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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:CTU2-MLYCD (FusionGDB2 ID:20607)

Fusion Gene Summary for CTU2-MLYCD

Fusion gene summary

Fusion gene information	Fusion gene name: CTU2-MLYCD
	Fusion gene ID: 20607
		Hgene	Tgene
	Gene symbol	CTU2	MLYCD
	Gene ID	348180	23417
	Gene name	cytosolic thiouridylase subunit 2	malonyl-CoA decarboxylase
	Synonyms	C16orf84\|MFRG\|NCS2\|UPF0432	MCD
	Cytomap	16q24.3	16q23.3
	Type of gene	protein-coding	protein-coding
	Description	cytoplasmic tRNA 2-thiolation protein 2cytosolic thiouridylase subunit 2 homolog	malonyl-CoA decarboxylase, mitochondrialmalonyl coenzyme A decarboxylase
	Modification date	20200320	20200313
	UniProtAcc	Q2VPK5	O95822
	Ensembl transtripts involved in fusion gene	ENST00000312060, ENST00000378384, ENST00000453996, ENST00000567949,	ENST00000262430,
Fusion gene scores	* DoF score	3 X 3 X 3=27	2 X 2 X 2=8
	# samples	3	2
	** MAII score	log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(2/8*10)=1.32192809488736
Context	PubMed: CTU2 [Title/Abstract] AND MLYCD [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	CTU2(88779313)-MLYCD(83945823), # samples:1
Anticipated loss of major functional domain due to fusion event.	CTU2-MLYCD seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. CTU2-MLYCD seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. CTU2-MLYCD seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
Tgene	MLYCD	GO:0006085	acetyl-CoA biosynthetic process	9869665\|10417274\|10455107
Tgene	MLYCD	GO:0006633	fatty acid biosynthetic process	15003260
Tgene	MLYCD	GO:2001294	malonyl-CoA catabolic process	10417274\|10455107\|15003260

Fusion gene breakpoints across CTU2 (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 MLYCD (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	BRCA	TCGA-BH-A1FD-01A	CTU2	chr16	88779313	+	MLYCD	chr16	83945823	+

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Fusion Gene ORF analysis for CTU2-MLYCD

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
Frame-shift	ENST00000312060	ENST00000262430	CTU2	chr16	88779313	+	MLYCD	chr16	83945823	+
Frame-shift	ENST00000378384	ENST00000262430	CTU2	chr16	88779313	+	MLYCD	chr16	83945823	+
Frame-shift	ENST00000453996	ENST00000262430	CTU2	chr16	88779313	+	MLYCD	chr16	83945823	+
Frame-shift	ENST00000567949	ENST00000262430	CTU2	chr16	88779313	+	MLYCD	chr16	83945823	+

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)

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

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Fusion Genomic Features for CTU2-MLYCD

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)
CTU2	chr16	88779313	+	MLYCD	chr16	83945822	+	0.9889637	0.011036223
CTU2	chr16	88779313	+	MLYCD	chr16	83945822	+	0.9889637	0.011036223

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 CTU2-MLYCD

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:88779313/:83945823)
- 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
CTU2 Q2VPK5	MLYCD O95822
FUNCTION: Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). May act by forming a heterodimer with CTU1/ATPBD3 that ligates sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wobble position. {ECO:0000255\|HAMAP-Rule:MF_03054, ECO:0000269\|PubMed:19017811}.	FUNCTION: Catalyzes the conversion of malonyl-CoA to acetyl-CoA. In the fatty acid biosynthesis MCD selectively removes malonyl-CoA and thus assures that methyl-malonyl-CoA is the only chain elongating substrate for fatty acid synthase and that fatty acids with multiple methyl side chains are produced. In peroxisomes it may be involved in degrading intraperoxisomal malonyl-CoA, which is generated by the peroxisomal beta-oxidation of odd chain-length dicarboxylic fatty acids. Plays a role in the metabolic balance between glucose and lipid oxidation in muscle independent of alterations in insulin signaling. May play a role in controlling the extent of ischemic injury by promoting glucose oxidation. {ECO:0000269\|PubMed:10455107, ECO:0000269\|PubMed:15003260, ECO:0000269\|PubMed:18314420, ECO:0000269\|PubMed:23482565}.

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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Fusion Gene Sequence for CTU2-MLYCD

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.

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Fusion Gene PPI Analysis for CTU2-MLYCD

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 CTU2-MLYCD

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 CTU2-MLYCD

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source