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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:SLX1B-FOXRED1 (FusionGDB2 ID:83155)

Fusion Gene Summary for SLX1B-FOXRED1

check button Fusion gene summary
Fusion gene informationFusion gene name: SLX1B-FOXRED1
Fusion gene ID: 83155
HgeneTgene
Gene symbol

SLX1B

FOXRED1

Gene ID

79008

55572

Gene nameSLX1 homolog B, structure-specific endonuclease subunitFAD dependent oxidoreductase domain containing 1
SynonymsGIYD2FP634|H17|MC1DN19
Cytomap

16p11.2

11q24.2

Type of geneprotein-codingprotein-coding
Descriptionstructure-specific endonuclease subunit SLX1GIY-YIG domain-containing protein 1SLX1 structure-specific endonuclease subunit homolog BFAD-dependent oxidoreductase domain-containing protein 1
Modification date2020031320200320
UniProtAcc.

Q96CU9

Ensembl transtripts involved in fusion geneENST00000330181, ENST00000351581, 
ENST00000263578, ENST00000534011, 
ENST00000442061, ENST00000532125, 
Fusion gene scores* DoF score3 X 2 X 3=185 X 4 X 4=80
# samples 35
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SLX1B [Title/Abstract] AND FOXRED1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSLX1B(29467206)-FOXRED1(126146965), # 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 SLX1B (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 FOXRED1 (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
ChimerDB4OVTCGA-30-1862SLX1Bchr16

29467206

+FOXRED1chr11

126146965

+


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Fusion Gene ORF analysis for SLX1B-FOXRED1

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
In-frameENST00000330181ENST00000263578SLX1Bchr16

29467206

+FOXRED1chr11

126146965

+
5CDS-3UTRENST00000330181ENST00000534011SLX1Bchr16

29467206

+FOXRED1chr11

126146965

+
5CDS-3UTRENST00000330181ENST00000442061SLX1Bchr16

29467206

+FOXRED1chr11

126146965

+
5CDS-3UTRENST00000330181ENST00000532125SLX1Bchr16

29467206

+FOXRED1chr11

126146965

+
intron-3CDSENST00000351581ENST00000263578SLX1Bchr16

29467206

+FOXRED1chr11

126146965

+
intron-3UTRENST00000351581ENST00000534011SLX1Bchr16

29467206

+FOXRED1chr11

126146965

+
intron-3UTRENST00000351581ENST00000442061SLX1Bchr16

29467206

+FOXRED1chr11

126146965

+
intron-3UTRENST00000351581ENST00000532125SLX1Bchr16

29467206

+FOXRED1chr11

126146965

+

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)
ENST00000330181SLX1Bchr1629467206+ENST00000263578FOXRED1chr11126146965+161982451183392

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
ENST00000330181ENST00000263578SLX1Bchr1629467206+FOXRED1chr11126146965+0.222692330.7773077

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Fusion Genomic Features for SLX1B-FOXRED1


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)
SLX1Bchr1629467206+FOXRED1chr11126146965+4.79E-060.99999523
SLX1Bchr1629467206+FOXRED1chr11126146965+4.79E-060.99999523

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 SLX1B-FOXRED1


check button Go to

FGviewer for the breakpoints of chr16:29467206-chr11:126146965

.
- 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
.FOXRED1

Q96CU9

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: Required for the assembly of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) (PubMed:20858599, PubMed:25678554). Involved in mid-late stages of complex I assembly (PubMed:25678554). {ECO:0000269|PubMed:20858599, ECO:0000269|PubMed:25678554}.

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
HgeneSLX1Bchr16:29467206chr11:126146965ENST00000330181+3612_95194.0276.0DomainGIY-YIG

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSLX1Bchr16:29467206chr11:126146965ENST00000351581+1512_950162.0DomainGIY-YIG
HgeneSLX1Bchr16:29467206chr11:126146965ENST00000330181+36186_238194.0276.0Zinc fingerSLX1-type
HgeneSLX1Bchr16:29467206chr11:126146965ENST00000351581+15186_2380162.0Zinc fingerSLX1-type
TgeneFOXRED1chr16:29467206chr11:126146965ENST0000026357881162_82367.0487.0TransmembraneHelical
TgeneFOXRED1chr16:29467206chr11:126146965ENST0000053212581162_82353.0473.0TransmembraneHelical


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Fusion Gene Sequence for SLX1B-FOXRED1


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.
>In-frame_ENST00000330181_ENST00000263578_TCGA-30-1862_SLX1B_chr16_29467206_+_FOXRED1_chr11_126146965_length(transcript)=1619nt_BP=824nt
GCTGAATGGTACGCGCTCGCCGACTGGACAGCAGTCTGGCTTCCGCGGTCGGACTTCTACACCCGCCTCCAGACAGGAGAGGGGCACGTA
CCGGCGCTACGGCTTCCTGCAGGCTGCCTCCGGATAGTCCCCGAGAGCTTGTTCCGAAGCAAGCACCCTGCAGCCCTAGCGATCCAGCCC
TCCCCTGGACCCTAGGTCACGGCAATCAACCCCCTGCTGTGGTTCCCGAACCCCAAGGCCCGATGGGTCCCGCGGGGGTCGCGGCGAGGC
CAGGGCGCTTTTTCGGCGTCTACCTGCTCTACTGCCTGAACCCCCGGTACCGGGGCCGCGTCTACGTGGGGTTCACTGTCAACACTGCTC
GTCGGGTCCAGCAGCACAATGGGGGCCGCAAAAAAGGCGGGGCCTGGCGGACCAGCGGGCGAGGGCCCTGGGAGATGGTGCTCGTCGTGC
ACGGCTTCCCGTCCTCCGTGGCCGCCCTTCGGTTTGAGTGGGCTTGGCAGCACCCGCACGCCTCGCGCCGCCTGGCGCACGTGGGGCCTC
GCCTGCGAGGAGAGACAGCCTTCGCTTTCCACCTGCGCGTGCTGGCGCACATGCTGCGCGCACCGCCCTGGGCTCGCCTCCCGCTCACGC
TGCGCTGGGTGCGCCCAGACCTCCGCCAGGACCTCTGCCTCCCGCCGCCGCCGCACGTGCCTCTGGCCTTCGGGCCTCCACCGCCCCAGG
CCCCGGCCCCAAGGCGCCGCGCAGGTCCCTTTGATGACGCGGAGCCTGAGCCAGACCAGGGGGATCCAGGGGCCTGCTGCTCCCTGTGCG
CCCAGACCATCCAGCAGGAAGAACCGGACCCGGCGAACCTGGAAGTGGACCATGATTTCTTCCAGGACAAGGTGTGGCCCCATTTGGCCC
TGAGGGTCCCAGCTTTTGAGACTCTGAAGGTTCAGAGCGCCTGGGCCGGCTATTACGACTACAACACCTTTGACCAGAATGGCGTGGTGG
GCCCCCACCCGCTAGTTGTCAACATGTACTTTGCTACTGGCTTCAGTGGTCACGGGCTCCAGCAGGCCCCTGGCATTGGGCGAGCTGTAG
CAGAGATGGTACTGAAGGGCAGGTTCCAGACCATCGACCTGAGCCCCTTCCTCTTTACCCGCTTTTACTTGGGAGAGAAGATCCAGGAGA
ACAACATCATCTGAGCATGTGTGCTCTGCACTGGCTCCACTGGCTTGCATCCTGGCTGTGTTCACAGCCTTGTTTGCTGCTTCCATCTTC
CCCAGTACTGTGCCAGGCCTTCTCCCCCTCCCCAGTGTCCTCTCCTCTCAGGCAGGCCATTGCACCCATATGGCTGGGCAGGCACAGGCA
GTGAGGCCGAGGCCAATAGCGAGTGATGAGCGGGATCCTAGGACTGATCTGTAGCCCATGCTGATGTCACCCACCAGGGCAATCCATCTG
GAGGCCTGAGCACCCTGGCCCAGGACTGGCTTCATCCTGGCACTGACCAGGAAAGACTGCCTCTGACCCTCTTAGCAGACAGAGCCCAGG

>In-frame_ENST00000330181_ENST00000263578_TCGA-30-1862_SLX1B_chr16_29467206_+_FOXRED1_chr11_126146965_length(amino acids)=392AA_start in transcript=5_stop in transcript=1183
MVRARRLDSSLASAVGLLHPPPDRRGARTGATASCRLPPDSPRELVPKQAPCSPSDPALPWTLGHGNQPPAVVPEPQGPMGPAGVAARPG
RFFGVYLLYCLNPRYRGRVYVGFTVNTARRVQQHNGGRKKGGAWRTSGRGPWEMVLVVHGFPSSVAALRFEWAWQHPHASRRLAHVGPRL
RGETAFAFHLRVLAHMLRAPPWARLPLTLRWVRPDLRQDLCLPPPPHVPLAFGPPPPQAPAPRRRAGPFDDAEPEPDQGDPGACCSLCAQ
TIQQEEPDPANLEVDHDFFQDKVWPHLALRVPAFETLKVQSAWAGYYDYNTFDQNGVVGPHPLVVNMYFATGFSGHGLQQAPGIGRAVAE

--------------------------------------------------------------

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Fusion Gene PPI Analysis for SLX1B-FOXRED1


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 SLX1B-FOXRED1


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 SLX1B-FOXRED1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneFOXRED1C0023264Leigh Disease6CLINGEN
TgeneFOXRED1C1838951LEIGH SYNDROME DUE TO MITOCHONDRIAL COMPLEX I DEFICIENCY6CLINGEN
TgeneFOXRED1C1850597Leigh Syndrome Due To Mitochondrial Complex II Deficiency6CLINGEN
TgeneFOXRED1C1850598Leigh Syndrome due to Mitochondrial Complex III Deficiency6CLINGEN
TgeneFOXRED1C1850599Leigh Syndrome due to Mitochondrial Complex IV Deficiency6CLINGEN
TgeneFOXRED1C1850600Leigh Syndrome due to Mitochondrial Complex V Deficiency6CLINGEN
TgeneFOXRED1C2931891Necrotizing encephalopathy, infantile subacute, of Leigh6CLINGEN
TgeneFOXRED1C1838979MITOCHONDRIAL COMPLEX I DEFICIENCY4GENOMICS_ENGLAND;ORPHANET
TgeneFOXRED1C4748791MITOCHONDRIAL COMPLEX I DEFICIENCY, NUCLEAR TYPE 193GENOMICS_ENGLAND;UNIPROT
TgeneFOXRED1C0751651Mitochondrial Diseases2CTD_human;GENOMICS_ENGLAND
TgeneFOXRED1C0162666Mitochondrial Encephalomyopathies1CTD_human
TgeneFOXRED1C0949855Electron Transport Chain Deficiencies, Mitochondrial1CTD_human
TgeneFOXRED1C0949856Oxidative Phosphorylation Deficiencies1CTD_human
TgeneFOXRED1C0949857Mitochondrial Respiratory Chain Deficiencies1CTD_human