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Fusion gene ID: 29419

FusionGeneSummary for PTPN13_AFF1

Fusion gene summary

Fusion gene information	Fusion gene name: PTPN13_AFF1
	Fusion gene ID: 29419
		Hgene	Tgene
	Gene symbol	PTPN13	AFF1
	Gene ID	5783	4299
	Gene name	protein tyrosine phosphatase, non-receptor type 13	AF4/FMR2 family member 1
	Synonyms	FAP-1\|PNP1\|PTP-BAS\|PTP-BL\|PTP1E\|PTPL1\|PTPLE\|hPTP1E	AF4\|MLLT2\|PBM1
	Cytomap	4q21.3	4q21.3-q22.1
	Type of gene	protein-coding	protein-coding
	Description	tyrosine-protein phosphatase non-receptor type 13fas-associated protein-tyrosine phosphatase 1hPTPE1protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)protein-tyrosine phosphatase 1Eprotein-tyrosine phosphatas	AF4/FMR2 family member 1ALL1-fused gene from chromosome 4 proteinmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 2pre-B-cell monocytic leukemia partner 1proto-oncogene AF4
	Modification date	20180519	20180523
	UniProtAcc	Q12923	P51825
	Ensembl transtripts involved in fusion gene	ENST00000427191, ENST00000436978, ENST00000502971, ENST00000411767, ENST00000316707, ENST00000511467,	ENST00000395146, ENST00000307808, ENST00000544085, ENST00000511996,
Fusion gene scores	* DoF score	5 X 6 X 3=90	10 X 25 X 4=1000
	# samples	6	31
	** MAII score	log2(6/90*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(31/1000*10)=-1.68965987938785 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: PTPN13 [Title/Abstract] AND AFF1 [Title/Abstract] AND fusion [Title/Abstract]
Functional or gene categories assigned by FusionGDB annotation	Oncogene involved fusion gene, in-frame and retained their domain. Tumor suppressor gene involved fusion gene, in-frame but not retained their domain. Tumor suppressor gene involved fusion gene, retained protein feature but frameshift. DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain.

* 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	PTPN13	GO:0006470	protein dephosphorylation	17657516
Hgene	PTPN13	GO:0014066	regulation of phosphatidylinositol 3-kinase signaling	23604317

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
TCGA	LD	CESC	TCGA-DS-A0VN-01A	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
TCGA	LD	CESC	TCGA-EA-A5ZD-01A	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+

* 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
5CDS-intron	ENST00000427191	ENST00000395146	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000427191	ENST00000307808	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000427191	ENST00000544085	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-3UTR	ENST00000427191	ENST00000511996	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000436978	ENST00000395146	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000436978	ENST00000307808	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000436978	ENST00000544085	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-3UTR	ENST00000436978	ENST00000511996	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
intron-intron	ENST00000502971	ENST00000395146	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
intron-intron	ENST00000502971	ENST00000307808	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
intron-intron	ENST00000502971	ENST00000544085	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
intron-3UTR	ENST00000502971	ENST00000511996	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000411767	ENST00000395146	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000411767	ENST00000307808	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000411767	ENST00000544085	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-3UTR	ENST00000411767	ENST00000511996	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000316707	ENST00000395146	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000316707	ENST00000307808	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000316707	ENST00000544085	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-3UTR	ENST00000316707	ENST00000511996	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000511467	ENST00000395146	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000511467	ENST00000307808	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-intron	ENST00000511467	ENST00000544085	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
5CDS-3UTR	ENST00000511467	ENST00000511996	PTPN13	chr4	87695684	+	AFF1	chr4	87894982	+
In-frame	ENST00000427191	ENST00000395146	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
In-frame	ENST00000427191	ENST00000307808	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-5UTR	ENST00000427191	ENST00000544085	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-intron	ENST00000427191	ENST00000511996	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
In-frame	ENST00000436978	ENST00000395146	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
In-frame	ENST00000436978	ENST00000307808	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-5UTR	ENST00000436978	ENST00000544085	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-intron	ENST00000436978	ENST00000511996	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
In-frame	ENST00000502971	ENST00000395146	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
In-frame	ENST00000502971	ENST00000307808	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-5UTR	ENST00000502971	ENST00000544085	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-intron	ENST00000502971	ENST00000511996	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
In-frame	ENST00000411767	ENST00000395146	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
In-frame	ENST00000411767	ENST00000307808	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-5UTR	ENST00000411767	ENST00000544085	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-intron	ENST00000411767	ENST00000511996	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
In-frame	ENST00000316707	ENST00000395146	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
In-frame	ENST00000316707	ENST00000307808	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-5UTR	ENST00000316707	ENST00000544085	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-intron	ENST00000316707	ENST00000511996	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
In-frame	ENST00000511467	ENST00000395146	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
In-frame	ENST00000511467	ENST00000307808	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-5UTR	ENST00000511467	ENST00000544085	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+
5CDS-intron	ENST00000511467	ENST00000511996	PTPN13	chr4	87610343	+	AFF1	chr4	88005272	+

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FusionProtFeatures for PTPN13_AFF1

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

Hgene	Tgene
PTPN13 Q12923	AFF1 P51825

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Fusion gene ID: 29419

FusionGeneSummary for PTPN13_AFF1

FusionProtFeatures for PTPN13_AFF1