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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:KIAA1109-UBE2D3 (FusionGDB2 ID:42048)

Fusion Gene Summary for KIAA1109-UBE2D3

check button Fusion gene summary
Fusion gene informationFusion gene name: KIAA1109-UBE2D3
Fusion gene ID: 42048
HgeneTgene
Gene symbol

KIAA1109

UBE2D3

Gene ID

84162

7323

Gene nameKIAA1109ubiquitin conjugating enzyme E2 D3
SynonymsALKKUCS|FSA|TweekE2(17)KB3|UBC4/5|UBCH5C
Cytomap

4q27

4q24

Type of geneprotein-codingprotein-coding
Descriptiontransmembrane protein KIAA1109fragile site-associated proteinubiquitin-conjugating enzyme E2 D3(E3-independent) E2 ubiquitin-conjugating enzyme D3E2 ubiquitin-conjugating enzyme D3ubiquitin carrier protein D3ubiquitin conjugating enzyme E2D 3ubiquitin-conjugating enzyme E2(17)KB 3ubiquitin-conjugating enzyme
Modification date2020032720200313
UniProtAcc

Q2LD37

.
Ensembl transtripts involved in fusion geneENST00000264501, ENST00000455637, 
ENST00000388738, ENST00000495260, 
ENST00000453744, ENST00000394801, 
ENST00000394803, ENST00000394804, 
ENST00000343106, ENST00000321805, 
ENST00000350435, ENST00000338145, 
ENST00000349311, ENST00000504211, 
ENST00000357194, ENST00000505207, 
ENST00000507845, ENST00000502404, 
ENST00000513098, 
Fusion gene scores* DoF score11 X 9 X 8=7928 X 5 X 7=280
# samples 139
** MAII scorelog2(13/792*10)=-2.60698880705116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/280*10)=-1.63742992061529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KIAA1109 [Title/Abstract] AND UBE2D3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKIAA1109(123075267)-UBE2D3(103731012), # 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
TgeneUBE2D3

GO:0000209

protein polyubiquitination

14765125|16522193

TgeneUBE2D3

GO:0006513

protein monoubiquitination

20347421

TgeneUBE2D3

GO:0016567

protein ubiquitination

9990509|21532592

TgeneUBE2D3

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

20347421

TgeneUBE2D3

GO:0051865

protein autoubiquitination

21068390

TgeneUBE2D3

GO:0070936

protein K48-linked ubiquitination

20061386

TgeneUBE2D3

GO:0070979

protein K11-linked ubiquitination

20061386


check buttonFusion gene breakpoints across KIAA1109 (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 UBE2D3 (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
ChimerDB4STADTCGA-HU-A4GJ-01AKIAA1109chr4

123075267

+UBE2D3chr4

103731012

-


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Fusion Gene ORF analysis for KIAA1109-UBE2D3

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
5UTR-3CDSENST00000264501ENST00000453744KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-3CDSENST00000264501ENST00000394801KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-3CDSENST00000264501ENST00000394803KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-3CDSENST00000264501ENST00000394804KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-3CDSENST00000264501ENST00000343106KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-3CDSENST00000264501ENST00000321805KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-3CDSENST00000264501ENST00000350435KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-3CDSENST00000264501ENST00000338145KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-3CDSENST00000264501ENST00000349311KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-5UTRENST00000264501ENST00000504211KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-5UTRENST00000264501ENST00000357194KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-5UTRENST00000264501ENST00000505207KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-5UTRENST00000264501ENST00000507845KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-5UTRENST00000264501ENST00000502404KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
5UTR-5UTRENST00000264501ENST00000513098KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000455637ENST00000453744KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000455637ENST00000394801KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000455637ENST00000394803KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000455637ENST00000394804KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000455637ENST00000343106KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000455637ENST00000321805KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000455637ENST00000350435KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000455637ENST00000338145KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000455637ENST00000349311KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000455637ENST00000504211KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000455637ENST00000357194KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000455637ENST00000505207KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000455637ENST00000507845KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000455637ENST00000502404KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000455637ENST00000513098KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000388738ENST00000453744KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000388738ENST00000394801KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000388738ENST00000394803KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000388738ENST00000394804KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000388738ENST00000343106KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000388738ENST00000321805KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000388738ENST00000350435KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000388738ENST00000338145KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000388738ENST00000349311KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000388738ENST00000504211KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000388738ENST00000357194KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000388738ENST00000505207KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000388738ENST00000507845KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000388738ENST00000502404KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000388738ENST00000513098KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000495260ENST00000453744KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000495260ENST00000394801KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000495260ENST00000394803KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000495260ENST00000394804KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000495260ENST00000343106KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000495260ENST00000321805KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000495260ENST00000350435KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000495260ENST00000338145KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-3CDSENST00000495260ENST00000349311KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000495260ENST00000504211KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000495260ENST00000357194KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000495260ENST00000505207KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000495260ENST00000507845KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000495260ENST00000502404KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-
intron-5UTRENST00000495260ENST00000513098KIAA1109chr4

123075267

+UBE2D3chr4

103731012

-

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)

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

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Fusion Genomic Features for KIAA1109-UBE2D3


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 KIAA1109-UBE2D3


check button Go to

FGviewer for the breakpoints of :-:

.
- 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
KIAA1109

Q2LD37

.
FUNCTION: Plays a role in endosomal trafficking and endosome recycling. Also involved in the actin cytoskeleton and cilia structural dynamics (PubMed:30906834). Acts as regulator of phagocytosis (PubMed:31540829). {ECO:0000269|PubMed:30906834, ECO:0000269|PubMed:31540829}.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


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Fusion Gene Sequence for KIAA1109-UBE2D3


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.

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Fusion Gene PPI Analysis for KIAA1109-UBE2D3


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 KIAA1109-UBE2D3


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 KIAA1109-UBE2D3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKIAA1109C4693347ALKURAYA-KUCINSKAS SYNDROME4GENOMICS_ENGLAND;UNIPROT
HgeneKIAA1109C0036572Seizures1GENOMICS_ENGLAND