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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:USP6NL-CCDC23 (FusionGDB2 ID:96939)

Fusion Gene Summary for USP6NL-CCDC23

check button Fusion gene summary
Fusion gene informationFusion gene name: USP6NL-CCDC23
Fusion gene ID: 96939
HgeneTgene
Gene symbol

USP6NL

CCDC23

Gene ID

9712

374969

Gene nameUSP6 N-terminal likesmall vasohibin binding protein
SynonymsRNTRE|TRE2NL|USP6NL-IT1CCDC23|NEDAHM
Cytomap

10p14

1p34.2

Type of geneprotein-codingprotein-coding
DescriptionUSP6 N-terminal-like proteinrelated to the N-terminus of tresmall vasohibin-binding proteincoiled-coil domain containing 23coiled-coil domain-containing protein 23
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000609104, ENST00000277575, 
ENST00000379237, ENST00000443016, 
ENST00000609853, 		ENST00000372522, 
ENST00000372521, ENST00000537227, 
ENST00000497437, 
Fusion gene scores* DoF score23 X 16 X 11=40483 X 2 X 2=12
# samples 305
** MAII scorelog2(30/4048*10)=-3.75417488419843
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/12*10)=2.05889368905357
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: USP6NL [Title/Abstract] AND CCDC23 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointUSP6NL(11639630)-CCDC23(43282251), # samples:1
USP6NL(11639630)-CCDC23(43273171), # 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneUSP6NL

GO:0043547

positive regulation of GTPase activity

17562788

TgeneCCDC23

GO:0006508

proteolysis

29146869

TgeneCCDC23

GO:0009306

protein secretion

20736312

TgeneCCDC23

GO:0031397

negative regulation of protein ubiquitination

20736312


check buttonFusion gene breakpoints across USP6NL (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across CCDC23 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4OVTCGA-30-1718-01AUSP6NLchr10

11639630

-CCDC23chr1

43282251

-
ChimerDB4OVTCGA-30-1718-01AUSP6NLchr10

11639630

-CCDC23chr1

43273171

-


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Fusion Gene ORF analysis for USP6NL-CCDC23

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-5UTRENST00000609104ENST00000372522USP6NLchr10

11639630

-CCDC23chr1

43282251

-
5CDS-5UTRENST00000609104ENST00000372521USP6NLchr10

11639630

-CCDC23chr1

43282251

-
5CDS-5UTRENST00000609104ENST00000537227USP6NLchr10

11639630

-CCDC23chr1

43282251

-
5CDS-5UTRENST00000609104ENST00000497437USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000277575ENST00000372522USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000277575ENST00000372521USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000277575ENST00000537227USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000277575ENST00000497437USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000379237ENST00000372522USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000379237ENST00000372521USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000379237ENST00000537227USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000379237ENST00000497437USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000443016ENST00000372522USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000443016ENST00000372521USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000443016ENST00000537227USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000443016ENST00000497437USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000609853ENST00000372522USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000609853ENST00000372521USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000609853ENST00000537227USP6NLchr10

11639630

-CCDC23chr1

43282251

-
intron-5UTRENST00000609853ENST00000497437USP6NLchr10

11639630

-CCDC23chr1

43282251

-
Frame-shiftENST00000609104ENST00000372522USP6NLchr10

11639630

-CCDC23chr1

43273171

-
In-frameENST00000609104ENST00000372521USP6NLchr10

11639630

-CCDC23chr1

43273171

-
In-frameENST00000609104ENST00000537227USP6NLchr10

11639630

-CCDC23chr1

43273171

-
5CDS-intronENST00000609104ENST00000497437USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000277575ENST00000372522USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000277575ENST00000372521USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000277575ENST00000537227USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-intronENST00000277575ENST00000497437USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000379237ENST00000372522USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000379237ENST00000372521USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000379237ENST00000537227USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-intronENST00000379237ENST00000497437USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000443016ENST00000372522USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000443016ENST00000372521USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000443016ENST00000537227USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-intronENST00000443016ENST00000497437USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000609853ENST00000372522USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000609853ENST00000372521USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-3CDSENST00000609853ENST00000537227USP6NLchr10

11639630

-CCDC23chr1

43273171

-
intron-intronENST00000609853ENST00000497437USP6NLchr10

11639630

-CCDC23chr1

43273171

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000609104USP6NLchr1011639630-ENST00000372521CCDC23chr143273171-844399797393134
ENST00000609104USP6NLchr1011639630-ENST00000537227CCDC23chr143273171-649399287096

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000609104ENST00000372521USP6NLchr1011639630-CCDC23chr143273171-0.508007050.4919929
ENST00000609104ENST00000537227USP6NLchr1011639630-CCDC23chr143273171-0.236931790.7630682

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Fusion Genomic Features for USP6NL-CCDC23


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution 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.

check buttonDistribution 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 USP6NL-CCDC23


check button Go to

FGviewer for the breakpoints of chr10:11639630-chr1:43273171

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
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: 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.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneUSP6NLchr10:11639630chr1:43273171ENST00000277575-114100_2920846.0DomainRab-GAP TBC
HgeneUSP6NLchr10:11639630chr1:43273171ENST00000379237-114100_2920852.0DomainRab-GAP TBC
TgeneCCDC23chr10:11639630chr1:43273171ENST00000372521135_5238.067.0Coiled coilOntology_term=ECO:0000255
TgeneCCDC23chr10:11639630chr1:43273171ENST00000372522135_5238.067.0Coiled coilOntology_term=ECO:0000255
TgeneCCDC23chr10:11639630chr1:43273171ENST00000537227145_5238.069.0Coiled coilOntology_term=ECO:0000255


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Fusion Gene Sequence for USP6NL-CCDC23


check button 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_ENST00000609104_ENST00000372521_TCGA-30-1718-01A_USP6NL_chr10_11639630_-_CCDC23_chr1_43273171_length(transcript)=844nt_BP=399nt
CGGCCGCTGCGGTGACGGTTGGCGGCGGCCGGTGAGGCGGGCGGGGCCGGAGGCGCGGAGGCGGGGTCCCGGGCGAGCCGCCCTGGGAGG
CGGGGGCCGTTTCCATAGCGGCGGCAGGAGGTGTCGCGCCGGGGAACTTCCTGGTTCCCGGGCTCGGCTTCGCCGGGATCCTCTTGGAAG
GGAAACAATGGGGCGGAGGGCACTGCGGTAGCCGCCGCCGCCGCCGCGCCGCGCCGCGCCGGATCTGCTCGGCCGCCCGGGACCGCCAGC
TCTGTCCGCTGCCCACAGCCTAGCAGTCGGGACCGTACTGAGGACATGTATTCCTCTGAGAAACCTTGGACAGCAGATTTTGGTTTAATA
TCTGATTGGGACAACATTCAGACCCATTTCCAGTCATGAATCTATGCCCTCAACAGAGTCATGACAGAACTGGAGCAGCAGCAGTTTGAT
GAGTTCTGTAAACAGATGCAGCCTCCTGGAGAATGAGGCCCCAGGTTCAAACCAGATGGGATCCTGAGAGCTTTGAGAGGGTGTTGCCAG
TTTTAAGCTGAGATGGCCCATTTGGAGCCTTACAGAACTAGACCAGAAGACATTTGTGGATAAATCTGAACTCACTTCCTGTGTGTAACT
TCTAACTTCACTGGTTCCTCCCATCTGAATTGGCCACATGCTTGCTGAAGAGACTTGTTTTCTTCTTCTAAGACAGTGGTTTTGTTTTTT
GGGTTTTTTTAAAAAAAAAAAAAAAACACACACAAAAAACACTTTTTCTATTGTTTGAGAAAAATCAGTGTTTCTCATGAAACTCTATAT

>In-frame_ENST00000609104_ENST00000372521_TCGA-30-1718-01A_USP6NL_chr10_11639630_-_CCDC23_chr1_43273171_length(amino acids)=134AA_start in transcript=797_stop in transcript=393
MRNTDFSQTIEKVFFVCVFFFFLKKPKKQNHCLRRRKQVSSASMWPIQMGGTSEVRSYTQEVSSDLSTNVFWSSSVRLQMGHLSLKLATP

--------------------------------------------------------------
>In-frame_ENST00000609104_ENST00000537227_TCGA-30-1718-01A_USP6NL_chr10_11639630_-_CCDC23_chr1_43273171_length(transcript)=649nt_BP=399nt
CGGCCGCTGCGGTGACGGTTGGCGGCGGCCGGTGAGGCGGGCGGGGCCGGAGGCGCGGAGGCGGGGTCCCGGGCGAGCCGCCCTGGGAGG
CGGGGGCCGTTTCCATAGCGGCGGCAGGAGGTGTCGCGCCGGGGAACTTCCTGGTTCCCGGGCTCGGCTTCGCCGGGATCCTCTTGGAAG
GGAAACAATGGGGCGGAGGGCACTGCGGTAGCCGCCGCCGCCGCCGCGCCGCGCCGCGCCGGATCTGCTCGGCCGCCCGGGACCGCCAGC
TCTGTCCGCTGCCCACAGCCTAGCAGTCGGGACCGTACTGAGGACATGTATTCCTCTGAGAAACCTTGGACAGCAGATTTTGGTTTAATA
TCTGATTGGGACAACATTCAGACCCATTTCCAGTCATGAATCTATGCCCTCAACAGAGTCATGACAGAACTGGAGCAGCAGCAGTTTGAT
GAGTTCTGTAAACAGATGCAGCCTCCTGGAGAATGAGGCCCCAGGTTCAAACCAGAAGACATTTGTGGATAAATCTGAACTCACTTCCTG
TGTGTAACTTCTAACTTCACTGGTTCCTCCCATCTGAATTGGCCACATGCTTGCTGAAGAGACTTGTTTTCTTCTTCTAAGACAGTGGTT

>In-frame_ENST00000609104_ENST00000537227_TCGA-30-1718-01A_USP6NL_chr10_11639630_-_CCDC23_chr1_43273171_length(amino acids)=96AA_start in transcript=287_stop in transcript=0
MWAADRAGGPGRPSRSGAARRGGGGGYRSALRPIVSLPRGSRRSRAREPGSSPARHLLPPLWKRPPPPRAARPGPRLRASGPARLTGRRQ

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

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Fusion Gene PPI Analysis for USP6NL-CCDC23


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for USP6NL-CCDC23


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for USP6NL-CCDC23


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneUSP6NLC0025202melanoma1CTD_human