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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:RIPK4-NEB (FusionGDB2 ID:73730)

Fusion Gene Summary for RIPK4-NEB

check button Fusion gene summary
Fusion gene informationFusion gene name: RIPK4-NEB
Fusion gene ID: 73730
HgeneTgene
Gene symbol

RIPK4

NEB

Gene ID

54101

4703

Gene namereceptor interacting serine/threonine kinase 4nebulin
SynonymsANKK2|ANKRD3|CHANDS|DIK|NKRD3|PKK|PPS2|RIP4NEB177D|NEM2
Cytomap

21q22.3

2q23.3

Type of geneprotein-codingprotein-coding
Descriptionreceptor-interacting serine/threonine-protein kinase 4PKC-delta-interacting protein kinaseankyrin repeat domain-containing protein 3protein kinase C-associated kinaseserine/threonine-protein kinase ANKRD3nebulinnemaline myopathy type 2
Modification date2020031320200328
UniProtAcc.

O76041

Ensembl transtripts involved in fusion geneENST00000332512, ENST00000352483, 
ENST00000542057, ENST00000544709, 
ENST00000409198, ENST00000397345, 
ENST00000427231, ENST00000172853, 
ENST00000604864, ENST00000603639, 
ENST00000397336, ENST00000509223, 
ENST00000498015, 
Fusion gene scores* DoF score5 X 5 X 2=505 X 5 X 2=50
# samples 55
** MAII scorelog2(5/50*10)=0log2(5/50*10)=0
Context

PubMed: RIPK4 [Title/Abstract] AND NEB [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNEB(152468732)-RIPK4(43166181), # samples:1
RIPK4(43166181)-NEB(152468732), # 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 RIPK4 (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 NEB (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/ABE717807RIPK4chr21

43166181

+NEBchr2

152468732

+


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Fusion Gene ORF analysis for RIPK4-NEB

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-3CDSENST00000332512ENST00000409198RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000332512ENST00000397345RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000332512ENST00000427231RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000332512ENST00000172853RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000332512ENST00000604864RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000332512ENST00000603639RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000332512ENST00000397336RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000332512ENST00000509223RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000332512ENST00000498015RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000352483ENST00000409198RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000352483ENST00000397345RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000352483ENST00000427231RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000352483ENST00000172853RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000352483ENST00000604864RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000352483ENST00000603639RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000352483ENST00000397336RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000352483ENST00000509223RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000352483ENST00000498015RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000542057ENST00000409198RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000542057ENST00000397345RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000542057ENST00000427231RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000542057ENST00000172853RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000542057ENST00000604864RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000542057ENST00000603639RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000542057ENST00000397336RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000542057ENST00000509223RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000542057ENST00000498015RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000544709ENST00000409198RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000544709ENST00000397345RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000544709ENST00000427231RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000544709ENST00000172853RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000544709ENST00000604864RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-3CDSENST00000544709ENST00000603639RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000544709ENST00000397336RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000544709ENST00000509223RIPK4chr21

43166181

+NEBchr2

152468732

+
intron-intronENST00000544709ENST00000498015RIPK4chr21

43166181

+NEBchr2

152468732

+

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 RIPK4-NEB


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 RIPK4-NEB


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
.NEB

O76041

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: Binds to actin and plays an important role in the assembly of the Z-disk. May functionally link sarcomeric actin to the desmin intermediate filaments in the heart muscle sarcomeres (PubMed:27733623). Isoform 2 might play a role in the assembly of focal adhesion (PubMed:15004028). {ECO:0000269|PubMed:15004028, ECO:0000269|PubMed:27733623}.

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 RIPK4-NEB


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 RIPK4-NEB


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 RIPK4-NEB


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 RIPK4-NEB


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRIPK4C0406733Curly hair-ankyloblepharon-nail dysplasia syndrome4ORPHANET;UNIPROT
HgeneRIPK4C1849718POPLITEAL PTERYGIUM SYNDROME, LETHAL TYPE3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneNEBC1850569Nemaline Myopathy 212CLINGEN;CTD_human;GENOMICS_ENGLAND
TgeneNEBC0206157Myopathies, Nemaline2GENOMICS_ENGLAND
TgeneNEBC0270960Congenital myopathy (disorder)1GENOMICS_ENGLAND
TgeneNEBC1854678MULTIPLE PTERYGIUM SYNDROME, LETHAL TYPE1ORPHANET