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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:SRGAP3-JAGN1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SRGAP3-JAGN1
FusionPDB ID: 86390
FusionGDB2.0 ID: 86390
HgeneTgene
Gene symbol

SRGAP3

JAGN1

Gene ID

23380

84522

Gene nameSLIT-ROBO Rho GTPase activating protein 2jagunal homolog 1
SynonymsARHGAP34|FNBP2|SRGAP2A|SRGAP3GL009|SCN6
Cytomap

1q32.1

3p25.3

Type of geneprotein-codingprotein-coding
DescriptionSLIT-ROBO Rho GTPase-activating protein 2SLIT-ROBO GAP2formin-binding protein 2rho GTPase-activating protein 34protein jagunal homolog 1
Modification date2020031320200313
UniProtAcc.

Q8N5M9

Ensembl transtripts involved in fusion geneENST idsENST00000360413, ENST00000383836, 
ENST00000433332, 
ENST00000489724, 
ENST00000307768, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score12 X 10 X 10=12003 X 2 X 3=18
# samples 183
** MAII scorelog2(18/1200*10)=-2.73696559416621
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SRGAP3 [Title/Abstract] AND JAGN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SRGAP3(9290569)-JAGN1(9934599), # samples:1
Anticipated loss of major functional domain due to fusion event.SRGAP3-JAGN1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
SRGAP3-JAGN1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
HgeneSRGAP3

GO:0043547

positive regulation of GTPase activity

21148482

HgeneSRGAP3

GO:0046847

filopodium assembly

22559944

HgeneSRGAP3

GO:0051014

actin filament severing

21148482

HgeneSRGAP3

GO:0060996

dendritic spine development

22559944

HgeneSRGAP3

GO:2001223

negative regulation of neuron migration

22559944


check buttonFusion gene breakpoints across SRGAP3 (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 JAGN1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4OVTCGA-24-2288-01ASRGAP3chr3

9290569

-JAGN1chr3

9934599

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000383836SRGAP3chr39290569-ENST00000307768JAGN1chr39934599+1930495523957144
ENST00000360413SRGAP3chr39290569-ENST00000307768JAGN1chr39934599+1764329357791144

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
ENST00000383836ENST00000307768SRGAP3chr39290569-JAGN1chr39934599+0.329386650.67061335
ENST00000360413ENST00000307768SRGAP3chr39290569-JAGN1chr39934599+0.135433840.86456615

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>86390_86390_1_SRGAP3-JAGN1_SRGAP3_chr3_9290569_ENST00000360413_JAGN1_chr3_9934599_ENST00000307768_length(amino acids)=144AA_BP=
MIYVHLVIWLLLVAKMSVGHLRLLSHDQVAMPYQWEYPYLLSILPSLLGLLSFPRNNISYLVLSMISMGLFSIAPLIYGSMEMFPAAQQL

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

>86390_86390_2_SRGAP3-JAGN1_SRGAP3_chr3_9290569_ENST00000383836_JAGN1_chr3_9934599_ENST00000307768_length(amino acids)=144AA_BP=
MIYVHLVIWLLLVAKMSVGHLRLLSHDQVAMPYQWEYPYLLSILPSLLGLLSFPRNNISYLVLSMISMGLFSIAPLIYGSMEMFPAAQQL

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

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Fusion Protein Functional Features


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/chr3:9290569/chr3:9934599)
- 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
.JAGN1

Q8N5M9

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: Endoplasmic reticulum transmembrane protein involved in vesicle-mediated transport, which is required for neutrophil function. Required for vesicle-mediated transport; it is however unclear whether it is involved in early secretory pathway or intracellular protein transport. Acts as a regulator of neutrophil function, probably via its role in vesicle-mediated transport: required for defense against fungal pathogens and for granulocyte colony-stimulating factor (GM-CSF) signaling pathway; possibly by regulating glycosylation and/or targeting of proteins contributing to the viability and migration of neutrophils. {ECO:0000269|PubMed:25129144, 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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneJAGN1chr3:9290569chr3:9934599ENST0000030776802118_13729.666666666666668184.0Topological domainLumenal
TgeneJAGN1chr3:9290569chr3:9934599ENST0000030776802159_18329.666666666666668184.0Topological domainCytoplasmic
TgeneJAGN1chr3:9290569chr3:9934599ENST000003077680261_7129.666666666666668184.0Topological domainLumenal
TgeneJAGN1chr3:9290569chr3:9934599ENST000003077680293_9629.666666666666668184.0Topological domainCytoplasmic
TgeneJAGN1chr3:9290569chr3:9934599ENST0000030776802138_15829.666666666666668184.0TransmembraneHelical
TgeneJAGN1chr3:9290569chr3:9934599ENST000003077680240_6029.666666666666668184.0TransmembraneHelical
TgeneJAGN1chr3:9290569chr3:9934599ENST000003077680272_9229.666666666666668184.0TransmembraneHelical
TgeneJAGN1chr3:9290569chr3:9934599ENST000003077680297_11729.666666666666668184.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSRGAP3chr3:9290569chr3:9934599ENST00000360413-122352_39222.3333333333333321076.0Coiled coilOntology_term=ECO:0000255
HgeneSRGAP3chr3:9290569chr3:9934599ENST00000360413-122952_98722.3333333333333321076.0Coiled coilOntology_term=ECO:0000255
HgeneSRGAP3chr3:9290569chr3:9934599ENST00000383836-122352_39222.3333333333333321100.0Coiled coilOntology_term=ECO:0000255
HgeneSRGAP3chr3:9290569chr3:9934599ENST00000383836-122952_98722.3333333333333321100.0Coiled coilOntology_term=ECO:0000255
HgeneSRGAP3chr3:9290569chr3:9934599ENST00000360413-12219_31422.3333333333333321076.0DomainF-BAR
HgeneSRGAP3chr3:9290569chr3:9934599ENST00000360413-122482_67022.3333333333333321076.0DomainRho-GAP
HgeneSRGAP3chr3:9290569chr3:9934599ENST00000360413-122744_80322.3333333333333321076.0DomainSH3
HgeneSRGAP3chr3:9290569chr3:9934599ENST00000383836-12219_31422.3333333333333321100.0DomainF-BAR
HgeneSRGAP3chr3:9290569chr3:9934599ENST00000383836-122482_67022.3333333333333321100.0DomainRho-GAP
HgeneSRGAP3chr3:9290569chr3:9934599ENST00000383836-122744_80322.3333333333333321100.0DomainSH3
TgeneJAGN1chr3:9290569chr3:9934599ENST00000307768021_3929.666666666666668184.0Topological domainCytoplasmic


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
SRGAP3
JAGN1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to SRGAP3-JAGN1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to SRGAP3-JAGN1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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