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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:TRAPPC11-KCNN4 (FusionGDB2 ID:93778)

Fusion Gene Summary for TRAPPC11-KCNN4

check button Fusion gene summary
Fusion gene informationFusion gene name: TRAPPC11-KCNN4
Fusion gene ID: 93778
HgeneTgene
Gene symbol

TRAPPC11

KCNN4

Gene ID

60684

3783

Gene nametrafficking protein particle complex 11potassium calcium-activated channel subfamily N member 4
SynonymsC4orf41|FOIGR|GRY|LGMD2S|LGMDR18DHS2|IK|IK1|IKCA1|KCA4|KCa3.1|SK4|hIKCa1|hKCa4|hSK4
Cytomap

4q35.1

19q13.31

Type of geneprotein-codingprotein-coding
Descriptiontrafficking protein particle complex subunit 11foie gras homologgryzun homologintermediate conductance calcium-activated potassium channel protein 4SKCa 4SKCa4potassium channel, calcium activated intermediate/small conductance subfamily N alpha, member 4potassium intermediate/small conductance calcium-activated channel, subfami
Modification date2020031320200329
UniProtAcc

Q7Z392

.
Ensembl transtripts involved in fusion geneENST00000511409, ENST00000334690, 
ENST00000357207, ENST00000512476, 
ENST00000262888, 
Fusion gene scores* DoF score7 X 7 X 5=2457 X 6 X 6=252
# samples 78
** MAII scorelog2(7/245*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/252*10)=-1.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TRAPPC11 [Title/Abstract] AND KCNN4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTRAPPC11(184589270)-KCNN4(44276287), # samples:2
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
TgeneKCNN4

GO:0006816

calcium ion transport

18796614

TgeneKCNN4

GO:0030322

stabilization of membrane potential

18796614

TgeneKCNN4

GO:0050862

positive regulation of T cell receptor signaling pathway

18796614


check buttonFusion gene breakpoints across TRAPPC11 (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 KCNN4 (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
ChimerDB4UCECTCGA-EY-A4KR-01ATRAPPC11chr4

184589270

+KCNN4chr19

44276287

-


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Fusion Gene ORF analysis for TRAPPC11-KCNN4

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
3UTR-3CDSENST00000511409ENST00000262888TRAPPC11chr4

184589270

+KCNN4chr19

44276287

-
In-frameENST00000334690ENST00000262888TRAPPC11chr4

184589270

+KCNN4chr19

44276287

-
In-frameENST00000357207ENST00000262888TRAPPC11chr4

184589270

+KCNN4chr19

44276287

-
intron-3CDSENST00000512476ENST00000262888TRAPPC11chr4

184589270

+KCNN4chr19

44276287

-

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)
ENST00000334690TRAPPC11chr4184589270+ENST00000262888KCNN4chr1944276287-1923762101362450
ENST00000357207TRAPPC11chr4184589270+ENST00000262888KCNN4chr1944276287-1897736321336434

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
ENST00000334690ENST00000262888TRAPPC11chr4184589270+KCNN4chr1944276287-0.0080278960.9919721
ENST00000357207ENST00000262888TRAPPC11chr4184589270+KCNN4chr1944276287-0.0086705160.99132943

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Fusion Genomic Features for TRAPPC11-KCNN4


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.
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.

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Fusion Protein Features for TRAPPC11-KCNN4


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/chr4:184589270/chr19:44276287)
- 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
TRAPPC11

Q7Z392

.
FUNCTION: Involved in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage. {ECO:0000269|PubMed:21525244, ECO:0000269|PubMed:27862579}.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}.

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
TgeneKCNN4chr4:184589270chr19:44276287ENST0000026288829241_261227452.6666666666667IntramembranePore-forming%3B Name%3DSegment H5
TgeneKCNN4chr4:184589270chr19:44276287ENST0000026288829286_347227452.6666666666667RegionNote=Calmodulin-binding
TgeneKCNN4chr4:184589270chr19:44276287ENST0000026288829265_285227452.6666666666667TransmembraneHelical%3B Name%3DSegment S6

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneKCNN4chr4:184589270chr19:44276287ENST0000026288829108_128227452.6666666666667TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNN4chr4:184589270chr19:44276287ENST0000026288829143_163227452.6666666666667TransmembraneHelical%3B Name%3DSegment S4
TgeneKCNN4chr4:184589270chr19:44276287ENST0000026288829207_227227452.6666666666667TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNN4chr4:184589270chr19:44276287ENST000002628882929_49227452.6666666666667TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNN4chr4:184589270chr19:44276287ENST000002628882959_79227452.6666666666667TransmembraneHelical%3B Name%3DSegment S2


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Fusion Gene Sequence for TRAPPC11-KCNN4


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.
>93778_93778_1_TRAPPC11-KCNN4_TRAPPC11_chr4_184589270_ENST00000334690_KCNN4_chr19_44276287_ENST00000262888_length(transcript)=1923nt_BP=762nt
AAAGTGCTTCCTGTGCCGGGGGAGGTGGGTACAGGGAAGTCTCGCCTGTTGGAACTGGCTGTGGGGCTGCGGCGGTGGGGACGGGCCACG
GCGTTCTGTGACATCCCCCCGCCTCCCCTCGTCTTCTCCCGGCTGGCGGCGACCGGCCTCAGCTGCAGCGGGCCCGGGGCGTGGGGCCTG
GGTTTTTTGTGACATCGTAAACATGAGCCCCACACAGTGGGACTTCCCTGTGGAATTATGTTGCCGGCCTATGGCCTTTGTTACTCTAAC
GGGCCTGGATGTAGTTTATAATGCAGTCCATCGAGCTGTCTGGGACGCCTTCTGTGCAAATCGGAGAGCTGATCGAGTACCAATTTCTTT
CAAGGTGCTCCCAGGTGACCATGAGTATCCCAAATGTAGACCCAAGAGAACTTCATATGAGTGGTACATTCCTAAAGGGATCTTAAAGAC
TGGCTGGATGAATAAGCATCTGAATCTGGTGCCAGCCCTGGTGGTTGTGTTCTATGAACTGGACTGGGATGAGCCTCAGTGGAAAGAAAA
GCAGTCTGAGTGCGCCACCAGAGTGGAAATAGTCAGGCAAAGTTTACAAGGAAGAAACACAAAAGTTGCAGTGGTTCTGATTCAGAAGAA
AACCCCTTTGCCCCCAGGAGAAGATGTCATTGCTTCAGAAAGGGCTGCAGCTTTATGCAATGCATGTGAACTCTCAGGAAAGTCTTTGTT
TGTACTGCCGCACACTGACCACCTTGTGGGTTATATTATAAGGCAGGCTGTTAATGCCACTGGGCACCTTTCAGACACACTTTGGCTGAT
CCCCATCACATTCCTGACCATCGGCTATGGTGACGTGGTGCCGGGCACCATGTGGGGCAAGATCGTCTGCCTGTGCACTGGAGTCATGGG
TGTCTGCTGCACAGCCCTGCTGGTGGCCGTGGTGGCCCGGAAGCTGGAGTTTAACAAGGCAGAGAAGCACGTGCACAACTTCATGATGGA
TATCCAGTATACCAAAGAGATGAAGGAGTCCGCTGCCCGAGTGCTACAAGAAGCCTGGATGTTCTACAAACATACTCGCAGGAAGGAGTC
TCATGCTGCCCGCAGGCATCAGCGCAAGCTGCTGGCCGCCATCAACGCGTTCCGCCAGGTGCGGCTGAAACACCGGAAGCTCCGGGAACA
AGTGAACTCCATGGTGGACATCTCCAAGATGCACATGATCCTGTATGACCTGCAGCAGAATCTGAGCAGCTCACACCGGGCCCTGGAGAA
ACAGATTGACACGCTGGCGGGGAAGCTGGATGCCCTGACTGAGCTGCTTAGCACTGCCCTGGGGCCGAGGCAGCTTCCAGAACCCAGCCA
GCAGTCCAAGTAGCTGGACCCACGAGGAGGAACCAGGCTACTTTCCCCAGTACTGAGGTGGTGGACATCGTCTCTGCCACTCCTGACCCA
GCCCTGAACAAAGCACCTCAAGTGCAAGGACCAAAGGGGGCCCTGGCTTGGAGTGGGTTGGCTTGCTGATGGCTGCTGGAGGGGACGCTG
GCTAAAGTGGGTAGGCCTTGGCCCACCTGAGGCCCCAGGTGGGAACATGGTCACCCCCACTCTGCATACCCTCATCAAAAACACTCTCAC
TATGCTGCTATGGACGACCTCCAGCTCTCAGTTACAAGTGCAGGCGACTGGAGGCAGGACTCCTGGGTCCCTGGGAAAGAGGGTACTAGG
GGCCCGGATCCAGGATTCTGGGAGGCTTCAGTTACCGCTGGCCGAGCTGAAGAACTGGGTATGAGGCTGGGGCGGGGCTGGAGGTGGCGC
CCCCTGGTGGGACAACAAAGAGGACACCATTTTTCCAGAGCTGCAGAGAGCACCTGGTGGGGAGGAAGAAGTGTAACTCACCAGCCTCTG

>93778_93778_1_TRAPPC11-KCNN4_TRAPPC11_chr4_184589270_ENST00000334690_KCNN4_chr19_44276287_ENST00000262888_length(amino acids)=450AA_BP=250
MCRGRWVQGSLACWNWLWGCGGGDGPRRSVTSPRLPSSSPGWRRPASAAAGPGRGAWVFCDIVNMSPTQWDFPVELCCRPMAFVTLTGLD
VVYNAVHRAVWDAFCANRRADRVPISFKVLPGDHEYPKCRPKRTSYEWYIPKGILKTGWMNKHLNLVPALVVVFYELDWDEPQWKEKQSE
CATRVEIVRQSLQGRNTKVAVVLIQKKTPLPPGEDVIASERAAALCNACELSGKSLFVLPHTDHLVGYIIRQAVNATGHLSDTLWLIPIT
FLTIGYGDVVPGTMWGKIVCLCTGVMGVCCTALLVAVVARKLEFNKAEKHVHNFMMDIQYTKEMKESAARVLQEAWMFYKHTRRKESHAA
RRHQRKLLAAINAFRQVRLKHRKLREQVNSMVDISKMHMILYDLQQNLSSSHRALEKQIDTLAGKLDALTELLSTALGPRQLPEPSQQSK

--------------------------------------------------------------
>93778_93778_2_TRAPPC11-KCNN4_TRAPPC11_chr4_184589270_ENST00000357207_KCNN4_chr19_44276287_ENST00000262888_length(transcript)=1897nt_BP=736nt
GGGTACAGGGAAGTCTCGCCTGTTGGAACTGGCTGTGGGGCTGCGGCGGTGGGGACGGGCCACGGCGTTCTGTGACATCCCCCCGCCTCC
CCTCGTCTTCTCCCGGCTGGCGGCGACCGGCCTCAGCTGCAGCGGGCCCGGGGCGTGGGGCCTGGGTTTTTTGTGACATCGTAAACATGA
GCCCCACACAGTGGGACTTCCCTGTGGAATTATGTTGCCGGCCTATGGCCTTTGTTACTCTAACGGGCCTGGATGTAGTTTATAATGCAG
TCCATCGAGCTGTCTGGGACGCCTTCTGTGCAAATCGGAGAGCTGATCGAGTACCAATTTCTTTCAAGGTGCTCCCAGGTGACCATGAGT
ATCCCAAATGTAGACCCAAGAGAACTTCATATGAGTGGTACATTCCTAAAGGGATCTTAAAGACTGGCTGGATGAATAAGCATCTGAATC
TGGTGCCAGCCCTGGTGGTTGTGTTCTATGAACTGGACTGGGATGAGCCTCAGTGGAAAGAAAAGCAGTCTGAGTGCGCCACCAGAGTGG
AAATAGTCAGGCAAAGTTTACAAGGAAGAAACACAAAAGTTGCAGTGGTTCTGATTCAGAAGAAAACCCCTTTGCCCCCAGGAGAAGATG
TCATTGCTTCAGAAAGGGCTGCAGCTTTATGCAATGCATGTGAACTCTCAGGAAAGTCTTTGTTTGTACTGCCGCACACTGACCACCTTG
TGGGTTATATTATAAGGCAGGCTGTTAATGCCACTGGGCACCTTTCAGACACACTTTGGCTGATCCCCATCACATTCCTGACCATCGGCT
ATGGTGACGTGGTGCCGGGCACCATGTGGGGCAAGATCGTCTGCCTGTGCACTGGAGTCATGGGTGTCTGCTGCACAGCCCTGCTGGTGG
CCGTGGTGGCCCGGAAGCTGGAGTTTAACAAGGCAGAGAAGCACGTGCACAACTTCATGATGGATATCCAGTATACCAAAGAGATGAAGG
AGTCCGCTGCCCGAGTGCTACAAGAAGCCTGGATGTTCTACAAACATACTCGCAGGAAGGAGTCTCATGCTGCCCGCAGGCATCAGCGCA
AGCTGCTGGCCGCCATCAACGCGTTCCGCCAGGTGCGGCTGAAACACCGGAAGCTCCGGGAACAAGTGAACTCCATGGTGGACATCTCCA
AGATGCACATGATCCTGTATGACCTGCAGCAGAATCTGAGCAGCTCACACCGGGCCCTGGAGAAACAGATTGACACGCTGGCGGGGAAGC
TGGATGCCCTGACTGAGCTGCTTAGCACTGCCCTGGGGCCGAGGCAGCTTCCAGAACCCAGCCAGCAGTCCAAGTAGCTGGACCCACGAG
GAGGAACCAGGCTACTTTCCCCAGTACTGAGGTGGTGGACATCGTCTCTGCCACTCCTGACCCAGCCCTGAACAAAGCACCTCAAGTGCA
AGGACCAAAGGGGGCCCTGGCTTGGAGTGGGTTGGCTTGCTGATGGCTGCTGGAGGGGACGCTGGCTAAAGTGGGTAGGCCTTGGCCCAC
CTGAGGCCCCAGGTGGGAACATGGTCACCCCCACTCTGCATACCCTCATCAAAAACACTCTCACTATGCTGCTATGGACGACCTCCAGCT
CTCAGTTACAAGTGCAGGCGACTGGAGGCAGGACTCCTGGGTCCCTGGGAAAGAGGGTACTAGGGGCCCGGATCCAGGATTCTGGGAGGC
TTCAGTTACCGCTGGCCGAGCTGAAGAACTGGGTATGAGGCTGGGGCGGGGCTGGAGGTGGCGCCCCCTGGTGGGACAACAAAGAGGACA
CCATTTTTCCAGAGCTGCAGAGAGCACCTGGTGGGGAGGAAGAAGTGTAACTCACCAGCCTCTGCTCTTATCTTTGTAATAAATGTTAAA

>93778_93778_2_TRAPPC11-KCNN4_TRAPPC11_chr4_184589270_ENST00000357207_KCNN4_chr19_44276287_ENST00000262888_length(amino acids)=434AA_BP=234
MWGCGGGDGPRRSVTSPRLPSSSPGWRRPASAAAGPGRGAWVFCDIVNMSPTQWDFPVELCCRPMAFVTLTGLDVVYNAVHRAVWDAFCA
NRRADRVPISFKVLPGDHEYPKCRPKRTSYEWYIPKGILKTGWMNKHLNLVPALVVVFYELDWDEPQWKEKQSECATRVEIVRQSLQGRN
TKVAVVLIQKKTPLPPGEDVIASERAAALCNACELSGKSLFVLPHTDHLVGYIIRQAVNATGHLSDTLWLIPITFLTIGYGDVVPGTMWG
KIVCLCTGVMGVCCTALLVAVVARKLEFNKAEKHVHNFMMDIQYTKEMKESAARVLQEAWMFYKHTRRKESHAARRHQRKLLAAINAFRQ

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

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Fusion Gene PPI Analysis for TRAPPC11-KCNN4


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 TRAPPC11-KCNN4


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 TRAPPC11-KCNN4


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