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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:ARRDC3-CNTF (FusionGDB2 ID:6870)

Fusion Gene Summary for ARRDC3-CNTF

Fusion gene summary

Fusion gene information	Fusion gene name: ARRDC3-CNTF
	Fusion gene ID: 6870
		Hgene	Tgene
	Gene symbol	ARRDC3	CNTF
	Gene ID	57561	1270
	Gene name	arrestin domain containing 3	ciliary neurotrophic factor
	Synonyms	TLIMP	HCNTF
	Cytomap	5q14.3	11q12.1
	Type of gene	protein-coding	protein-coding
	Description	arrestin domain-containing protein 3TBP-2-like inducible membrane proteinalpha-arrestin 3	ciliary neurotrophic factorCiliary Neuronotrophic Factor
	Modification date	20200313	20200313
	UniProtAcc	Q96B67	P26992
	Ensembl transtripts involved in fusion gene	ENST00000265138, ENST00000503192,	ENST00000361987,
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: ARRDC3 [Title/Abstract] AND CNTF [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	ARRDC3(90678629)-CNTF(58391506), # 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
Tgene	CNTF	GO:0010628	positive regulation of gene expression	24129709
Tgene	CNTF	GO:0042531	positive regulation of tyrosine phosphorylation of STAT protein	12643274\|21912637
Tgene	CNTF	GO:0043524	negative regulation of neuron apoptotic process	10966616
Tgene	CNTF	GO:0070120	ciliary neurotrophic factor-mediated signaling pathway	12643274

Fusion gene breakpoints across ARRDC3 (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 CNTF (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	Non-Cancer	61N	ARRDC3	chr5	90678629	-	CNTF	chr11	58391506	+

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Fusion Gene ORF analysis for ARRDC3-CNTF

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	ENST00000265138	ENST00000361987	ARRDC3	chr5	90678629	-	CNTF	chr11	58391506	+
intron-3CDS	ENST00000503192	ENST00000361987	ARRDC3	chr5	90678629	-	CNTF	chr11	58391506	+

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)

ENST00000265138

ARRDC3

chr5

90678629

ENST00000361987

CNTF

chr11

58391506

2239

547

532

1035

167

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
ENST00000265138	ENST00000361987	ARRDC3	chr5	90678629	-	CNTF	chr11	58391506	+	0.009589709	0.9904103

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Fusion Genomic Features for ARRDC3-CNTF

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)
ARRDC3	chr5	90678629	-	CNTF	chr11	58391506	+	0.014676096	0.98532385
ARRDC3	chr5	90678629	-	CNTF	chr11	58391506	+	0.014676096	0.98532385

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 ARRDC3-CNTF

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:90678629/chr11:58391506)
- 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
ARRDC3 Q96B67	CNTF P26992
FUNCTION: Adapter protein that plays a role in regulating cell-surface expression of adrenergic receptors and probably also other G protein-coupled receptors (PubMed:20559325, PubMed:21982743, PubMed:23208550). Plays a role in NEDD4-mediated ubiquitination and endocytosis af activated ADRB2 and subsequent ADRB2 degradation (PubMed:20559325, PubMed:23208550). May recruit NEDD4 to ADRB2 (PubMed:20559325). Alternatively, may function as adapter protein that does not play a major role in recruiting NEDD4 to ADRB2, but rather plays a role in a targeting ADRB2 to endosomes (PubMed:23208550). {ECO:0000269\|PubMed:20559325, ECO:0000269\|PubMed:23208550}.	FUNCTION: Binds to CNTF. The alpha subunit provides the receptor specificity. Receptor for heterodimeric neurotropic cytokine composed of CLCF1/CLC and CRLF1/CLF-1 (PubMed:26858303). {ECO:0000269\|PubMed:26858303}.

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 ARRDC3-CNTF

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.

>6870_6870_1_ARRDC3-CNTF_ARRDC3_chr5_90678629_ENST00000265138_CNTF_chr11_58391506_ENST00000361987_length(transcript)=2239nt_BP=547nt
ACAAAGCTGCTCTTAAAGTGAGCTGGCAGCTTTTAGCCGCCCGTCTTTGTAAGGAGACCACTGAGACGAGCGGGAGCGCGGAGCAGCAGC
CTCTGCTGCCCTGACTTTTTAAGAAATCTCAATGAACTATTTGTAGAGAATCACTGATCCGGCCTGCAAGCATTTTGCACGGCAAAAATA
TCGATCAGTGTTAAGTGAAGATCACATTTTATATGCGATCTTGACTTTTTTGTCTTACATTATATTTTTATAGATTTTGTTATAAACATG
GTGCTGGGAAAGGTGAAGAGTTTGACAATAAGCTTTGACTGTCTTAATGACAGCAATGTCCCTGTGTATTCTAGTGGGGATACCGTCTCA
GGAAGGGTAAATTTAGAAGTTACTGGGGAAATCAGAGTAAAATCTCTTAAAATTCATGCAAGAGGACATGCGAAAGTACGCTGGACTGAA
TCTAGAAACGCCGGCTCCAATACTGCCTATACACAGAATTACACTGAAGAAGTAGAGTATTTCAACCATAAAGACATCTTAATTGGGCAC
GAAAGAGGTGAAGCATCAGGGCCTGAACAAGAACATCAACCTGGACTCTGCGGATGGGATGCCAGTGGCAAGCACTGATCAGTGGAGTGA
GCTGACCGAGGCAGAGCGACTCCAAGAGAACCTTCAAGCTTATCGTACCTTCCATGTTTTGTTGGCCAGGCTCTTAGAAGACCAGCAGGT
GCATTTTACCCCAACCGAAGGTGACTTCCATCAAGCTATACATACCCTTCTTCTCCAAGTCGCTGCCTTTGCATACCAGATAGAGGAGTT
AATGATACTCCTGGAATACAAGATCCCCCGCAATGAGGCTGATGGGATGCCTATTAATGTTGGAGATGGTGGTCTCTTTGAGAAGAAGCT
GTGGGGCCTAAAGGTGCTGCAGGAGCTTTCACAGTGGACAGTAAGGTCCATCCATGACCTTCGTTTCATTTCTTCTCATCAGACTGGGAT
CCCAGCACGTGGGAGCCATTATATTGCTAACAACAAGAAAATGTAGCAGTTAGTCCCTTCTCTCTTCCTTGCTTTCTCTTCTAATGGAAT
ATGCGTAGTTCCCTGGGGCCTCGCTTTCCCATCTTAAATTTCTAAAAACAGTTAAGACAACAGGCATTTTCTTTCTTTTTTCTCTGACCA
CCTGCAGCCTGTTGAAGGACTACAGGTATTTTCATCAAGTAGCGTTGGAGACATACACAAATGGGCATACAAGTTTAGCCTGGGGGGTGT
GATTTGTGTGCGTGCTTGCATGTGCTGCAGGTGTAAGAGAGTGGGAGCAGGGACAACGTCCTTCCACTTCAGGGTTCTAACCTTTCTAAC
CCACTAAGTAACCTCTACAGGCATTTAACTGCCTTACAGACAGAATATACATATGTTAATTCTAGTCCTGGATGACTCGGTCTGAGAAGA
TTCAATTTAAAATCAGACTCTTTAGTTGATTTAAACTCTTAGAGAATAAGAATAATAATGGCTAACTTTTATTATCTTCTATATTAAGGC
AGTATGCCAAGGGTCTTTATGTATATTATGTACAGCGTTTACAACCTTGTGAGCAAGGTGGTGTTACTCCCATTAGGTAGATGAGAAAAC
AGGCTCACAGAGATTTGGTTAAGCTCACACAGCTAACAAGTAGCACACTGAGTTTGAACACAGATCATTCTCCTTGTAAAAGCCTATGTG
CCTTTCACTTTAGAGGCTTGATCATGAATCACTGCACCTCTTTGTCACAGGGTGTTGGAAGATGCATCCATGTAATCTATTCCCATCGCT
GGAAAACAGCTGCTGTTAGATGTCCTCAGAAGTCAGTTGCAAATTTTAGCGTTAAAGTCAGGATTTATTGTTCATACTTGGCGGTGAGGA
GGGCAGCTGGAGATCTTAAGATTCCATTTTGGAAAATGATTAGGCCCGCCAAACTTCTGAACTTTGGAAGCTGGGGATGTTTAGTAATAC
AGCCTGGTTTTTAAGTACTCACTAAAAGTTCTCAAATATTGGGTTGGGCACGGCTTATACCAGGTTACCTCACTTTTAATTAGTGATGCA
GGCAGTGTAACCCAAGCATTTGTGGACAATGAGTGGAATACTAAAGTTAAAAAGTCAAACTTTCACCTCAGATTTTCTGGACTTAGTCAT

>6870_6870_1_ARRDC3-CNTF_ARRDC3_chr5_90678629_ENST00000265138_CNTF_chr11_58391506_ENST00000361987_length(amino acids)=167AA_BP=5
MGTKEVKHQGLNKNINLDSADGMPVASTDQWSELTEAERLQENLQAYRTFHVLLARLLEDQQVHFTPTEGDFHQAIHTLLLQVAAFAYQI

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Fusion Gene PPI Analysis for ARRDC3-CNTF

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 ARRDC3-CNTF

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 ARRDC3-CNTF

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source