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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:SEL1L3-COQ10A (FusionGDB2 ID:80205)

Fusion Gene Summary for SEL1L3-COQ10A

check button Fusion gene summary
Fusion gene informationFusion gene name: SEL1L3-COQ10A
Fusion gene ID: 80205
HgeneTgene
Gene symbol

SEL1L3

COQ10A

Gene ID

23231

93058

Gene nameSEL1L family member 3coenzyme Q10A
SynonymsSel-1L3-
Cytomap

4p15.2

12q13.3

Type of geneprotein-codingprotein-coding
Descriptionprotein sel-1 homolog 3sel-1 suppressor of lin-12-like 3suppressor of lin-12-like protein 3coenzyme Q-binding protein COQ10 homolog A, mitochondrialcoenzyme Q10 homolog A
Modification date2020031320200313
UniProtAcc.

Q96MF6

Ensembl transtripts involved in fusion geneENST00000264868, ENST00000399878, 
ENST00000502949, ENST00000513364, 
ENST00000308197, ENST00000433805, 
ENST00000546544, 
Fusion gene scores* DoF score11 X 12 X 7=9242 X 1 X 2=4
# samples 122
** MAII scorelog2(12/924*10)=-2.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/4*10)=2.32192809488736
Context

PubMed: SEL1L3 [Title/Abstract] AND COQ10A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSEL1L3(25803905)-COQ10A(56661578), # 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 SEL1L3 (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 COQ10A (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 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
ChimerDB4SARCTCGA-DX-A3LW-01ASEL1L3chr4

25803905

-COQ10Achr12

56661578

+


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Fusion Gene ORF analysis for SEL1L3-COQ10A

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
Frame-shiftENST00000264868ENST00000308197SEL1L3chr4

25803905

-COQ10Achr12

56661578

+
Frame-shiftENST00000264868ENST00000433805SEL1L3chr4

25803905

-COQ10Achr12

56661578

+
Frame-shiftENST00000264868ENST00000546544SEL1L3chr4

25803905

-COQ10Achr12

56661578

+
Frame-shiftENST00000399878ENST00000308197SEL1L3chr4

25803905

-COQ10Achr12

56661578

+
Frame-shiftENST00000399878ENST00000433805SEL1L3chr4

25803905

-COQ10Achr12

56661578

+
Frame-shiftENST00000399878ENST00000546544SEL1L3chr4

25803905

-COQ10Achr12

56661578

+
Frame-shiftENST00000502949ENST00000308197SEL1L3chr4

25803905

-COQ10Achr12

56661578

+
Frame-shiftENST00000502949ENST00000433805SEL1L3chr4

25803905

-COQ10Achr12

56661578

+
In-frameENST00000502949ENST00000546544SEL1L3chr4

25803905

-COQ10Achr12

56661578

+
intron-3CDSENST00000513364ENST00000308197SEL1L3chr4

25803905

-COQ10Achr12

56661578

+
intron-3CDSENST00000513364ENST00000433805SEL1L3chr4

25803905

-COQ10Achr12

56661578

+
intron-3CDSENST00000513364ENST00000546544SEL1L3chr4

25803905

-COQ10Achr12

56661578

+

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)
ENST00000502949SEL1L3chr425803905-ENST00000546544COQ10Achr1256661578+31541898172506829

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
ENST00000502949ENST00000546544SEL1L3chr425803905-COQ10Achr1256661578+0.0007037470.9992962

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Fusion Genomic Features for SEL1L3-COQ10A


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)
SEL1L3chr425803904-COQ10Achr1256661577+0.0023517510.9976483
SEL1L3chr425803904-COQ10Achr1256661577+0.0023517510.9976483

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 SEL1L3-COQ10A


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/chr4:25803905/chr12:56661578)
- 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
.COQ10A

Q96MF6

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: Required for the function of coenzyme Q in the respiratory chain. May serve as a chaperone or may be involved in the transport of Q6 from its site of synthesis to the catalytic sites of the respiratory complexes (Probable). {ECO:0000305}.

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
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000264868-1124575_6096171098.0RepeatNote=Sel1-like 1
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000399878-1124575_6096521133.0RepeatNote=Sel1-like 1
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000399878-1124611_6476521133.0RepeatNote=Sel1-like 2

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000264868-1124611_6476171098.0RepeatNote=Sel1-like 2
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000264868-1124694_7306171098.0RepeatNote=Sel1-like 3
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000264868-1124732_7676171098.0RepeatNote=Sel1-like 4
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000264868-1124768_8006171098.0RepeatNote=Sel1-like 5
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000264868-1124801_8396171098.0RepeatNote=Sel1-like 6
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000264868-1124840_8776171098.0RepeatNote=Sel1-like 7
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000264868-1124952_9886171098.0RepeatNote=Sel1-like 8
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000399878-1124694_7306521133.0RepeatNote=Sel1-like 3
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000399878-1124732_7676521133.0RepeatNote=Sel1-like 4
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000399878-1124768_8006521133.0RepeatNote=Sel1-like 5
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000399878-1124801_8396521133.0RepeatNote=Sel1-like 6
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000399878-1124840_8776521133.0RepeatNote=Sel1-like 7
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000399878-1124952_9886521133.0RepeatNote=Sel1-like 8
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000502949-1124575_609499980.0RepeatNote=Sel1-like 1
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000502949-1124611_647499980.0RepeatNote=Sel1-like 2
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000502949-1124694_730499980.0RepeatNote=Sel1-like 3
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000502949-1124732_767499980.0RepeatNote=Sel1-like 4
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000502949-1124768_800499980.0RepeatNote=Sel1-like 5
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000502949-1124801_839499980.0RepeatNote=Sel1-like 6
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000502949-1124840_877499980.0RepeatNote=Sel1-like 7
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000502949-1124952_988499980.0RepeatNote=Sel1-like 8
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000264868-11241057_10776171098.0TransmembraneHelical
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000399878-11241057_10776521133.0TransmembraneHelical
HgeneSEL1L3chr4:25803905chr12:56661578ENST00000502949-11241057_1077499980.0TransmembraneHelical


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Fusion Gene Sequence for SEL1L3-COQ10A


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.
>80205_80205_1_SEL1L3-COQ10A_SEL1L3_chr4_25803905_ENST00000502949_COQ10A_chr12_56661578_ENST00000546544_length(transcript)=3154nt_BP=1898nt
CACACTCGCCCTGCGCCCTGCGGGAATGGCGCCCCGGCCAAAAAAGCAACCAGACAAAAACCCATTGCACGGGCGGGAACTGGTCTGTGC
GACCCGCAAAAGGGAATGTTGTACCATCTTTGGGTAGGCAGACTTCCCTGACGACATCAGTGATACCCAAAGCTGAGCAGAGCGTGGCTT
ACAAAGACTTTATTTATTTTACTGTCTTTGAAGGAAACGTTCGCAACGTTTCTGAAGTCTCGGTTGAGTATTTATGCTCTCAGCCTTGTG
TTGTCAATTTGGAAGCAGTTGTTTCATCTGAGTTCAGAAGTAGCATTCCCGTGTACAAAAAAAGGTGGAAGAATGAGAAACATCTTCACA
CCAGCAGGACACAAATAGTACATGTGAAATTTCCAAGCATTATGGTTTACAGAGATGATTATTTCATCAGACATTCCATCTCTGTATCTG
CAGTGATAGTACGCGCCTGGATTACTCACAAATACAGTGGCAGAGACTGGAATGTTAAATGGGAGGAAAACTTGCTCCATGCTGTAGCAA
AGAATTATACCCTCCTGCAGACCATCCCGCCTTTTGAACGCCCTTTCAAAGATCATCAAGTGTGCCTTGAGTGGAACATGGGTTATATTT
GGAACCTTCGGGCAAACAGGATTCCACAGTGTCCTCTGGAAAATGATGTGGTTGCCCTGCTTGGCTTTCCTTATGCCTCCAGTGGAGAAA
ACACAGGCATTGTCAAGAAGTTCCCGAGGTTTCGGAACCGAGAGCTGGAGGCCACTCGACGCCAGAGGATGGATTACCCAGTGTTTACTG
TTTCATTGTGGCTTTATTTACTCCATTATTGCAAGGCCAACCTCTGTGGGATTCTGTACTTTGTTGACTCTAATGAGATGTACGGCACAC
CTTCTGTATTTCTTACGGAAGAGGGCTATTTGCATATTCAGATGCATCTTGTCAAAGGGGAAGACCTTGCTGTAAAAACTAAATTCATCA
TACCTTTGAAGGAGTGGTTTCGACTGGATATCTCTTTTAACGGAGGCCAGATAGTAGTAACCACTAGCATTGGACAGGATTTGAAAAGCT
ACCACAATCAGACCATTAGCTTCCGGGAGGATTTCCATTATAATGACACAGCTGGGTACTTCATTATTGGAGGGAGCAGGTATGTGGCTG
GCATTGAAGGGTTTTTTGGACCCCTGAAGTACTATCGCCTTCGCAGTCTGCACCCCGCCCAGATTTTTAATCCCCTCCTTGAGAAGCAAC
TTGCTGAACAAATCAAGTTATATTATGAAAGGTGTGCTGAGGTTCAAGAAATAGTATCTGTGTATGCATCTGCAGCAAAGCACGGGGGCG
AGAGACAAGAAGCATGCCACCTCCACAACTCCTACCTGGACCTCCAGCGCAGGTATGGGAGACCCTCGATGTGCAGAGCCTTCCCCTGGG
AGAAGGAGCTGAAAGACAAACACCCCAGCTTGTTCCAGGCATTGCTGGAGATGGATCTGCTGACCGTGCCAAGGAACCAAAATGAATCTG
TATCAGAAATCGGTGGGAAGATATTTGAGAAGGCTGTAAAGAGACTCTCTAGCATTGATGGTCTTCACCAAATTAGCTCTATCGTCCCCT
TTCTGACGGATTCCAGCTGCTGTGGATACCATAAAGCATCCTACTACCTTGCAGTCTTTTATGAGACTGGATTAAATGTTCCTCGGGATC
AGCTGCAGGGCATGTTGTATAGTTTGGTTGGAGGCCAGGGGAGTGAGAGGCTGTCTTCAATGAATCTTGGGTATAAACACTACCAGGGTA
TTGACAACTACCCCCTGGACTGGGAACTGTCGTATGCCTACTACAGCAACATTGCCACCAAGACACCCCTTGACCAGCACACACTGCAAG
GAGATCAGTTTCTGACCTCCTGCAGCCTCCTCTTGCCTCGGGCTGCCCAGATCTTGGCGGCTGAGGCTGGCTTACCTTCGAGCCGTTCCT
TCATGGGATTTGCTGCTCCCTTCACCAACAAGCGAAAGGCTTACTCGGAGCGTAGAATCATGGGGTACTCAATGCAGGAGATGTATGAGG
TGGTGTCCAACGTCCAGGAGTATCGTGAGTTTGTGCCCTGGTGTAAGAAGTCTCTGGTGGTATCCAGCCGTAAGGGTCATTTGAAAGCCC
AGCTGGAGGTTGGCTTTCCACCTGTCATGGAACGTTACACCTCTGCAGTTTCCATGGTCAAACCTCACATGGTCAAGGCTGTTTGTACTG
ATGGCAAGCTCTTCAACCACTTAGAGACTATTTGGCGATTCAGCCCTGGTATTCCTGCCTATCCTCGAACCTGCACTGTGGACTTTTCGA
TTTCCTTTGAATTTCGTTCTCTGCTGCACTCCCAGCTGGCCACCATGTTTTTTGATGAGGTTGTCAAACAGAATGTTGCTGCCTTTGAGC
GTCGGGCAGCCACCAAGTTTGGTCCAGAAACAGCCATCCCCCGTGAACTGATGTTCCATGAGGTGCACCAGACTTGAGGCAAGGGATTGC
TCCCTGACCTCCCTTCTACCCCACTTCCCTACACAATTCTCTTATTTATTTGGTTTGGCTCCTGTTCCAATTTGAAAGGAGTCTGTGTTC
ATAATACTGTTTCTCCTCTCAATTTCCCAGAAATTGGGTTCTATGCTGGCTGGAAATGTTGGGGGAAAGAGAAGGCAAAGGATGTGGAAA
TGAGATGTGCTTAGGAAAGGGTCAGGCCCATCGTAGGAGCACCATATGCCTGCAGCCTTTTCACTACGAATTAGAATAAGGACTATGTGG
TTGTCTCTGGACCTTATCAAGACACCTTAGTGTCTGACCAGGGGACGATAGTAACTTTTCTAAGGATTGAATAAATTGAGCTTTTCTTCT
GGCACAGAGGTACTGAGTGGTAAGTAACTTTTACCCTGCCTGAGATTCCTCAGGAGAAAAGGCAACCTGCCTCCAGCCTGAAATACATAA
AGCCTCATTTTAAGACTGTAAGTCCATGCTGCCTGGCTACTAGAGAGCAAGGGGCTTTCTTACCACCAGTGCTGAGGAGAAAAGTACTGA
ACGGAAACGGAGTTGTCTTTGTACTCTTGAGTTGTACCTTATTCTTCCACTTGGCCTGAGTTTTTATAAAATTTCAATAAATTGTGACAG

>80205_80205_1_SEL1L3-COQ10A_SEL1L3_chr4_25803905_ENST00000502949_COQ10A_chr12_56661578_ENST00000546544_length(amino acids)=829AA_BP=627
MREWRPGQKSNQTKTHCTGGNWSVRPAKGNVVPSLGRQTSLTTSVIPKAEQSVAYKDFIYFTVFEGNVRNVSEVSVEYLCSQPCVVNLEA
VVSSEFRSSIPVYKKRWKNEKHLHTSRTQIVHVKFPSIMVYRDDYFIRHSISVSAVIVRAWITHKYSGRDWNVKWEENLLHAVAKNYTLL
QTIPPFERPFKDHQVCLEWNMGYIWNLRANRIPQCPLENDVVALLGFPYASSGENTGIVKKFPRFRNRELEATRRQRMDYPVFTVSLWLY
LLHYCKANLCGILYFVDSNEMYGTPSVFLTEEGYLHIQMHLVKGEDLAVKTKFIIPLKEWFRLDISFNGGQIVVTTSIGQDLKSYHNQTI
SFREDFHYNDTAGYFIIGGSRYVAGIEGFFGPLKYYRLRSLHPAQIFNPLLEKQLAEQIKLYYERCAEVQEIVSVYASAAKHGGERQEAC
HLHNSYLDLQRRYGRPSMCRAFPWEKELKDKHPSLFQALLEMDLLTVPRNQNESVSEIGGKIFEKAVKRLSSIDGLHQISSIVPFLTDSS
CCGYHKASYYLAVFYETGLNVPRDQLQGMLYSLVGGQGSERLSSMNLGYKHYQGIDNYPLDWELSYAYYSNIATKTPLDQHTLQGDQFLT
SCSLLLPRAAQILAAEAGLPSSRSFMGFAAPFTNKRKAYSERRIMGYSMQEMYEVVSNVQEYREFVPWCKKSLVVSSRKGHLKAQLEVGF
PPVMERYTSAVSMVKPHMVKAVCTDGKLFNHLETIWRFSPGIPAYPRTCTVDFSISFEFRSLLHSQLATMFFDEVVKQNVAAFERRAATK

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Fusion Gene PPI Analysis for SEL1L3-COQ10A


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 SEL1L3-COQ10A


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 SEL1L3-COQ10A


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