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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:TMEM135-MIPEP (FusionGDB2 ID:91682)

Fusion Gene Summary for TMEM135-MIPEP

Fusion gene summary

Fusion gene information	Fusion gene name: TMEM135-MIPEP
	Fusion gene ID: 91682
		Hgene	Tgene
	Gene symbol	TMEM135	MIPEP
	Gene ID	65084	4285
	Gene name	transmembrane protein 135	mitochondrial intermediate peptidase
	Synonyms	PMP52	COXPD31\|HMIP\|MIP
	Cytomap	11q14.2	13q12.12
	Type of gene	protein-coding	protein-coding
	Description	transmembrane protein 135peroxisomal membrane protein 52	mitochondrial intermediate peptidase
	Modification date	20200313	20200313
	UniProtAcc	.	Q99797
	Ensembl transtripts involved in fusion gene	ENST00000305494, ENST00000340353, ENST00000355734, ENST00000535167, ENST00000532959,	ENST00000469167, ENST00000382172,
Fusion gene scores	* DoF score	17 X 12 X 8=1632	10 X 7 X 7=490
	# samples	20	14
	** MAII score	log2(20/1632*10)=-3.02856915219677 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(14/490*10)=-1.8073549220576 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: TMEM135 [Title/Abstract] AND MIPEP [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	TMEM135(86749228)-MIPEP(24304584), # samples:3
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 TMEM135 (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 MIPEP (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	OV	TCGA-24-1556-01A	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-
ChimerDB4	OV	TCGA-24-1556	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-

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Fusion Gene ORF analysis for TMEM135-MIPEP

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	ENST00000305494	ENST00000469167	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-
5CDS-intron	ENST00000340353	ENST00000469167	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-
5CDS-intron	ENST00000355734	ENST00000469167	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-
5UTR-3CDS	ENST00000535167	ENST00000382172	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-
5UTR-intron	ENST00000535167	ENST00000469167	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-
In-frame	ENST00000305494	ENST00000382172	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-
In-frame	ENST00000340353	ENST00000382172	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-
In-frame	ENST00000355734	ENST00000382172	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-
intron-3CDS	ENST00000532959	ENST00000382172	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-
intron-intron	ENST00000532959	ENST00000469167	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-

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)
ENST00000340353	TMEM135	chr11	86749228	+	ENST00000382172	MIPEP	chr13	24304584	-	600	343	11	319	102
ENST00000305494	TMEM135	chr11	86749228	+	ENST00000382172	MIPEP	chr13	24304584	-	437	180	27	218	63
ENST00000355734	TMEM135	chr11	86749228	+	ENST00000382172	MIPEP	chr13	24304584	-	459	202	10	240	76

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
ENST00000340353	ENST00000382172	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-	0.8132001	0.18679988
ENST00000305494	ENST00000382172	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-	0.8017992	0.19820082
ENST00000355734	ENST00000382172	TMEM135	chr11	86749228	+	MIPEP	chr13	24304584	-	0.8085867	0.19141328

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Fusion Genomic Features for TMEM135-MIPEP

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 TMEM135-MIPEP

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:86749228/chr13:24304584)
- 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
.	MIPEP Q99797
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.	FUNCTION: Cleaves proteins, imported into the mitochondrion, to their mature size.

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

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000305494

149_169

459.0

Transmembrane

Helical

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000305494

298_318

459.0

Transmembrane

Helical

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000305494

331_351

459.0

Transmembrane

Helical

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000305494

380_400

459.0

Transmembrane

Helical

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000305494

68_88

459.0

Transmembrane

Helical

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000305494

96_116

459.0

Transmembrane

Helical

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000340353

149_169

437.0

Transmembrane

Helical

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000340353

298_318

437.0

Transmembrane

Helical

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000340353

331_351

437.0

Transmembrane

Helical

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000340353

380_400

437.0

Transmembrane

Helical

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000340353

68_88

437.0

Transmembrane

Helical

Hgene

TMEM135

chr11:86749228

chr13:24304584

ENST00000340353

96_116

437.0

Transmembrane

Helical

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Fusion Gene Sequence for TMEM135-MIPEP

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.

>91682_91682_1_TMEM135-MIPEP_TMEM135_chr11_86749228_ENST00000305494_MIPEP_chr13_24304584_ENST00000382172_length(transcript)=437nt_BP=180nt
GGCTCTCCCCCTCCTGTCTTCTCCGCGCTGTTCCTCGTCATGGCGGCCCTCAGCAAGTCCATCCCTCATAACTGCTATGAGATCGGCCAC
ACTTGGCACCCTTCCTGCCGGGTCTCCTTCCTGCAGATCACCGGGGGCGCCCTGGAGGAGTCCCTGAAGATCTATGCTCCTCTGTACTTG
GTATGCTTCAGAAGTGTCCTTCTGTTGATGACTTCGTAAGTGCCCTCGTTTCCGACTTGGATCTGGACTTCGAAACTTTCCTCATGGATT
CTGAATAAAAGAAACACTCTACACCTCTTAAATCAAGGTCATGTAGATAATGACTTTGTTATAAATGCTACAGCTGTGAGAGCTTGTTTC

>91682_91682_1_TMEM135-MIPEP_TMEM135_chr11_86749228_ENST00000305494_MIPEP_chr13_24304584_ENST00000382172_length(amino acids)=63AA_BP=

--------------------------------------------------------------
>91682_91682_2_TMEM135-MIPEP_TMEM135_chr11_86749228_ENST00000340353_MIPEP_chr13_24304584_ENST00000382172_length(transcript)=600nt_BP=343nt
GTCCCGCCCCCTTGAGCTGCGATACGCCGAGCGCTCAACATCCGAGGACTTTGGCCCAGAGTAACCCCGCTCTCGTGACCTTTCCCCTCC
ATTCCGCACCTCCGAGTGCTGGCCGGGCGAGAGGCTGGCGGCTGGGCTCTCGCGCCCCTCCCTGCAGGGCTCAGGCTCTCCCCCTCCTGT
CTTCTCCGCGCTGTTCCTCGTCATGGCGGCCCTCAGCAAGTCCATCCCTCATAACTGCTATGAGATCGGCCACACTTGGCACCCTTCCTG
CCGGGTCTCCTTCCTGCAGATCACCGGGGGCGCCCTGGAGGAGTCCCTGAAGATCTATGCTCCTCTGTACTTGGTATGCTTCAGAAGTGT
CCTTCTGTTGATGACTTCGTAAGTGCCCTCGTTTCCGACTTGGATCTGGACTTCGAAACTTTCCTCATGGATTCTGAATAAAAGAAACAC
TCTACACCTCTTAAATCAAGGTCATGTAGATAATGACTTTGTTATAAATGCTACAGCTGTGAGAGCTTGTTTCTGATTTCATTGTTCGCT

>91682_91682_2_TMEM135-MIPEP_TMEM135_chr11_86749228_ENST00000340353_MIPEP_chr13_24304584_ENST00000382172_length(amino acids)=102AA_BP=
MSCDTPSAQHPRTLAQSNPALVTFPLHSAPPSAGRARGWRLGSRAPPCRAQALPLLSSPRCSSSWRPSASPSLITAMRSATLGTLPAGSP

--------------------------------------------------------------
>91682_91682_3_TMEM135-MIPEP_TMEM135_chr11_86749228_ENST00000355734_MIPEP_chr13_24304584_ENST00000382172_length(transcript)=459nt_BP=202nt
GCGCCCCTCCCTGCAGGGCTCAGGCTCTCCCCCTCCTGTCTTCTCCGCGCTGTTCCTCGTCATGGCGGCCCTCAGCAAGTCCATCCCTCA
TAACTGCTATGAGATCGGCCACACTTGGCACCCTTCCTGCCGGGTCTCCTTCCTGCAGATCACCGGGGGCGCCCTGGAGGAGTCCCTGAA
GATCTATGCTCCTCTGTACTTGGTATGCTTCAGAAGTGTCCTTCTGTTGATGACTTCGTAAGTGCCCTCGTTTCCGACTTGGATCTGGAC
TTCGAAACTTTCCTCATGGATTCTGAATAAAAGAAACACTCTACACCTCTTAAATCAAGGTCATGTAGATAATGACTTTGTTATAAATGC
TACAGCTGTGAGAGCTTGTTTCTGATTTCATTGTTCGCTTCTGTAATTCTGAAAAACTTTAAACTGGTAGAACTTGGAATAAATAATTTG

>91682_91682_3_TMEM135-MIPEP_TMEM135_chr11_86749228_ENST00000355734_MIPEP_chr13_24304584_ENST00000382172_length(amino acids)=76AA_BP=

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

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Fusion Gene PPI Analysis for TMEM135-MIPEP

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 TMEM135-MIPEP

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 TMEM135-MIPEP

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source