Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:COX6A1-CAPZA1 (FusionGDB2 ID:HG1337TG829)

Fusion Gene Summary for COX6A1-CAPZA1

check button Fusion gene summary
Fusion gene informationFusion gene name: COX6A1-CAPZA1
Fusion gene ID: hg1337tg829
HgeneTgene
Gene symbol

COX6A1

CAPZA1

Gene ID

1337

829

Gene namecytochrome c oxidase subunit 6A1capping actin protein of muscle Z-line subunit alpha 1
SynonymsCMTRID|COX6A|COX6ALCAPPA1|CAPZ|CAZ1
Cytomap('COX6A1')('CAPZA1')

12q24.31|12q24.2

1p13.2

Type of geneprotein-codingprotein-coding
Descriptioncytochrome c oxidase subunit 6A1, mitochondrialCOX VIa-Lcytochrome C oxidase subunit VIa homologcytochrome c oxidase polypeptide VIa-livercytochrome c oxidase subunit VIA-livercytochrome c oxidase subunit VIa polypeptide 1F-actin-capping protein subunit alpha-1Cap ZcapZ alpha-1capping actin protein of muscle Z-line alpha subunit 1capping protein (actin filament) muscle Z-line, alpha 1
Modification date2020031320200327
UniProtAcc.

P52907

Ensembl transtripts involved in fusion geneENST00000229379, 
Fusion gene scores* DoF score5 X 4 X 3=6010 X 11 X 5=550
# samples 510
** MAII scorelog2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/550*10)=-2.4594316186373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COX6A1 [Title/Abstract] AND CAPZA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOX6A1(120876324)-CAPZA1(113201643), # 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 COX6A1 (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 CAPZA1 (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
* 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-09-2056COX6A1chr12

120876324

+CAPZA1chr1

113201643

+


Top

Fusion Gene ORF analysis for COX6A1-CAPZA1

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-3UTRENST00000229379ENST00000476936COX6A1chr12

120876324

+CAPZA1chr1

113201643

+
In-frameENST00000229379ENST00000263168COX6A1chr12

120876324

+CAPZA1chr1

113201643

+

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)
ENST00000229379COX6A1chr12120876324+ENST00000263168CAPZA1chr1113201643+220528316717233

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
ENST00000229379ENST00000263168COX6A1chr12120876324+CAPZA1chr1113201643+0.0004900310.99950993

Top

Fusion Genomic Features for COX6A1-CAPZA1


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)
COX6A1chr12120876324+CAPZA1chr1113201643+7.67E-121
COX6A1chr12120876324+CAPZA1chr1113201643+7.67E-121

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%

Top

Fusion Protein Features for COX6A1-CAPZA1


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/chr12:120876324/chr1:113201643)
- 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
.CAPZA1

P52907

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: F-actin-capping proteins bind in a Ca(2+)-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike other capping proteins (such as gelsolin and severin), these proteins do not sever actin filaments. May play a role in the formation of epithelial cell junctions. {ECO:0000269|PubMed:22891260}.

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
HgeneCOX6A1chr12:120876324chr1:113201643ENST00000229379+2325_3482110.0Topological domainMitochondrial matrix
HgeneCOX6A1chr12:120876324chr1:113201643ENST00000229379+2335_5982110.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCOX6A1chr12:120876324chr1:113201643ENST00000229379+2360_10982110.0Topological domainMitochondrial intermembrane


Top

Fusion Gene Sequence for COX6A1-CAPZA1


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.
>18802_18802_1_COX6A1-CAPZA1_COX6A1_chr12_120876324_ENST00000229379_CAPZA1_chr1_113201643_ENST00000263168_length(transcript)=2205nt_BP=283nt
ACTTCCGCTTCCGGCGCTGCGGCAGTCCAGATCAAAAATGGCGGTAGTTGGTGTGTCCTCGGTTTCTCGGCTGCTGGGTCGGTCCCGCCC
ACAGCTGGGGCGGCCTATGTCGAGTGGCGCCCATGGCGAAGAGGGCTCAGCTCGCATGTGGAAGACTCTCACCTTCTTCGTCGCGCTCCC
CGGGGTGGCAGTCAGCATGCTGAATGTGTACCTGAAGTCGCACCACGGAGAGCACGAGAGACCCGAGTTCATCGCCTACCCCCATCTCCG
CATCAGGACCAAGGTTTATGCTAAAACTATCGATGGGCAACAGACTATTATTGCATGTATTGAAAGCCACCAGTTTCAGCCTAAAAACTT
CTGGAATGGTCGTTGGAGATCAGAGTGGAAGTTCACCATCACACCACCTACAGCCCAGGTGGTTGGCGTGCTTAAGATTCAGGTTCACTA
TTATGAAGATGGCAATGTTCAGTTGGTTAGTCATAAAGATGTACAGGATTCACTAACTGTTTCGAATGAAGCCCAAACTGCCAAGGAGTT
TATTAAAATCATAGAGAATGCAGAAAATGAGTATCAGACAGCAATTAGTGAAAACTATCAAACAATGTCAGATACCACATTCAAGGCCTT
GCGCCGGCAGCTTCCAGTTACCCGCACCAAAATCGACTGGAACAAGATACTCAGCTACAAGATTGGCAAAGAAATGCAGAATGCTTAAAG
GCTGAATGTAGGATTCTTCAGTATGTGGAAAGACAAGGATTCAACGTGTGGTCATATGATAAATAAGTGATTTATAAACAAGAGTGATAT
TTTGCTAGGGCTTTCAAAGTTAACCGGTTTTCTAGCCTCATGGAATACTGTTGAACCTATAGCGTTGTCTTGATTCTTTTGTGTTCTCTG
CCTTGTAATTTTCTGTTACTGCTATATCTACGTGTAAATCTTTTTTTCTTTTTTTTTTTTTTTTTTTGGTTAATTCTGCCACATTTAATG
TTGGTGAGAGAGTGATCTATCCTAATGACATTTTACTGTTTAAAAAAGTTTCCTAGCCATGAAGCCCTGCTACTGATTTAGACAAGGTAT
TATGGTCATTACTTTGTACCCCTATCCTTCCAAGCACTTCTGGTACTTCAGTCGTTTTTACTGATCCACCAACACCTAAAGAGGCTATGC
TACAGTCTCTAGCTAAATGGAAGACACATTCATCCTTCTCCCTCTGACTGCTTTGATCATCATTTATTGCATCTCATAACTAATTTTCTA
AAGTTTGGATTGGGACTTTTCAGGTCCTTTTTGGAGGGCAAAGGAAGTGCCAGCTTCTCTGGGGAACTTGTTTTTAAATCCAAAGACTTG
AACCACATTCCCTGCACATGAACATGTTTGCTTTTATCCCTTCTCTCATTGTCTCCTTCCCATCTTAGTACCATTGTAGTTATAAACATC
TGCATTTTTTAGAAGCATTTTACCCATTTATTTTTTTAAACATTCAAGAACTGCTGACGTACTGTGGATGTAGAGTATAAAACTTGAAAA
ATGCAGATGTTGAAGGAATAATAGGTATCTTGTGCTTTAATACTTTATGGCAGGATTGTACTATAAGCAAATGAATTAAACAGCTATGTA
AATCATAAAGAAAAACTAAAAATGAACCAAAGTGAAAGGATAACTTCCAGGCAGTATCTTTCTATTGTAACCTGTTATTTAAGGAAATAC
TAGTGATTTCTTCTAAATAGGATGTAAAACTTCTTTCAAATTACTCTTCCTCAGTCCTGCCTGCCAAGAACTCAAGTGTAACTGTGATAA
AATAACCTTTCCCAGGTATATTGGCAGGTATGTGTGTAATCTCAGAATACACAGGTGACATAGATATGATATGACAACTGGTAATGGTGG
ATTCATTTACATTGTTTACACTTCTATGACCAGGCCTTAAGGGAAGGTCAGTTTTTTAAAAAACCAAGTAGTGTCTTCCTACCTATCTCC
AGATACATGTCAAAAAAAGAAAGGTGTTTGTGCTTCCGTTTTGTTTCTGCTCAGTAATATAGTCAAGCAAGTTTGTTCCAGGTGACCCAT
TGAGCTGTGTATGCATTTTTGTTTATTTCAATAAAATATATTTGTATTATTTGTCCTTCATACTATCCATCCATACCACACTATCTTCTG

>18802_18802_1_COX6A1-CAPZA1_COX6A1_chr12_120876324_ENST00000229379_CAPZA1_chr1_113201643_ENST00000263168_length(amino acids)=233AA_BP=89
MRQSRSKMAVVGVSSVSRLLGRSRPQLGRPMSSGAHGEEGSARMWKTLTFFVALPGVAVSMLNVYLKSHHGEHERPEFIAYPHLRIRTKV
YAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSLTVSNEAQTAKEFIKIIE

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

Top

Fusion Gene PPI Analysis for COX6A1-CAPZA1


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


Top

Related Drugs for COX6A1-CAPZA1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for COX6A1-CAPZA1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOX6A1C4015029CHARCOT-MARIE-TOOTH DISEASE, RECESSIVE INTERMEDIATE D1CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0279626Squamous cell carcinoma of esophagus1CTD_human