006508	proteolysis	7890620\|8811434
Hgene	CTSB	GO:0030574	collagen catabolic process	22952693
Hgene	CTSB	GO:0051603	proteolysis involved in cellular protein catabolic process	22952693

Fusion gene breakpoints across CTSB (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 UBAP2L (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	OV	TCGA-61-2008	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+

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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)
ENST00000434271	CTSB	chr8	11710837	-	ENST00000343815	UBAP2L	chr1	154234067	+	873	364	817	401	138
ENST00000434271	CTSB	chr8	11710837	-	ENST00000428931	UBAP2L	chr1	154234067	+	1389	364	238	831	197
ENST00000434271	CTSB	chr8	11710837	-	ENST00000271877	UBAP2L	chr1	154234067	+	862	364	238	771	177
ENST00000434271	CTSB	chr8	11710837	-	ENST00000361546	UBAP2L	chr1	154234067	+	1390	364	238	831	197
ENST00000530640	CTSB	chr8	11710837	-	ENST00000343815	UBAP2L	chr1	154234067	+	772	263	716	300	138
ENST00000530640	CTSB	chr8	11710837	-	ENST00000428931	UBAP2L	chr1	154234067	+	1288	263	137	730	197
ENST00000530640	CTSB	chr8	11710837	-	ENST00000271877	UBAP2L	chr1	154234067	+	761	263	137	670	177
ENST00000530640	CTSB	chr8	11710837	-	ENST00000361546	UBAP2L	chr1	154234067	+	1289	263	137	730	197
ENST00000415599	CTSB	chr8	11710837	-	ENST00000343815	UBAP2L	chr1	154234067	+	707	198	651	235	138
ENST00000415599	CTSB	chr8	11710837	-	ENST00000428931	UBAP2L	chr1	154234067	+	1223	198	72	665	197
ENST00000415599	CTSB	chr8	11710837	-	ENST00000271877	UBAP2L	chr1	154234067	+	696	198	72	605	177
ENST00000415599	CTSB	chr8	11710837	-	ENST00000361546	UBAP2L	chr1	154234067	+	1224	198	72	665	197
ENST00000533455	CTSB	chr8	11710837	-	ENST00000343815	UBAP2L	chr1	154234067	+	854	345	798	382	138
ENST00000533455	CTSB	chr8	11710837	-	ENST00000428931	UBAP2L	chr1	154234067	+	1370	345	219	812	197
ENST00000533455	CTSB	chr8	11710837	-	ENST00000271877	UBAP2L	chr1	154234067	+	843	345	219	752	177
ENST00000533455	CTSB	chr8	11710837	-	ENST00000361546	UBAP2L	chr1	154234067	+	1371	345	219	812	197

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
ENST00000434271	ENST00000343815	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.52296996	0.47703004
ENST00000434271	ENST00000428931	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.015650302	0.98434967
ENST00000434271	ENST00000271877	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.008325049	0.99167496
ENST00000434271	ENST00000361546	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.015490466	0.9845095
ENST00000530640	ENST00000343815	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.39361292	0.606387
ENST00000530640	ENST00000428931	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.010002761	0.98999727
ENST00000530640	ENST00000271877	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.002836654	0.99716336
ENST00000530640	ENST00000361546	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.009885254	0.9901148
ENST00000415599	ENST00000343815	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.57264173	0.4273583
ENST00000415599	ENST00000428931	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.010309302	0.98969066
ENST00000415599	ENST00000271877	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.003078716	0.9969213
ENST00000415599	ENST00000361546	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.010242282	0.98975766
ENST00000533455	ENST00000343815	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.4436393	0.5563607
ENST00000533455	ENST00000428931	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.013185445	0.9868146
ENST00000533455	ENST00000271877	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.004706887	0.9952931
ENST00000533455	ENST00000361546	CTSB	chr8	11710837	-	UBAP2L	chr1	154234067	+	0.013055465	0.9869445

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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

>20480_20480_1_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000415599_UBAP2L_chr1_154234067_ENST00000271877_length(amino acids)=177AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD

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

>20480_20480_2_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000415599_UBAP2L_chr1_154234067_ENST00000343815_length(amino acids)=138AA_BP=
MKLHAFQKSKATAGVCIDASKVLHRLNLKWVRQGQTHGGEGNGGGASSKAQKVSTNSFPQATQAMASAQQALLSGLVSETRLQCKFIHTH

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

>20480_20480_3_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000415599_UBAP2L_chr1_154234067_ENST00000361546_length(amino acids)=197AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD
ISGSVYSKTQQSFEKQGFHSGTPAASFNLPSALGSGGPINPATAAAYPPAPFMHILTPHQQPHSQILHHHLQQDGQTGSGQRSQTSSIPQ

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

>20480_20480_4_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000415599_UBAP2L_chr1_154234067_ENST00000428931_length(amino acids)=197AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD
ISGSVYSKTQQSFEKQGFHSGTPAASFNLPSALGSGGPINPATAAAYPPAPFMHILTPHQQPHSQILHHHLQQDGQTGSGQRSQTSSIPQ

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

>20480_20480_5_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000434271_UBAP2L_chr1_154234067_ENST00000271877_length(amino acids)=177AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD

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

>20480_20480_6_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000434271_UBAP2L_chr1_154234067_ENST00000343815_length(amino acids)=138AA_BP=
MKLHAFQKSKATAGVCIDASKVLHRLNLKWVRQGQTHGGEGNGGGASSKAQKVSTNSFPQATQAMASAQQALLSGLVSETRLQCKFIHTH

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

>20480_20480_7_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000434271_UBAP2L_chr1_154234067_ENST00000361546_length(amino acids)=197AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD
ISGSVYSKTQQSFEKQGFHSGTPAASFNLPSALGSGGPINPATAAAYPPAPFMHILTPHQQPHSQILHHHLQQDGQTGSGQRSQTSSIPQ

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

>20480_20480_8_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000434271_UBAP2L_chr1_154234067_ENST00000428931_length(amino acids)=197AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD
ISGSVYSKTQQSFEKQGFHSGTPAASFNLPSALGSGGPINPATAAAYPPAPFMHILTPHQQPHSQILHHHLQQDGQTGSGQRSQTSSIPQ

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

>20480_20480_9_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000530640_UBAP2L_chr1_154234067_ENST00000271877_length(amino acids)=177AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD

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

>20480_20480_10_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000530640_UBAP2L_chr1_154234067_ENST00000343815_length(amino acids)=138AA_BP=
MKLHAFQKSKATAGVCIDASKVLHRLNLKWVRQGQTHGGEGNGGGASSKAQKVSTNSFPQATQAMASAQQALLSGLVSETRLQCKFIHTH

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

>20480_20480_11_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000530640_UBAP2L_chr1_154234067_ENST00000361546_length(amino acids)=197AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD
ISGSVYSKTQQSFEKQGFHSGTPAASFNLPSALGSGGPINPATAAAYPPAPFMHILTPHQQPHSQILHHHLQQDGQTGSGQRSQTSSIPQ

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

>20480_20480_12_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000530640_UBAP2L_chr1_154234067_ENST00000428931_length(amino acids)=197AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD
ISGSVYSKTQQSFEKQGFHSGTPAASFNLPSALGSGGPINPATAAAYPPAPFMHILTPHQQPHSQILHHHLQQDGQTGSGQRSQTSSIPQ

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

>20480_20480_13_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000533455_UBAP2L_chr1_154234067_ENST00000271877_length(amino acids)=177AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD

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

>20480_20480_14_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000533455_UBAP2L_chr1_154234067_ENST00000343815_length(amino acids)=138AA_BP=
MKLHAFQKSKATAGVCIDASKVLHRLNLKWVRQGQTHGGEGNGGGASSKAQKVSTNSFPQATQAMASAQQALLSGLVSETRLQCKFIHTH

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

>20480_20480_15_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000533455_UBAP2L_chr1_154234067_ENST00000361546_length(amino acids)=197AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD
ISGSVYSKTQQSFEKQGFHSGTPAASFNLPSALGSGGPINPATAAAYPPAPFMHILTPHQQPHSQILHHHLQQDGQTGSGQRSQTSSIPQ

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

>20480_20480_16_CTSB-UBAP2L_CTSB_chr8_11710837_ENST00000533455_UBAP2L_chr1_154234067_ENST00000428931_length(amino acids)=197AA_BP=42
MWQLWASLCCLLVLANARSRPSFHPLSDELVNYVNKRNTTWQVAPTSSKQHGVNVSVNASATPFQQPSGYGSHGYNTGVSVTSSNTGVPD
ISGSVYSKTQQSFEKQGFHSGTPAASFNLPSALGSGGPINPATAAAYPPAPFMHILTPHQQPHSQILHHHLQQDGQTGSGQRSQTSSIPQ

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

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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/chr8:11710837/chr1:154234067)
- 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
CTSB P07858	.
FUNCTION: Thiol protease which is believed to participate in intracellular degradation and turnover of proteins (PubMed:12220505). Cleaves matrix extracellular phosphoglycoprotein MEPE (PubMed:12220505). Involved in the solubilization of cross-linked TG/thyroglobulin in the thyroid follicle lumen (By similarity). Has also been implicated in tumor invasion and metastasis (PubMed:3972105). {ECO:0000250\|UniProtKB:P10605, ECO:0000269\|PubMed:12220505, ECO:0000269\|PubMed:3972105}.	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.

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

Tgene

UBAP2L

chr8:11710837

chr1:154234067

ENST00000343815

49_89

932.0

984.0

Domain

UBA

Tgene

UBAP2L

chr8:11710837

chr1:154234067

ENST00000361546

49_89

932.0

1088.0

Domain

UBA

Tgene

UBAP2L

chr8:11710837

chr1:154234067

ENST00000428931

49_89

932.0

1088.0

Domain

UBA

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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
CTSB
UBAP2L

- 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 CTSB-UBAP2L

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 CTSB-UBAP2L

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