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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:TSPAN5-METAP1 (FusionGDB2 ID:94117)

Fusion Gene Summary for TSPAN5-METAP1

Fusion gene summary

Fusion gene information	Fusion gene name: TSPAN5-METAP1
	Fusion gene ID: 94117
		Hgene	Tgene
	Gene symbol	TSPAN5	METAP1
	Gene ID	10098	23173
	Gene name	tetraspanin 5	methionyl aminopeptidase 1
	Synonyms	NET-4\|NET4\|TM4SF9\|TSPAN-5	MAP1A\|MetAP1A
	Cytomap	4q23	4q23
	Type of gene	protein-coding	protein-coding
	Description	tetraspanin-5tetraspan NET-4tetraspan TM4SFtransmembrane 4 superfamily member 9transmembrane 4 superfamily, member 8	methionine aminopeptidase 1MAP 1metAP 1peptidase M 1
	Modification date	20200313	20200313
	UniProtAcc	.	Q6UB28
	Ensembl transtripts involved in fusion gene	ENST00000305798, ENST00000505184, ENST00000509168,	ENST00000296411, ENST00000506548, ENST00000544031,
Fusion gene scores	* DoF score	7 X 4 X 6=168	4 X 4 X 2=32
	# samples	9	4
	** MAII score	log2(9/168*10)=-0.900464326449086 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/32*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context	PubMed: TSPAN5 [Title/Abstract] AND METAP1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	TSPAN5(99579297)-METAP1(99950018), # 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

Fusion gene breakpoints across TSPAN5 (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 METAP1 (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	STAD	TCGA-BR-8678-01A	TSPAN5	chr4	99579297	-	METAP1	chr4	99950018	+

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Fusion Gene ORF analysis for TSPAN5-METAP1

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
In-frame	ENST00000305798	ENST00000296411	TSPAN5	chr4	99579297	-	METAP1	chr4	99950018	+
5CDS-3UTR	ENST00000305798	ENST00000506548	TSPAN5	chr4	99579297	-	METAP1	chr4	99950018	+
5CDS-intron	ENST00000305798	ENST00000544031	TSPAN5	chr4	99579297	-	METAP1	chr4	99950018	+
intron-3CDS	ENST00000505184	ENST00000296411	TSPAN5	chr4	99579297	-	METAP1	chr4	99950018	+
intron-3UTR	ENST00000505184	ENST00000506548	TSPAN5	chr4	99579297	-	METAP1	chr4	99950018	+
intron-intron	ENST00000505184	ENST00000544031	TSPAN5	chr4	99579297	-	METAP1	chr4	99950018	+
intron-3CDS	ENST00000509168	ENST00000296411	TSPAN5	chr4	99579297	-	METAP1	chr4	99950018	+
intron-3UTR	ENST00000509168	ENST00000506548	TSPAN5	chr4	99579297	-	METAP1	chr4	99950018	+
intron-intron	ENST00000509168	ENST00000544031	TSPAN5	chr4	99579297	-	METAP1	chr4	99950018	+

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)

ENST00000305798

TSPAN5

chr4

99579297

ENST00000296411

METAP1

chr4

99950018

3027

484

403

1530

375

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
ENST00000305798	ENST00000296411	TSPAN5	chr4	99579297	-	METAP1	chr4	99950018	+	0.000281788	0.99971825

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Fusion Genomic Features for TSPAN5-METAP1

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)
TSPAN5	chr4	99579296	-	METAP1	chr4	99950017	+	0.16109884	0.83890116
TSPAN5	chr4	99579296	-	METAP1	chr4	99950017	+	0.16109884	0.83890116

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 TSPAN5-METAP1

Go to
FGviewer for the breakpoints of chr4:99579297-chr4:99950018
.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.

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

Hgene	Tgene
.	METAP1 Q6UB28
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: Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed (By similarity). May play a role in colon tumorigenesis. {ECO:0000255\|HAMAP-Rule:MF_03174, ECO:0000269\|PubMed:16568094}.

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

Hgene

TSPAN5

chr4:99579297

chr4:99950018

ENST00000305798

1_17

27.0

269.0

Topological domain

Cytoplasmic

- 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

TSPAN5

chr4:99579297

chr4:99950018

ENST00000305798

114_232

27.0

269.0

Topological domain

Extracellular

Hgene

TSPAN5

chr4:99579297

chr4:99950018

ENST00000305798

254_268

27.0

269.0

Topological domain

Cytoplasmic

Hgene

TSPAN5

chr4:99579297

chr4:99950018

ENST00000305798

39_61

27.0

269.0

Topological domain

Extracellular

Hgene

TSPAN5

chr4:99579297

chr4:99950018

ENST00000305798

83_92

27.0

269.0

Topological domain

Cytoplasmic

Hgene

TSPAN5

chr4:99579297

chr4:99950018

ENST00000305798

18_38

27.0

269.0

Transmembrane

Helical

Hgene

TSPAN5

chr4:99579297

chr4:99950018

ENST00000305798

233_253

27.0

269.0

Transmembrane

Helical

Hgene

TSPAN5

chr4:99579297

chr4:99950018

ENST00000305798

62_82

27.0

269.0

Transmembrane

Helical

Hgene

TSPAN5

chr4:99579297

chr4:99950018

ENST00000305798

93_113

27.0

269.0

Transmembrane

Helical

Tgene

METAP1

chr4:99579297

chr4:99950018

ENST00000296411

9_52

38.0

387.0

Region

Zinc finger-like%3B important for proper ribosome association

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Fusion Gene Sequence for TSPAN5-METAP1

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.

>In-frame_ENST00000305798_ENST00000296411_TCGA-BR-8678-01A_TSPAN5_chr4_99579297_-_METAP1_chr4_99950018_length(transcript)=3027nt_BP=484nt
GCGAACGGGCGGGCGAGCAAGCGAGCGGCGTCTCCACCAGCATCTGCCGCGGCCGCCTTTGCCCGAAGCCCGGGGACGAACCGACGGACC
GACCGCCTGGCGCACGGACGCGGGCGCTCGCTTTGTGTTCGGGGCTAGCGTCGGCGAGGCTTGAGCTTGCAGCGCGCGGCTTCCCTGCTT
TCTCGCGGCCACCCCGGCTCCGGCGGCCTCGGCGCGCGAGGGGCTGGAGGTGCGGGAGCCGCTCTCCGCCGGTCGGTCCCCGCGCGGCTG
AGCCCAGGCCGCCAGCGCCGCGGCCCCGTGCGGTGTCCCTGAGCTCCTGCTCCCCGCCGGGCTGCTCCGAGCAACGGTGCTTCGGAGCTC
CAAACTCGGGCTGCCGGGGCAAGTGTCTTCATGAACCCAGAGGATGTCCGGGAAGCACTACAAGGGTCCTGAAGTCAGTTGTTGCATCAA
ATACTTCATATTTGGCTTCAATGTCATATTTTGGGAATGTTTTAAAGGAAGTTGGGCTACTCACAAGTTACTACATAAGAAAGCAAAAGA
TGAAAAGGCGAAGCGAGAAGTGTCTTCCTGGACTGTGGAAGGTGATATTAATACTGACCCATGGGCAGGTTATCGATATACTGGTAAACT
CAGACCACATTATCCACTGATGCCAACAAGGCCAGTGCCAAGTTATATTCAAAGACCAGATTATGCTGATCATCCCTTAGGAATGTCTGA
ATCTGAACAGGCTCTTAAAGGTACTTCTCAGATTAAATTACTCTCATCTGAAGATATAGAAGGGATGCGACTTGTATGTAGGCTTGCTAG
AGAAGTTTTGGATGTTGCTGCCGGCATGATTAAACCAGGTGTAACTACTGAAGAAATAGATCACGCTGTACACTTAGCATGTATTGCAAG
AAATTGCTACCCTTCTCCCCTGAATTATTATAATTTCCCAAAGTCTTGTTGTACCTCAGTGAATGAAGTCATTTGCCATGGAATACCAGA
CAGAAGGCCCTTACAAGAAGGTGACATTGTTAATGTGGATATCACTCTTTATCGCAATGGTTATCATGGGGACCTGAATGAGACATTTTT
TGTTGGAGAAGTGGATGATGGAGCACGGAAACTTGTTCAGACCACATATGAGTGCCTGATGCAAGCCATTGATGCAGTGAAGCCTGGTGT
TCGGTACAGAGAATTGGGAAACATTATCCAGAAGCATGCCCAAGCAAATGGGTTTTCAGTTGTTCGAAGCTATTGTGGGCATGGAATCCA
CAAGCTTTTTCATACAGCTCCCAATGTACCCCACTATGCTAAAAATAAAGCAGTTGGAGTGATGAAGTCGGGCCATGTATTTACAATTGA
GCCAATGATTTGTGAAGGCGGATGGCAGGATGAAACCTGGCCAGATGGTTGGACTGCGGTGACAAGAGACGGAAAGCGGTCTGCTCAGTT
TGAGCACACCCTCCTGGTCACAGACACTGGCTGTGAAATCCTAACCCGGCGACTTGACAGTGCACGGCCTCACTTCATGTCTCAATTTTA
ATTTCTCCCAAGATGGCACATCTCAGTACCTTCTTACTGTGCTATGCATTTTATTGAGAGTACAGAAAGGAAGAGGAACCTTTTTTTAAT
CACTTGTTTTGTTTTGACTATAGATAAGAAAGGACTACAGCATTTGATGTGTGTCCTCAAGAACTTGTCTTGGGTCTGAAAAAGCTGAGA
AGAATAAAGGAAACATTGCTCAACTCTTCAGCCCCCTCCCCCTGCACACCTGTTTTCTCATTTGCCCTTTGAGCACTTTTACTTAAACTT
GCTTGTAGTTGCTTTTATCACTGCCGCAAAACAGCCATCAAGAGCCATCTGCTTTCCAGGTGAACATTGGAAATGAGAATCTTTGAAACT
TAGCAATATGTGTTGCACCAGATTTTTTAAATTATATATATGGAAATATATATGTATACATTTTAAGTTCTGTATACATAATTACCAAAC
ACTATGTGACCTGGAGTTTGTGTTGTTTCTGCTCTGACAGGTTTATATGTTCTTACAAATGGATCCATAGTTTGCAGTGATTTAATTCCT
GGTTGGGATTTGGCCTCCCCTCTCCCCCATGCTAATTATTTACCCTTGTAATTGTGCATAGGGAAGCACTCACCCAATGAGACTTTCTCC
AATGTGGACTCTGTGTGTCAGTGAATGAATGTAGTAAAATTCACTTTGGAAGGTTATCAGGCTTTTAAAAATCTAGTTTATGGCAAAAAT
AGCCATTTTCCAAGTGGTGGCTGACTGTTGCAGGGAATGAGAATTTCATAATACACTGCTATTTCAGACCTCTGTTTGGTCAGAAATGGA
AAAGAAAAAGCCCCCTTTCTTCCCTTTTCTGTTTTACTTCAAGGGCATACCTTGGAGGTGCTCAGAGAAGCGTGAAGTTTGCACTATGGT
GGAGGATGGGGAAAGAGTTCTAAAGTGTCTCCAGCTGTGAACCCAGGAGGTCAAGTGGGCTATTAAAATCTAACGTTGAGTAAATGTGAT
AGTGATGAGAAAGGAATTTTGTGTACTGTAACCTTGCAGTAGAGATGCAGCTGTCCTTCGTGTGTGGAAACACACCTCTCCTTTACATAG
TTGGGAACCTCATTAGAAATGACCTCAGCTGCCCCATATCTACGTTCCTTTCAGCAGTTGTCCAAGTAGGAGTGTATCCAGTGAAGACAT
ATCAAATCACAAAGTCATTGTCATTAGAGTGTACTTGATTACTGGGCATCCTTGTAATATAATTTCATACCACTGACACATTATACTTGT
AAGAGAACATCTTTCCCAGAGTGCCTCAGACCTTATTGCTTTAAAATATAATAATGTTTTCATTACTTTTATTATTTGAATGATTTAGTA
AAGTTGACTGAATCTGGTATAGACTTTGGGAGTATGTGTGTGAAGTTTTTATCAAACTGTAATATTTGTGAATGGAATGCCTTGCAATAT

>In-frame_ENST00000305798_ENST00000296411_TCGA-BR-8678-01A_TSPAN5_chr4_99579297_-_METAP1_chr4_99950018_length(amino acids)=375AA_start in transcript=403_stop in transcript=1530
MSGKHYKGPEVSCCIKYFIFGFNVIFWECFKGSWATHKLLHKKAKDEKAKREVSSWTVEGDINTDPWAGYRYTGKLRPHYPLMPTRPVPS
YIQRPDYADHPLGMSESEQALKGTSQIKLLSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCYPSPLNYYNFPK
SCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHGDLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHAQ
ANGFSVVRSYCGHGIHKLFHTAPNVPHYAKNKAVGVMKSGHVFTIEPMICEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEIL

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

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Fusion Gene PPI Analysis for TSPAN5-METAP1

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 TSPAN5-METAP1

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 TSPAN5-METAP1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source