	FusionGeneSummary
	FusionProtFeature
	FusionGeneSequence
	FusionGenePPI
	RelatedDrugs
	RelatedDiseases

Fusion gene ID: 41120

FusionGeneSummary for USP39_USP39

Fusion gene summary

Fusion gene information	Fusion gene name: USP39_USP39
	Fusion gene ID: 41120
		Hgene	Tgene
	Gene symbol	USP39	USP39
	Gene ID	10713	10713
	Gene name	ubiquitin specific peptidase 39	ubiquitin specific peptidase 39
	Synonyms	65K\|CGI-21\|HSPC332\|SAD1\|SNRNP65	65K\|CGI-21\|HSPC332\|SAD1\|SNRNP65
	Cytomap	2p11.2	2p11.2
	Type of gene	protein-coding	protein-coding
	Description	U4/U6.U5 tri-snRNP-associated protein 2SAD1 homologSnRNP assembly defective 1 homologU4/U6.U5 tri-snRNP-associated 65 kDa proteininactive ubiquitin-specific peptidase 39small nuclear ribonucleoprotein 65kDa (U4/U6.U5)ubiquitin specific protease 39	U4/U6.U5 tri-snRNP-associated protein 2SAD1 homologSnRNP assembly defective 1 homologU4/U6.U5 tri-snRNP-associated 65 kDa proteininactive ubiquitin-specific peptidase 39small nuclear ribonucleoprotein 65kDa (U4/U6.U5)ubiquitin specific protease 39
	Modification date	20180522	20180522
	UniProtAcc	Q53GS9	Q53GS9
	Ensembl transtripts involved in fusion gene	ENST00000459775, ENST00000450066, ENST00000409025, ENST00000409470, ENST00000323701, ENST00000409766,	ENST00000459775, ENST00000450066, ENST00000409025, ENST00000409470, ENST00000323701, ENST00000409766,
Fusion gene scores	* DoF score	9 X 8 X 7=504	6 X 6 X 4=144
	# samples	10	6
	** MAII score	log2(10/504*10)=-2.33342373372519 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/144*10)=-1.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: USP39 [Title/Abstract] AND USP39 [Title/Abstract] AND fusion [Title/Abstract]
Functional or gene categories assigned by FusionGDB annotation

* 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

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 type	Source	Cancer type	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChiTaRS3.1			BE839522	USP39	chr2	85833534	+	USP39	chr2	85833592	-

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

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
intron-intron	ENST00000459775	ENST00000459775	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000459775	ENST00000450066	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000459775	ENST00000409025	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000459775	ENST00000409470	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000459775	ENST00000323701	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000459775	ENST00000409766	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000450066	ENST00000459775	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000450066	ENST00000450066	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000450066	ENST00000409025	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000450066	ENST00000409470	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000450066	ENST00000323701	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000450066	ENST00000409766	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409025	ENST00000459775	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409025	ENST00000450066	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409025	ENST00000409025	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409025	ENST00000409470	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409025	ENST00000323701	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409025	ENST00000409766	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409470	ENST00000459775	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409470	ENST00000450066	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409470	ENST00000409025	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409470	ENST00000409470	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409470	ENST00000323701	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409470	ENST00000409766	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000323701	ENST00000459775	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000323701	ENST00000450066	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000323701	ENST00000409025	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000323701	ENST00000409470	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000323701	ENST00000323701	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000323701	ENST00000409766	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409766	ENST00000459775	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409766	ENST00000450066	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409766	ENST00000409025	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409766	ENST00000409470	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409766	ENST00000323701	USP39	chr2	85833534	+	USP39	chr2	85833592	-
intron-intron	ENST00000409766	ENST00000409766	USP39	chr2	85833534	+	USP39	chr2	85833592	-

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FusionProtFeatures for USP39_USP39

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

Hgene	Tgene
USP39 Q53GS9	USP39 Q53GS9

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

- 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

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FusionGeneSequence for USP39_USP39

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.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for USP39_USP39

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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RelatedDrugs for USP39_USP39

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for USP39_USP39

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

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Fusion gene ID: 41120

FusionGeneSummary for USP39_USP39

FusionProtFeatures for USP39_USP39

FusionGeneSequence for USP39_USP39

FusionGenePPI for USP39_USP39

RelatedDrugs for USP39_USP39

RelatedDiseases for USP39_USP39