UTHEALTH HOME    ABOUT SBMI    A-Z    WEBMAIL    INSIDE THE UNIVERSITY
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use
Center for Computational Systems Medicine level2
leaf

Fusion Gene Summary

leaf

Fusion Gene Sample Information

leaf

Fusion ORF Analysis

leaf

Fusion Amino Acid Sequences

leaf

Fusion Protein Functional Features

leaf

Fusion Protein Structure

leaf

pLDDT scores

leaf

Ramachandran Plot of Fusion Protein Structure

leaf

Fusion Protein-Protein Interaction

leaf

Related drugs with this fusion protein

leaf

Related disease with this fusion protein

Fusion Protein:APTX-ARL5B

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: APTX-ARL5B
FusionPDB ID: 5719
FusionGDB2.0 ID: 5719
HgeneTgene
Gene symbol

APTX

ARL5B

Gene ID

54840

221079

Gene nameaprataxinADP ribosylation factor like GTPase 5B
SynonymsAOA|AOA1|AXA1|EAOH|EOAHA|FHA-HITARL8
Cytomap

9p21.1

10p12.31

Type of geneprotein-codingprotein-coding
Descriptionaprataxinforkhead-associated domain histidine triad-like proteinADP-ribosylation factor-like protein 5BADP-ribosylation factor-like 5BADP-ribosylation factor-like 8ADP-ribosylation factor-like protein 8ADP-ribosylation-like factor 8
Modification date2020032020200313
UniProtAcc

Q7Z2E3

Q96KC2

Ensembl transtripts involved in fusion geneENST idsENST00000397172, ENST00000309615, 
ENST00000379813, ENST00000379817, 
ENST00000379819, ENST00000379825, 
ENST00000436040, ENST00000463596, 
ENST00000468275, ENST00000473270, 
ENST00000476858, 		ENST00000377275, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 9 X 6=5405 X 5 X 3=75
# samples 126
** MAII scorelog2(12/540*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/75*10)=-0.321928094887362
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: APTX [Title/Abstract] AND ARL5B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)APTX(32987758)-ARL5B(18961551), # samples:3
Anticipated loss of major functional domain due to fusion event.APTX-ARL5B 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.
APTX-ARL5B 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.
APTX-ARL5B 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.
APTX-ARL5B 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
HgeneAPTX

GO:0000012

single strand break repair

17519253

HgeneAPTX

GO:0042542

response to hydrogen peroxide

15044383


check buttonFusion gene breakpoints across APTX (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 ARL5B (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

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
ChimerDB4LUSCTCGA-39-5037-01AAPTXchr9

32987758

-ARL5Bchr10

18961551

+
ChimerDB4LUSCTCGA-39-5037APTXchr9

32987758

-ARL5Bchr10

18961551

+


Top

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)
ENST00000397172APTXchr932987758-ENST00000377275ARL5Bchr1018961551+70203123596197

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
ENST00000397172ENST00000377275APTXchr932987758-ARL5Bchr1018961551+0.001606330.9983936

Top

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

>5719_5719_1_APTX-ARL5B_APTX_chr9_32987758_ENST00000397172_ARL5B_chr10_18961551_ENST00000377275_length(amino acids)=197AA_BP=103
MSNVNLSVSDFWRVMMRVCWLVRQDSRHQRIRLPHLEAVVIGRGPETKITDKKCSRQQVQLKAECNKGYVKVKQVGVNPTSIDSVVIGKD
QEVKLQPGQVLHMFIILVVDSIDRERLAITKEELYRMLAHEDLRKAAVLIFANKQDMKGCMTAAEISKYLTLSSIKDHPWHIQSCCALTG

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

Top

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/chr9:32987758/chr10:18961551)
- 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
APTX

Q7Z2E3

ARL5B

Q96KC2

FUNCTION: DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair and base excision repair (PubMed:15380105, PubMed:15044383, PubMed:16964241, PubMed:17276982, PubMed:24362567). Resolves abortive DNA ligation intermediates formed either at base excision sites, or when DNA ligases attempt to repair non-ligatable breaks induced by reactive oxygen species (PubMed:16964241, PubMed:24362567). Catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined (PubMed:16964241, PubMed:17276982, PubMed:24362567). Also able to hydrolyze adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity (PubMed:16547001). Likewise, catalyzes the release of 3'-linked guanosine (DNAppG) and inosine (DNAppI) from DNA, but has higher specific activity with 5'-linked adenosine (AppDNA) (By similarity). {ECO:0000250|UniProtKB:O74859, ECO:0000269|PubMed:15044383, ECO:0000269|PubMed:15380105, ECO:0000269|PubMed:16547001, ECO:0000269|PubMed:16964241, ECO:0000269|PubMed:17276982, ECO:0000269|PubMed:24362567}.FUNCTION: Binds and exchanges GTP and GDP.

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
HgeneAPTXchr9:32987758chr10:18961551ENST00000397172-4838_87103.0285.0DomainNote=FHA-like
TgeneARL5Bchr9:32987758chr10:18961551ENST0000037727526125_12885.0180.0Nucleotide bindingNote=GTP

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneAPTXchr9:32987758chr10:18961551ENST00000309615-18182_2870307.0DomainHIT
HgeneAPTXchr9:32987758chr10:18961551ENST00000309615-1838_870307.0DomainNote=FHA-like
HgeneAPTXchr9:32987758chr10:18961551ENST00000379813-18182_2870343.0DomainHIT
HgeneAPTXchr9:32987758chr10:18961551ENST00000379813-1838_870343.0DomainNote=FHA-like
HgeneAPTXchr9:32987758chr10:18961551ENST00000379817-17182_2870343.0DomainHIT
HgeneAPTXchr9:32987758chr10:18961551ENST00000379817-1738_870343.0DomainNote=FHA-like
HgeneAPTXchr9:32987758chr10:18961551ENST00000379819-18182_2870.0357.0DomainHIT
HgeneAPTXchr9:32987758chr10:18961551ENST00000379819-1838_870.0357.0DomainNote=FHA-like
HgeneAPTXchr9:32987758chr10:18961551ENST00000379825-18182_2870307.0DomainHIT
HgeneAPTXchr9:32987758chr10:18961551ENST00000379825-1838_870307.0DomainNote=FHA-like
HgeneAPTXchr9:32987758chr10:18961551ENST00000397172-48182_287103.0285.0DomainHIT
HgeneAPTXchr9:32987758chr10:18961551ENST00000436040-16182_2870445.0DomainHIT
HgeneAPTXchr9:32987758chr10:18961551ENST00000436040-1638_870445.0DomainNote=FHA-like
HgeneAPTXchr9:32987758chr10:18961551ENST00000463596-18182_2870343.0DomainHIT
HgeneAPTXchr9:32987758chr10:18961551ENST00000463596-1838_870343.0DomainNote=FHA-like
HgeneAPTXchr9:32987758chr10:18961551ENST00000468275-18182_2870343.0DomainHIT
HgeneAPTXchr9:32987758chr10:18961551ENST00000468275-1838_870343.0DomainNote=FHA-like
HgeneAPTXchr9:32987758chr10:18961551ENST00000476858-17182_2870303.0DomainHIT
HgeneAPTXchr9:32987758chr10:18961551ENST00000476858-1738_870303.0DomainNote=FHA-like
HgeneAPTXchr9:32987758chr10:18961551ENST00000309615-18126_1310307.0MotifNuclear localization signal
HgeneAPTXchr9:32987758chr10:18961551ENST00000309615-18272_2760307.0MotifHistidine triad motif
HgeneAPTXchr9:32987758chr10:18961551ENST00000379813-18126_1310343.0MotifNuclear localization signal
HgeneAPTXchr9:32987758chr10:18961551ENST00000379813-18272_2760343.0MotifHistidine triad motif
HgeneAPTXchr9:32987758chr10:18961551ENST00000379817-17126_1310343.0MotifNuclear localization signal
HgeneAPTXchr9:32987758chr10:18961551ENST00000379817-17272_2760343.0MotifHistidine triad motif
HgeneAPTXchr9:32987758chr10:18961551ENST00000379819-18126_1310.0357.0MotifNuclear localization signal
HgeneAPTXchr9:32987758chr10:18961551ENST00000379819-18272_2760.0357.0MotifHistidine triad motif
HgeneAPTXchr9:32987758chr10:18961551ENST00000379825-18126_1310307.0MotifNuclear localization signal
HgeneAPTXchr9:32987758chr10:18961551ENST00000379825-18272_2760307.0MotifHistidine triad motif
HgeneAPTXchr9:32987758chr10:18961551ENST00000397172-48126_131103.0285.0MotifNuclear localization signal
HgeneAPTXchr9:32987758chr10:18961551ENST00000397172-48272_276103.0285.0MotifHistidine triad motif
HgeneAPTXchr9:32987758chr10:18961551ENST00000436040-16126_1310445.0MotifNuclear localization signal
HgeneAPTXchr9:32987758chr10:18961551ENST00000436040-16272_2760445.0MotifHistidine triad motif
HgeneAPTXchr9:32987758chr10:18961551ENST00000463596-18126_1310343.0MotifNuclear localization signal
HgeneAPTXchr9:32987758chr10:18961551ENST00000463596-18272_2760343.0MotifHistidine triad motif
HgeneAPTXchr9:32987758chr10:18961551ENST00000468275-18126_1310343.0MotifNuclear localization signal
HgeneAPTXchr9:32987758chr10:18961551ENST00000468275-18272_2760343.0MotifHistidine triad motif
HgeneAPTXchr9:32987758chr10:18961551ENST00000476858-17126_1310303.0MotifNuclear localization signal
HgeneAPTXchr9:32987758chr10:18961551ENST00000476858-17272_2760303.0MotifHistidine triad motif
HgeneAPTXchr9:32987758chr10:18961551ENST00000309615-18331_3530307.0Zinc fingerC2H2-type
HgeneAPTXchr9:32987758chr10:18961551ENST00000379813-18331_3530343.0Zinc fingerC2H2-type
HgeneAPTXchr9:32987758chr10:18961551ENST00000379817-17331_3530343.0Zinc fingerC2H2-type
HgeneAPTXchr9:32987758chr10:18961551ENST00000379819-18331_3530.0357.0Zinc fingerC2H2-type
HgeneAPTXchr9:32987758chr10:18961551ENST00000379825-18331_3530307.0Zinc fingerC2H2-type
HgeneAPTXchr9:32987758chr10:18961551ENST00000397172-48331_353103.0285.0Zinc fingerC2H2-type
HgeneAPTXchr9:32987758chr10:18961551ENST00000436040-16331_3530445.0Zinc fingerC2H2-type
HgeneAPTXchr9:32987758chr10:18961551ENST00000463596-18331_3530343.0Zinc fingerC2H2-type
HgeneAPTXchr9:32987758chr10:18961551ENST00000468275-18331_3530343.0Zinc fingerC2H2-type
HgeneAPTXchr9:32987758chr10:18961551ENST00000476858-17331_3530303.0Zinc fingerC2H2-type
TgeneARL5Bchr9:32987758chr10:18961551ENST000003772752623_3085.0180.0Nucleotide bindingNote=GTP
TgeneARL5Bchr9:32987758chr10:18961551ENST000003772752666_7085.0180.0Nucleotide bindingGTP


Top

Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>257_APTX_32987758_ARL5B_18961551_ranked_0.pdbAPTX3298775832987758ENST00000377275ARL5Bchr1018961551+
MSNVNLSVSDFWRVMMRVCWLVRQDSRHQRIRLPHLEAVVIGRGPETKITDKKCSRQQVQLKAECNKGYVKVKQVGVNPTSIDSVVIGKD
QEVKLQPGQVLHMFIILVVDSIDRERLAITKEELYRMLAHEDLRKAAVLIFANKQDMKGCMTAAEISKYLTLSSIKDHPWHIQSCCALTG
197


Top

pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
APTX_pLDDT.png
all structure
all structure
ARL5B_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


Top

Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

Top

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
APTX
ARL5B


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
HgeneAPTXchr9:32987758chr10:18961551ENST00000309615-18207_2110307.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000309615-18269_2700307.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000379813-18207_2110343.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000379813-18269_2700343.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000379817-17207_2110343.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000379817-17269_2700343.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000379819-18207_2110.0357.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000379819-18269_2700.0357.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000379825-18207_2110307.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000379825-18269_2700307.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000397172-48207_211103.0285.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000397172-48269_270103.0285.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000436040-16207_2110445.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000436040-16269_2700445.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000463596-18207_2110343.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000463596-18269_2700343.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000468275-18207_2110343.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000468275-18269_2700343.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000476858-17207_2110303.0DNA substrate
HgeneAPTXchr9:32987758chr10:18961551ENST00000476858-17269_2700303.0DNA substrate


Top

Related Drugs to APTX-ARL5B


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

Top

Related Diseases to APTX-ARL5B


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