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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:SEC23A-KNTC1 (FusionGDB2 ID:80045)

Fusion Gene Summary for SEC23A-KNTC1

check button Fusion gene summary
Fusion gene informationFusion gene name: SEC23A-KNTC1
Fusion gene ID: 80045
HgeneTgene
Gene symbol

SEC23A

KNTC1

Gene ID

10484

9735

Gene nameSec23 homolog A, COPII coat complex componentkinetochore associated 1
SynonymsCLSD|hSec23AROD
Cytomap

14q21.1

12q24.31

Type of geneprotein-codingprotein-coding
Descriptionprotein transport protein Sec23ASEC23-related protein ASec23 homolog A, coat complex II componentkinetochore-associated protein 1Rough Deal homolog, centromere/kinetochore protein
Modification date2020032720200313
UniProtAcc.

P50748

Ensembl transtripts involved in fusion geneENST00000307712, ENST00000536508, 
ENST00000545328, ENST00000548032, 
ENST00000553970, ENST00000557280, 
ENST00000537403, ENST00000553925, 
ENST00000333479, ENST00000450485, 
ENST00000436959, ENST00000534995, 
ENST00000537348, ENST00000545065, 
Fusion gene scores* DoF score10 X 12 X 6=72011 X 16 X 6=1056
# samples 1214
** MAII scorelog2(12/720*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/1056*10)=-2.91511110241349
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SEC23A [Title/Abstract] AND KNTC1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSEC23A(39572235)-KNTC1(123097658), # 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
HgeneSEC23A

GO:0090110

cargo loading into COPII-coated vesicle

17499046|18843296

TgeneKNTC1

GO:0007093

mitotic cell cycle checkpoint

11146660


check buttonFusion gene breakpoints across SEC23A (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 KNTC1 (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
ChimerDB4STADTCGA-BR-A4PDSEC23Achr14

39572235

-KNTC1chr12

123097658

+


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Fusion Gene ORF analysis for SEC23A-KNTC1

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-3CDSENST00000307712ENST00000333479SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-3CDSENST00000307712ENST00000450485SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-3CDSENST00000536508ENST00000333479SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-3CDSENST00000536508ENST00000450485SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-3CDSENST00000545328ENST00000333479SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-3CDSENST00000545328ENST00000450485SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-3CDSENST00000548032ENST00000333479SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-3CDSENST00000548032ENST00000450485SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-3CDSENST00000553970ENST00000333479SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-3CDSENST00000553970ENST00000450485SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-3CDSENST00000557280ENST00000333479SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-3CDSENST00000557280ENST00000450485SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-5UTRENST00000307712ENST00000436959SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-5UTRENST00000536508ENST00000436959SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-5UTRENST00000545328ENST00000436959SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-5UTRENST00000548032ENST00000436959SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-5UTRENST00000553970ENST00000436959SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-5UTRENST00000557280ENST00000436959SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000307712ENST00000534995SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000307712ENST00000537348SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000307712ENST00000545065SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000536508ENST00000534995SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000536508ENST00000537348SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000536508ENST00000545065SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000545328ENST00000534995SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000545328ENST00000537348SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000545328ENST00000545065SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000548032ENST00000534995SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000548032ENST00000537348SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000548032ENST00000545065SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000553970ENST00000534995SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000553970ENST00000537348SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000553970ENST00000545065SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000557280ENST00000534995SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000557280ENST00000537348SEC23Achr14

39572235

-KNTC1chr12

123097658

+
5UTR-intronENST00000557280ENST00000545065SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-3CDSENST00000537403ENST00000333479SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-3CDSENST00000537403ENST00000450485SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-3CDSENST00000553925ENST00000333479SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-3CDSENST00000553925ENST00000450485SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-5UTRENST00000537403ENST00000436959SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-5UTRENST00000553925ENST00000436959SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-intronENST00000537403ENST00000534995SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-intronENST00000537403ENST00000537348SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-intronENST00000537403ENST00000545065SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-intronENST00000553925ENST00000534995SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-intronENST00000553925ENST00000537348SEC23Achr14

39572235

-KNTC1chr12

123097658

+
intron-intronENST00000553925ENST00000545065SEC23Achr14

39572235

-KNTC1chr12

123097658

+

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 SEC23A-KNTC1


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)
SEC23Achr1439572235-KNTC1chr12123097658+5.07E-060.9999949
SEC23Achr1439572235-KNTC1chr12123097658+5.07E-060.9999949

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.
genomic feature of top 1%

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Fusion Protein Features for SEC23A-KNTC1


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/:39572235/:123097658)
- 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
.KNTC1

P50748

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: Essential component of the mitotic checkpoint, which prevents cells from prematurely exiting mitosis. Required for the assembly of the dynein-dynactin and MAD1-MAD2 complexes onto kinetochores (PubMed:11146660, PubMed:11590237, PubMed:15824131). Its function related to the spindle assembly machinery is proposed to depend on its association in the mitotic RZZ complex. {ECO:0000269|PubMed:11146660, ECO:0000269|PubMed:11590237, ECO:0000269|PubMed:15824131, 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

- 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 SEC23A-KNTC1


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 SEC23A-KNTC1


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 SEC23A-KNTC1


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 SEC23A-KNTC1


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