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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:KIAA1217-NELL1 (FusionGDB2 ID:42280)

Fusion Gene Summary for KIAA1217-NELL1

check button Fusion gene summary
Fusion gene informationFusion gene name: KIAA1217-NELL1
Fusion gene ID: 42280
HgeneTgene
Gene symbol

KIAA1217

NELL1

Gene ID

56243

4745

Gene nameKIAA1217neural EGFL like 1
SynonymsETL4|SKTIDH3GL|NRP1
Cytomap

10p12.2-p12.1

11p15.1

Type of geneprotein-codingprotein-coding
Descriptionsickle tail protein homologlikely orthologue of Mus musculus enhancer trap locus 4protein kinase C-binding protein NELL1nel-related protein 1neural epidermal growth factor-like 1
Modification date2020031320200313
UniProtAcc

Q5T5P2

Q92832

Ensembl transtripts involved in fusion geneENST00000376451, ENST00000376452, 
ENST00000376454, ENST00000376462, 
ENST00000396445, ENST00000458595, 
ENST00000307544, ENST00000396446, 
ENST00000430453, ENST00000481700, 
ENST00000298925, ENST00000325319, 
ENST00000357134, ENST00000529218, 
ENST00000532434, 
Fusion gene scores* DoF score22 X 21 X 11=508216 X 16 X 3=768
# samples 2416
** MAII scorelog2(24/5082*10)=-4.40429006444484
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/768*10)=-2.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KIAA1217 [Title/Abstract] AND NELL1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKIAA1217(24836573)-NELL1(21058768), # 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
TgeneNELL1

GO:0010468

regulation of gene expression

21723284

TgeneNELL1

GO:0030501

positive regulation of bone mineralization

21723284

TgeneNELL1

GO:0033689

negative regulation of osteoblast proliferation

21723284

TgeneNELL1

GO:0045669

positive regulation of osteoblast differentiation

21723284

TgeneNELL1

GO:1903363

negative regulation of cellular protein catabolic process

21723284


check buttonFusion gene breakpoints across KIAA1217 (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 NELL1 (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
ChiTaRS5.0N/AFN152849KIAA1217chr10

24836573

-NELL1chr11

21058768

+


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Fusion Gene ORF analysis for KIAA1217-NELL1

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
3UTR-intronENST00000376451ENST00000298925KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376451ENST00000325319KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376451ENST00000357134KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376451ENST00000529218KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376451ENST00000532434KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376452ENST00000298925KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376452ENST00000325319KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376452ENST00000357134KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376452ENST00000529218KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376452ENST00000532434KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376454ENST00000298925KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376454ENST00000325319KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376454ENST00000357134KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376454ENST00000529218KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376454ENST00000532434KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376462ENST00000298925KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376462ENST00000325319KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376462ENST00000357134KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376462ENST00000529218KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000376462ENST00000532434KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000396445ENST00000298925KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000396445ENST00000325319KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000396445ENST00000357134KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000396445ENST00000529218KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000396445ENST00000532434KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000458595ENST00000298925KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000458595ENST00000325319KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000458595ENST00000357134KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000458595ENST00000529218KIAA1217chr10

24836573

-NELL1chr11

21058768

+
3UTR-intronENST00000458595ENST00000532434KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000307544ENST00000298925KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000307544ENST00000325319KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000307544ENST00000357134KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000307544ENST00000529218KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000307544ENST00000532434KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000396446ENST00000298925KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000396446ENST00000325319KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000396446ENST00000357134KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000396446ENST00000529218KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000396446ENST00000532434KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000430453ENST00000298925KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000430453ENST00000325319KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000430453ENST00000357134KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000430453ENST00000529218KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000430453ENST00000532434KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000481700ENST00000298925KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000481700ENST00000325319KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000481700ENST00000357134KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000481700ENST00000529218KIAA1217chr10

24836573

-NELL1chr11

21058768

+
intron-intronENST00000481700ENST00000532434KIAA1217chr10

24836573

-NELL1chr11

21058768

+

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 KIAA1217-NELL1


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 KIAA1217-NELL1


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:24836573/:21058768)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
KIAA1217

Q5T5P2

NELL1

Q92832

FUNCTION: Required for normal development of intervertebral disks. {ECO:0000250|UniProtKB:A2AQ25}.FUNCTION: Plays a role in the control of cell growth and differentiation. Promotes osteoblast cell differentiation and terminal mineralization. {ECO:0000269|PubMed:21723284}.

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 KIAA1217-NELL1


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 KIAA1217-NELL1


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 KIAA1217-NELL1


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 KIAA1217-NELL1


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