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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:KIRREL3-NUMB (FusionGDB2 ID:42782)

Fusion Gene Summary for KIRREL3-NUMB

check button Fusion gene summary
Fusion gene informationFusion gene name: KIRREL3-NUMB
Fusion gene ID: 42782
HgeneTgene
Gene symbol

KIRREL3

NUMB

Gene ID

84623

8650

Gene namekirre like nephrin family adhesion molecule 3NUMB endocytic adaptor protein
SynonymsKIRRE|MRD4|NEPH2|PRO4502C14orf41|S171|c14_5527
Cytomap

11q24.2

14q24.2-q24.3

Type of geneprotein-codingprotein-coding
Descriptionkin of IRRE-like protein 3kin of IRRE like 3kin of irregular chiasm-like protein 3nephrin-like 2nephrin-like protein 2protein numb homologh-Numbnumb homolog
Modification date2020031320200313
UniProtAcc

Q8IZU9

NUMBL

Ensembl transtripts involved in fusion geneENST00000416561, ENST00000525144, 
ENST00000525704, ENST00000529097, 
ENST00000533026, 		ENST00000355058, 
ENST00000356296, ENST00000359560, 
ENST00000454166, ENST00000535282, 
ENST00000544991, ENST00000554521, 
ENST00000554546, ENST00000555238, 
ENST00000555394, ENST00000555738, 
ENST00000556600, ENST00000556772, 
ENST00000557597, ENST00000559312, 
ENST00000560335, 
Fusion gene scores* DoF score5 X 5 X 2=5010 X 9 X 5=450
# samples 510
** MAII scorelog2(5/50*10)=0log2(10/450*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KIRREL3 [Title/Abstract] AND NUMB [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKIRREL3(126327094)-NUMB(73861913), # 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

check buttonFusion gene breakpoints across KIRREL3 (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 NUMB (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/ACQ205481KIRREL3chr11

126327094

-NUMBchr14

73861913

+


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Fusion Gene ORF analysis for KIRREL3-NUMB

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
intron-intronENST00000416561ENST00000355058KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000356296KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000359560KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000454166KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000535282KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000544991KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000554521KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000554546KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000555238KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000555394KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000555738KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000556600KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000556772KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000557597KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000559312KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000416561ENST00000560335KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000355058KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000356296KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000359560KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000454166KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000535282KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000544991KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000554521KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000554546KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000555238KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000555394KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000555738KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000556600KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000556772KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000557597KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000559312KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525144ENST00000560335KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000355058KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000356296KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000359560KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000454166KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000535282KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000544991KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000554521KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000554546KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000555238KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000555394KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000555738KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000556600KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000556772KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000557597KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000559312KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000525704ENST00000560335KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000355058KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000356296KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000359560KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000454166KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000535282KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000544991KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000554521KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000554546KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000555238KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000555394KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000555738KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000556600KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000556772KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000557597KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000559312KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000529097ENST00000560335KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000355058KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000356296KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000359560KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000454166KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000535282KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000544991KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000554521KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000554546KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000555238KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000555394KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000555738KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000556600KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000556772KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000557597KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000559312KIRREL3chr11

126327094

-NUMBchr14

73861913

+
intron-intronENST00000533026ENST00000560335KIRREL3chr11

126327094

-NUMBchr14

73861913

+

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 KIRREL3-NUMB


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 KIRREL3-NUMB


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/:126327094/:73861913)
- 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
KIRREL3

Q8IZU9

NUMB

NUMBL

FUNCTION: Synaptic adhesion molecule required for the formation of target-specific synapses. Required for formation of target-specific synapses at hippocampal mossy fiber synapses. Required for formation of mossy fiber filopodia, the synaptic structures connecting dentate granule and GABA neurons. Probably acts as a homophilic adhesion molecule that promotes trans-cellular interactions and stabilize mossy fiber filipodia contact and subsequent synapse formation. Required for the coalescence of vomeronasal sensory neuron axons. May be involved in the hematopoietic supportive capacity of stroma cells; the secreted extracellular domain is directly responsible for supporting hematopoietic stem cells. {ECO:0000250|UniProtKB:Q8BR86}.609

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 KIRREL3-NUMB


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 KIRREL3-NUMB


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 KIRREL3-NUMB


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 KIRREL3-NUMB


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