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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:SEC31A-ARPC5 (FusionGDB2 ID:79611)

Fusion Gene Summary for SEC31A-ARPC5

check button Fusion gene summary
Fusion gene informationFusion gene name: SEC31A-ARPC5
Fusion gene ID: 79611
HgeneTgene
Gene symbol

SEC31A

ARPC5

Gene ID

22872

10092

Gene nameSEC31 homolog A, COPII coat complex componentactin related protein 2/3 complex subunit 5
SynonymsABP125|ABP130|HSPC275|HSPC334|NEDSOSB|SEC31L1ARC16|dJ127C7.3|p16-Arc
Cytomap

4q21.22

1q25.3

Type of geneprotein-codingprotein-coding
Descriptionprotein transport protein Sec31ASEC31 homolog A, COPII coating complex componentSEC31-like protein 1SEC31-related protein Aweb1-like proteinyeast Sec31p homologactin-related protein 2/3 complex subunit 5Arp2/3 protein complex subunit p16actin related protein 2/3 complex, subunit 5, 16kDaarp2/3 complex 16 kDa subunit
Modification date2020031320200313
UniProtAcc.

Q9BPX5

Ensembl transtripts involved in fusion geneENST00000348405, ENST00000513858, 
ENST00000395310, ENST00000443462, 
ENST00000509142, ENST00000326950, 
ENST00000432794, ENST00000311785, 
ENST00000448323, ENST00000505472, 
ENST00000500777, ENST00000508502, 
ENST00000355196, ENST00000264405, 
ENST00000505984, ENST00000508479, 
ENST00000436790, 		ENST00000367534, 
ENST00000462965, ENST00000359856, 
ENST00000294742, 
Fusion gene scores* DoF score22 X 23 X 10=50606 X 9 X 2=108
# samples 257
** MAII scorelog2(25/5060*10)=-4.33913738491959
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/108*10)=-0.625604485218502
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SEC31A [Title/Abstract] AND ARPC5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSEC31A(83745811)-ARPC5(183602237), # 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
HgeneSEC31A

GO:0051592

response to calcium ion

17196169

HgeneSEC31A

GO:0090110

cargo loading into COPII-coated vesicle

17499046|18843296

TgeneARPC5

GO:0034314

Arp2/3 complex-mediated actin nucleation

11741539


check buttonFusion gene breakpoints across SEC31A (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 ARPC5 (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
ChiTaRS5.0N/ABM992139SEC31Achr4

83745811

+ARPC5chr1

183602237

+


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Fusion Gene ORF analysis for SEC31A-ARPC5

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
intron-3CDSENST00000348405ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000348405ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000348405ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000348405ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000513858ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000513858ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000513858ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000513858ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000395310ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000395310ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000395310ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000395310ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000443462ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000443462ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000443462ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000443462ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000509142ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000509142ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000509142ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000509142ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000326950ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000326950ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000326950ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000326950ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000432794ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000432794ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000432794ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000432794ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000311785ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000311785ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000311785ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000311785ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000448323ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000448323ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000448323ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000448323ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000505472ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000505472ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000505472ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000505472ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000500777ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000500777ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000500777ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000500777ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000508502ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000508502ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000508502ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000508502ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000355196ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000355196ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000355196ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000355196ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000264405ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000264405ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000264405ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000264405ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000505984ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000505984ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000505984ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000505984ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000508479ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000508479ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000508479ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000508479ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-3CDSENST00000436790ENST00000367534SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000436790ENST00000462965SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000436790ENST00000359856SEC31Achr4

83745811

+ARPC5chr1

183602237

+
intron-5UTRENST00000436790ENST00000294742SEC31Achr4

83745811

+ARPC5chr1

183602237

+

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 SEC31A-ARPC5


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.

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 SEC31A-ARPC5


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.ARPC5

Q9BPX5

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: May function as component of the Arp2/3 complex which is involved in regulation of actin polymerization and together with an activating nucleation-promoting factor (NPF) mediates the formation of branched actin networks.

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 SEC31A-ARPC5


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 SEC31A-ARPC5


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 SEC31A-ARPC5


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 SEC31A-ARPC5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSEC31AC0079744Diffuse Large B-Cell Lymphoma1CTD_human