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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:COPZ1-HNRNPA1 (FusionGDB2 ID:18670)

Fusion Gene Summary for COPZ1-HNRNPA1

check button Fusion gene summary
Fusion gene informationFusion gene name: COPZ1-HNRNPA1
Fusion gene ID: 18670
HgeneTgene
Gene symbol

COPZ1

HNRNPA1

Gene ID

22818

3178

Gene nameCOPI coat complex subunit zeta 1heterogeneous nuclear ribonucleoprotein A1
SynonymsCGI-120|COPZ|HSPC181|zeta-COP|zeta1-COPALS19|ALS20|HNRPA1|HNRPA1L3|IBMPFD3|UP 1|hnRNP A1|hnRNP-A1
Cytomap

12q13.13

12q13.13

Type of geneprotein-codingprotein-coding
Descriptioncoatomer subunit zeta-1coatomer protein complex subunit zeta 1coatomer protein complex, subunit zetazeta-1 COPzeta-1-coat proteinheterogeneous nuclear ribonucleoprotein A1epididymis secretory sperm binding proteinhelix-destabilizing proteinheterogeneous nuclear ribonucleoprotein A1B proteinheterogeneous nuclear ribonucleoprotein B2 proteinheterogeneous nuclear ribonucleoprotei
Modification date2020031320200315
UniProtAcc

P61923

P09651

Ensembl transtripts involved in fusion geneENST00000262061, ENST00000455864, 
ENST00000549043, ENST00000551779, 
ENST00000552218, ENST00000552362, 
ENST00000553231, ENST00000548753, 
ENST00000416254, ENST00000548281, 
ENST00000549116, 		ENST00000547276, 
ENST00000551803, ENST00000330752, 
ENST00000340913, ENST00000546500, 
Fusion gene scores* DoF score12 X 4 X 10=4809 X 8 X 4=288
# samples 139
** MAII scorelog2(13/480*10)=-1.88452278258006
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/288*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COPZ1 [Title/Abstract] AND HNRNPA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOPZ1(54737100)-HNRNPA1(54677596), # samples:1
Anticipated loss of major functional domain due to fusion event.COPZ1-HNRNPA1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* 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
HgeneCOPZ1

GO:0006891

intra-Golgi vesicle-mediated transport

11056392

TgeneHNRNPA1

GO:0032212

positive regulation of telomere maintenance via telomerase

23935072

TgeneHNRNPA1

GO:0051168

nuclear export

8521471

TgeneHNRNPA1

GO:0051170

import into nucleus

8521471

TgeneHNRNPA1

GO:1903936

cellular response to sodium arsenite

27694260


check buttonFusion gene breakpoints across COPZ1 (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 HNRNPA1 (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
ChimerDB4LUADTCGA-MP-A4T8-01ACOPZ1chr12

54737100

+HNRNPA1chr12

54677596

+


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Fusion Gene ORF analysis for COPZ1-HNRNPA1

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-intronENST00000262061ENST00000547276COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000262061ENST00000551803COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000455864ENST00000547276COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000455864ENST00000551803COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000549043ENST00000547276COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000549043ENST00000551803COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000551779ENST00000547276COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000551779ENST00000551803COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000552218ENST00000547276COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000552218ENST00000551803COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000552362ENST00000547276COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000552362ENST00000551803COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000553231ENST00000547276COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5CDS-intronENST00000553231ENST00000551803COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5UTR-3CDSENST00000548753ENST00000330752COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5UTR-3CDSENST00000548753ENST00000340913COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5UTR-3CDSENST00000548753ENST00000546500COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5UTR-intronENST00000548753ENST00000547276COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
5UTR-intronENST00000548753ENST00000551803COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000262061ENST00000330752COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000262061ENST00000340913COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000262061ENST00000546500COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000455864ENST00000330752COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000455864ENST00000340913COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000455864ENST00000546500COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000549043ENST00000330752COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000549043ENST00000340913COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000549043ENST00000546500COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000551779ENST00000330752COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000551779ENST00000340913COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000551779ENST00000546500COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000552218ENST00000330752COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000552218ENST00000340913COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000552218ENST00000546500COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000552362ENST00000330752COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000552362ENST00000340913COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000552362ENST00000546500COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000553231ENST00000330752COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000553231ENST00000340913COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
Frame-shiftENST00000553231ENST00000546500COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-3CDSENST00000416254ENST00000330752COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-3CDSENST00000416254ENST00000340913COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-3CDSENST00000416254ENST00000546500COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-3CDSENST00000548281ENST00000330752COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-3CDSENST00000548281ENST00000340913COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-3CDSENST00000548281ENST00000546500COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-3CDSENST00000549116ENST00000330752COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-3CDSENST00000549116ENST00000340913COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-3CDSENST00000549116ENST00000546500COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-intronENST00000416254ENST00000547276COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-intronENST00000416254ENST00000551803COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-intronENST00000548281ENST00000547276COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-intronENST00000548281ENST00000551803COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-intronENST00000549116ENST00000547276COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+
intron-intronENST00000549116ENST00000551803COPZ1chr12

54737100

+HNRNPA1chr12

54677596

+

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 COPZ1-HNRNPA1


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)
COPZ1chr1254737100+HNRNPA1chr1254677595+0.050700840.94929916
COPZ1chr1254737100+HNRNPA1chr1254677595+0.050700840.94929916

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 COPZ1-HNRNPA1


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/:54737100/:54677596)
- 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
COPZ1

P61923

HNRNPA1

P09651

FUNCTION: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins (By similarity). The zeta subunit may be involved in regulating the coat assembly and, hence, the rate of biosynthetic protein transport due to its association-dissociation properties with the coatomer complex (By similarity). {ECO:0000250|UniProtKB:P53600}.FUNCTION: Involved in the packaging of pre-mRNA into hnRNP particles, transport of poly(A) mRNA from the nucleus to the cytoplasm and may modulate splice site selection (PubMed:17371836). May bind to specific miRNA hairpins (PubMed:28431233). Binds to the IRES and thereby inhibits the translation of the apoptosis protease activating factor APAF1 (PubMed:31498791). {ECO:0000269|PubMed:17371836, ECO:0000269|PubMed:28431233, ECO:0000269|PubMed:31498791}.; FUNCTION: (Microbial infection) May play a role in HCV RNA replication. {ECO:0000269|PubMed:17229681}.; FUNCTION: (Microbial infection) Cleavage by Enterovirus 71 protease 3C results in increased translation of apoptosis protease activating factor APAF1, leading to apoptosis. {ECO:0000269|PubMed:17229681}.

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 COPZ1-HNRNPA1


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 COPZ1-HNRNPA1


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 COPZ1-HNRNPA1


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 COPZ1-HNRNPA1


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