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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:ARL15-NDUFS4 (FusionGDB2 ID:HG54622TG4724)

Fusion Gene Summary for ARL15-NDUFS4

check button Fusion gene summary
Fusion gene informationFusion gene name: ARL15-NDUFS4
Fusion gene ID: hg54622tg4724
HgeneTgene
Gene symbol

ARL15

NDUFS4

Gene ID

54622

4724

Gene nameADP ribosylation factor like GTPase 15NADH:ubiquinone oxidoreductase subunit S4
SynonymsARFRP2AQDQ|CI-18|CI-18 kDa|CI-AQDQ|MC1DN1
Cytomap('ARL15')('NDUFS4')

5q11.2

5q11.2

Type of geneprotein-codingprotein-coding
DescriptionADP-ribosylation factor-like protein 15ADP-ribosylation factor-like 15ADP-ribosylation factor-related protein 2ARF-related protein 2NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialNADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzyme Q reductase)NADH-ubiquinone oxidoreductase 18 kDa subunitcomplex I 18kDa subunitcomplex I-AQDQmitochondrial respi
Modification date2020031320200313
UniProtAcc.

O43181

Ensembl transtripts involved in fusion geneENST00000502271, ENST00000504924, 
ENST00000507646, ENST00000510591, 
Fusion gene scores* DoF score18 X 13 X 7=16388 X 6 X 5=240
# samples 189
** MAII scorelog2(18/1638*10)=-3.18586654531133
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/240*10)=-1.41503749927884
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARL15 [Title/Abstract] AND NDUFS4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARL15(53606262)-NDUFS4(52942063), # 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 ARL15 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across NDUFS4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information
* 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
ChimerDB4Non-CancerTCGA-BH-A1FN-11AARL15chr5

53606262

-NDUFS4chr5

52942063

+


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Fusion Gene ORF analysis for ARL15-NDUFS4

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-3CDSENST00000502271ENST00000296684ARL15chr5

53606262

-NDUFS4chr5

52942063

+
In-frameENST00000504924ENST00000296684ARL15chr5

53606262

-NDUFS4chr5

52942063

+
In-frameENST00000507646ENST00000296684ARL15chr5

53606262

-NDUFS4chr5

52942063

+
intron-3CDSENST00000510591ENST00000296684ARL15chr5

53606262

-NDUFS4chr5

52942063

+

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)
ENST00000504924ARL15chr553606262-ENST00000296684NDUFS4chr552942063+6101421492163
ENST00000507646ARL15chr553606262-ENST00000296684NDUFS4chr552942063+6131451495164

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
ENST00000504924ENST00000296684ARL15chr553606262-NDUFS4chr552942063+0.0066008620.99339914
ENST00000507646ENST00000296684ARL15chr553606262-NDUFS4chr552942063+0.0067195480.9932805

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Fusion Genomic Features for ARL15-NDUFS4


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)
ARL15chr553606261-NDUFS4chr552942062+0.097931990.90206796
ARL15chr553606261-NDUFS4chr552942062+0.097931990.90206796

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.
genomic feature

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.
genomic feature of top 1%

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Fusion Protein Features for ARL15-NDUFS4


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/chr5:53606262/chr5:52942063)
- 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
.NDUFS4

O43181

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. {ECO:0000269|PubMed:11181577, ECO:0000269|PubMed:12611891, ECO:0000269|PubMed:9463323}.

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
HgeneARL15chr5:53606262chr5:52942063ENST00000504924-15142_14516205.0Nucleotide bindingGTP
HgeneARL15chr5:53606262chr5:52942063ENST00000504924-1539_4616205.0Nucleotide bindingGTP
HgeneARL15chr5:53606262chr5:52942063ENST00000504924-1582_8616205.0Nucleotide bindingGTP


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Fusion Gene Sequence for ARL15-NDUFS4


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.
>6566_6566_1_ARL15-NDUFS4_ARL15_chr5_53606262_ENST00000504924_NDUFS4_chr5_52942063_ENST00000296684_length(transcript)=610nt_BP=142nt
GTTGCTGGCTTTTTCAGGAGCTGCTCGCTCGCAGCCAGAGACGCTGCTTTTTTTTTCCGGGTTCGGAGCCGTTCCGGATGCTTTAGGCTG
CCGGATGTCTGATCTCCGAATAACTGAGGCGTTTCTGTACATGGATTATCTGGATATCACTACTTTAACTGGAGTTCCAGAAGAGCATAT
AAAAACTAGAAAAGTCAGGATCTTTGTTCCTGCTCGCAATAACATGCAGTCTGGAGTAAACAACACAAAGAAATGGAAGATGGAGTTTGA
TACCAGAGAGCGATGGGAAAATCCTTTGATGGGTTGGGCATCAACGGCTGATCCCTTATCCAACATGGTTCTAACCTTCAGTACTAAAGA
AGATGCAGTTTCCTTTGCAGAAAAAAATGGATGGAGCTATGACATTGAAGAGAGGAAGGTTCCAAAACCCAAGTCCAAGTCTTATGGTGC
AAACTTTTCTTGGAACAAAAGAACAAGAGTATCCACAAAATAGGTTGGCACTGACTATATCTCTGCTTGACTGTGAATAAAGTCAGCTGT

>6566_6566_1_ARL15-NDUFS4_ARL15_chr5_53606262_ENST00000504924_NDUFS4_chr5_52942063_ENST00000296684_length(amino acids)=163AA_BP=47
LLAFSGAARSQPETLLFFSGFGAVPDALGCRMSDLRITEAFLYMDYLDITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKKWKMEFD

--------------------------------------------------------------
>6566_6566_2_ARL15-NDUFS4_ARL15_chr5_53606262_ENST00000507646_NDUFS4_chr5_52942063_ENST00000296684_length(transcript)=613nt_BP=145nt
GCTGTTGCTGGCTTTTTCAGGAGCTGCTCGCTCGCAGCCAGAGACGCTGCTTTTTTTTTCCGGGTTCGGAGCCGTTCCGGATGCTTTAGG
CTGCCGGATGTCTGATCTCCGAATAACTGAGGCGTTTCTGTACATGGATTATCTGGATATCACTACTTTAACTGGAGTTCCAGAAGAGCA
TATAAAAACTAGAAAAGTCAGGATCTTTGTTCCTGCTCGCAATAACATGCAGTCTGGAGTAAACAACACAAAGAAATGGAAGATGGAGTT
TGATACCAGAGAGCGATGGGAAAATCCTTTGATGGGTTGGGCATCAACGGCTGATCCCTTATCCAACATGGTTCTAACCTTCAGTACTAA
AGAAGATGCAGTTTCCTTTGCAGAAAAAAATGGATGGAGCTATGACATTGAAGAGAGGAAGGTTCCAAAACCCAAGTCCAAGTCTTATGG
TGCAAACTTTTCTTGGAACAAAAGAACAAGAGTATCCACAAAATAGGTTGGCACTGACTATATCTCTGCTTGACTGTGAATAAAGTCAGC

>6566_6566_2_ARL15-NDUFS4_ARL15_chr5_53606262_ENST00000507646_NDUFS4_chr5_52942063_ENST00000296684_length(amino acids)=164AA_BP=48
LLLAFSGAARSQPETLLFFSGFGAVPDALGCRMSDLRITEAFLYMDYLDITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKKWKMEF

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Fusion Gene PPI Analysis for ARL15-NDUFS4


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 ARL15-NDUFS4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneNDUFS4O43181DB00157NADHSmall moleculeApproved|Nutraceutical

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Related Diseases for ARL15-NDUFS4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0023264Leigh Disease14CLINGEN;CTD_human;GENOMICS_ENGLAND
TgeneC1838951LEIGH SYNDROME DUE TO MITOCHONDRIAL COMPLEX I DEFICIENCY12CLINGEN
TgeneC1850597Leigh Syndrome Due To Mitochondrial Complex II Deficiency12CLINGEN
TgeneC1850598Leigh Syndrome due to Mitochondrial Complex III Deficiency12CLINGEN
TgeneC1850599Leigh Syndrome due to Mitochondrial Complex IV Deficiency12CLINGEN
TgeneC1850600Leigh Syndrome due to Mitochondrial Complex V Deficiency12CLINGEN
TgeneC2931891Necrotizing encephalopathy, infantile subacute, of Leigh12CLINGEN
TgeneC1838979MITOCHONDRIAL COMPLEX I DEFICIENCY10CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0751267Encephalopathy, Subacute Necrotizing, Infantile1CTD_human
TgeneC0751268Encephalopathy, Subacute Necrotizing, Juvenile1CTD_human
TgeneC0751651Mitochondrial Diseases1GENOMICS_ENGLAND