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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:BTNL9-KLC1 (FusionGDB2 ID:HG153579TG3831)

Fusion Gene Summary for BTNL9-KLC1

check button Fusion gene summary
Fusion gene informationFusion gene name: BTNL9-KLC1
Fusion gene ID: hg153579tg3831
HgeneTgene
Gene symbol

BTNL9

KLC1

Gene ID

153579

3831

Gene namebutyrophilin like 9kinesin light chain 1
SynonymsBTN3|BTN8|VDLS1900KLC|KNS2|KNS2A
Cytomap('BTNL9')('KLC1')

5q35.3

14q32.33

Type of geneprotein-codingprotein-coding
Descriptionbutyrophilin-like protein 9butyrophilin 3kinesin light chain 1kinesin 2 60/70kDamedulloblastoma antigen MU-MB-2.50
Modification date2020031320200313
UniProtAcc.

Q07866

Ensembl transtripts involved in fusion geneENST00000327705, ENST00000376841, 
ENST00000376842, ENST00000515271, 
ENST00000511589, 
Fusion gene scores* DoF score3 X 3 X 2=1820 X 16 X 10=3200
# samples 322
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(22/3200*10)=-3.86249647625007
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BTNL9 [Title/Abstract] AND KLC1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBTNL9(180477369)-KLC1(104166992), # 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 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
ChimerDB4BRCATCGA-B6-A0IE-01ABTNL9chr5

180477369

+KLC1chr14

104166992

+


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Fusion Gene ORF analysis for BTNL9-KLC1

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
5CDS-intronENST00000327705ENST00000246489BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000327705ENST00000334553BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000327705ENST00000347839BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000327705ENST00000380038BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000327705ENST00000389744BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000327705ENST00000445352BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000327705ENST00000452929BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000327705ENST00000553286BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000327705ENST00000554280BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000327705ENST00000555836BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000327705ENST00000557450BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000327705ENST00000557575BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000246489BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000334553BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000347839BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000380038BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000389744BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000445352BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000452929BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000553286BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000554280BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000555836BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000557450BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376841ENST00000557575BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000246489BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000334553BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000347839BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000380038BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000389744BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000445352BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000452929BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000553286BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000554280BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000555836BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000557450BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000376842ENST00000557575BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000246489BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000334553BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000347839BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000380038BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000389744BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000445352BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000452929BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000553286BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000554280BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000555836BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000557450BTNL9chr5

180477369

+KLC1chr14

104166992

+
5CDS-intronENST00000515271ENST00000557575BTNL9chr5

180477369

+KLC1chr14

104166992

+
Frame-shiftENST00000327705ENST00000348520BTNL9chr5

180477369

+KLC1chr14

104166992

+
Frame-shiftENST00000376841ENST00000348520BTNL9chr5

180477369

+KLC1chr14

104166992

+
Frame-shiftENST00000376842ENST00000348520BTNL9chr5

180477369

+KLC1chr14

104166992

+
Frame-shiftENST00000515271ENST00000348520BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-3CDSENST00000511589ENST00000348520BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000246489BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000334553BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000347839BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000380038BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000389744BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000445352BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000452929BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000553286BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000554280BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000555836BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000557450BTNL9chr5

180477369

+KLC1chr14

104166992

+
intron-intronENST00000511589ENST00000557575BTNL9chr5

180477369

+KLC1chr14

104166992

+

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 BTNL9-KLC1


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)
BTNL9chr5180477369+KLC1chr14104166991+0.0152623530.9847377
BTNL9chr5180477369+KLC1chr14104166991+0.0152623530.9847377


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 BTNL9-KLC1


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/:180477369/:104166992)
- 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
.KLC1

Q07866

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: Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport. The light chain may function in coupling of cargo to the heavy chain or in the modulation of its ATPase activity.

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 BTNL9-KLC1


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 BTNL9-KLC1


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 BTNL9-KLC1


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 BTNL9-KLC1


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