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 level1
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-Protein Interaction

leaf

Related drugs with this fusion protein

leaf

Related disease with this fusion protein

Fusion Protein:ABCC4-UPF3A

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ABCC4-UPF3A
FusionPDB ID: 291
FusionGDB2.0 ID: 291
HgeneTgene
Gene symbol

ABCC4

UPF3A

Gene ID

10257

65110

Gene nameATP binding cassette subfamily C member 4UPF3A regulator of nonsense mediated mRNA decay
SynonymsMOAT-B|MOATB|MRP4HUPF3A|RENT3A|UPF3
Cytomap

13q32.1

13q34

Type of geneprotein-codingprotein-coding
Descriptionmultidrug resistance-associated protein 4MRP/cMOAT-related ABC transporterbA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)canalicular multispecific organic anion transporter (ABC superfamily)multi-specific organic anion transporter regulator of nonsense transcripts 3AUPF3 regulator of nonsense transcripts homolog AhUpf3nonsense mRNA reducing factor 3Aup-frameshift suppressor 3 homolog A
Modification date2020031320200313
UniProtAcc

O15439

.
Ensembl transtripts involved in fusion geneENST idsENST00000538287, ENST00000376887, 
ENST00000412704, ENST00000431522, 
ENST00000536256, ENST00000474158, 
ENST00000351487, ENST00000375299, 
ENST00000475218, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score23 X 21 X 11=53137 X 7 X 5=245
# samples 257
** MAII scorelog2(25/5313*10)=-4.40952671281098
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/245*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: ABCC4 [Title/Abstract] AND UPF3A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ABCC4(95899228)-UPF3A(115070263), # samples:1
Anticipated loss of major functional domain due to fusion event.ABCC4-UPF3A 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.
ABCC4-UPF3A 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.
ABCC4-UPF3A 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.
ABCC4-UPF3A 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
HgeneABCC4

GO:0032310

prostaglandin secretion

25173977

TgeneUPF3A

GO:0000184

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

16601204

TgeneUPF3A

GO:0045727

positive regulation of translation

16601204


check buttonFusion gene breakpoints across ABCC4 (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 UPF3A (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
ChimerDB4OVTCGA-24-2020ABCC4chr13

95899228

-UPF3Achr13

115070263

+


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)
ENST00000412704ABCC4chr1395899228-ENST00000375299UPF3Achr13115070263+1445425119553144
ENST00000412704ABCC4chr1395899228-ENST00000351487UPF3Achr13115070263+1445425119553144
ENST00000376887ABCC4chr1395899228-ENST00000375299UPF3Achr13115070263+1441421115549144
ENST00000376887ABCC4chr1395899228-ENST00000351487UPF3Achr13115070263+1441421115549144
ENST00000536256ABCC4chr1395899228-ENST00000375299UPF3Achr13115070263+1445425119553144
ENST00000536256ABCC4chr1395899228-ENST00000351487UPF3Achr13115070263+1445425119553144
ENST00000431522ABCC4chr1395899228-ENST00000375299UPF3Achr13115070263+1445425119553144
ENST00000431522ABCC4chr1395899228-ENST00000351487UPF3Achr13115070263+1445425119553144

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
ENST00000412704ENST00000375299ABCC4chr1395899228-UPF3Achr13115070263+0.0170041490.9829958
ENST00000412704ENST00000351487ABCC4chr1395899228-UPF3Achr13115070263+0.0170041490.9829958
ENST00000376887ENST00000375299ABCC4chr1395899228-UPF3Achr13115070263+0.014533360.9854666
ENST00000376887ENST00000351487ABCC4chr1395899228-UPF3Achr13115070263+0.014533360.9854666
ENST00000536256ENST00000375299ABCC4chr1395899228-UPF3Achr13115070263+0.0170041490.9829958
ENST00000536256ENST00000351487ABCC4chr1395899228-UPF3Achr13115070263+0.0170041490.9829958
ENST00000431522ENST00000375299ABCC4chr1395899228-UPF3Achr13115070263+0.0170041490.9829958
ENST00000431522ENST00000351487ABCC4chr1395899228-UPF3Achr13115070263+0.0170041490.9829958

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

>291_291_1_ABCC4-UPF3A_ABCC4_chr13_95899228_ENST00000376887_UPF3A_chr13_115070263_ENST00000351487_length(amino acids)=144AA_BP=102
MLPVYQEVKPNPLQDANLCSRVFFWWLNPLFKIGHKRRLEEDDMYSVLPEDRSQHLGEELQGFWDKEVLRAENDAQKPSLTRAIIKCYWK

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

>291_291_2_ABCC4-UPF3A_ABCC4_chr13_95899228_ENST00000376887_UPF3A_chr13_115070263_ENST00000375299_length(amino acids)=144AA_BP=102
MLPVYQEVKPNPLQDANLCSRVFFWWLNPLFKIGHKRRLEEDDMYSVLPEDRSQHLGEELQGFWDKEVLRAENDAQKPSLTRAIIKCYWK

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

>291_291_3_ABCC4-UPF3A_ABCC4_chr13_95899228_ENST00000412704_UPF3A_chr13_115070263_ENST00000351487_length(amino acids)=144AA_BP=102
MLPVYQEVKPNPLQDANLCSRVFFWWLNPLFKIGHKRRLEEDDMYSVLPEDRSQHLGEELQGFWDKEVLRAENDAQKPSLTRAIIKCYWK

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

>291_291_4_ABCC4-UPF3A_ABCC4_chr13_95899228_ENST00000412704_UPF3A_chr13_115070263_ENST00000375299_length(amino acids)=144AA_BP=102
MLPVYQEVKPNPLQDANLCSRVFFWWLNPLFKIGHKRRLEEDDMYSVLPEDRSQHLGEELQGFWDKEVLRAENDAQKPSLTRAIIKCYWK

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

>291_291_5_ABCC4-UPF3A_ABCC4_chr13_95899228_ENST00000431522_UPF3A_chr13_115070263_ENST00000351487_length(amino acids)=144AA_BP=102
MLPVYQEVKPNPLQDANLCSRVFFWWLNPLFKIGHKRRLEEDDMYSVLPEDRSQHLGEELQGFWDKEVLRAENDAQKPSLTRAIIKCYWK

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

>291_291_6_ABCC4-UPF3A_ABCC4_chr13_95899228_ENST00000431522_UPF3A_chr13_115070263_ENST00000375299_length(amino acids)=144AA_BP=102
MLPVYQEVKPNPLQDANLCSRVFFWWLNPLFKIGHKRRLEEDDMYSVLPEDRSQHLGEELQGFWDKEVLRAENDAQKPSLTRAIIKCYWK

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

>291_291_7_ABCC4-UPF3A_ABCC4_chr13_95899228_ENST00000536256_UPF3A_chr13_115070263_ENST00000351487_length(amino acids)=144AA_BP=102
MLPVYQEVKPNPLQDANLCSRVFFWWLNPLFKIGHKRRLEEDDMYSVLPEDRSQHLGEELQGFWDKEVLRAENDAQKPSLTRAIIKCYWK

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

>291_291_8_ABCC4-UPF3A_ABCC4_chr13_95899228_ENST00000536256_UPF3A_chr13_115070263_ENST00000375299_length(amino acids)=144AA_BP=102
MLPVYQEVKPNPLQDANLCSRVFFWWLNPLFKIGHKRRLEEDDMYSVLPEDRSQHLGEELQGFWDKEVLRAENDAQKPSLTRAIIKCYWK

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

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/chr13:95899228/chr13:115070263)
- 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
ABCC4

O15439

.
FUNCTION: ATP-dependent transporter of the ATP-binding cassette (ABC) family that actively extrudes physiological compounds and xenobiotics from cells. Transports a range of endogenous molecules that have a key role in cellular communication and signaling, including cyclic nucleotides such as cyclic AMP (cAMP) and cyclic GMP (cGMP), bile acids, steroid conjugates, urate, and prostaglandins (PubMed:11856762, PubMed:12883481, PubMed:12523936, PubMed:12835412, PubMed:15364914, PubMed:15454390, PubMed:16282361, PubMed:17959747, PubMed:18300232, PubMed:26721430). Mediates the ATP-dependent efflux of glutathione conjugates such as leukotriene C4 (LTC4) and leukotriene B4 (LTB4) too. The presence of GSH is necessary for the ATP-dependent transport of LTB4, whereas GSH is not required for the transport of LTC4 (PubMed:17959747). Mediates the cotransport of bile acids with reduced glutathione (GSH) (PubMed:12883481, PubMed:12523936, PubMed:16282361). Transports a wide range of drugs and their metabolites, including anticancer, antiviral and antibiotics molecules (PubMed:11856762, PubMed:12105214, PubMed:15454390, PubMed:18300232, PubMed:17344354). Confers resistance to anticancer agents such as methotrexate (PubMed:11106685). {ECO:0000269|PubMed:11106685, ECO:0000269|PubMed:11856762, ECO:0000269|PubMed:12105214, ECO:0000269|PubMed:12523936, ECO:0000269|PubMed:12835412, ECO:0000269|PubMed:12883481, ECO:0000269|PubMed:15364914, ECO:0000269|PubMed:15454390, ECO:0000269|PubMed:16282361, ECO:0000269|PubMed:17344354, ECO:0000269|PubMed:17959747, ECO:0000269|PubMed:18300232, ECO:0000269|PubMed:26721430}.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.

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
TgeneUPF3Achr13:95899228chr13:115070263ENST0000035148779421_434401.0444.0RegionNote=Required for association with EIF4A3 and ECJ core components CASC3%2C MAGOH and RBM8A

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-3311041_1274102.01326.0DomainABC transporter 2
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331410_633102.01326.0DomainABC transporter 1
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331714_1005102.01326.0DomainABC transmembrane type-1 2
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-33192_377102.01326.0DomainABC transmembrane type-1 1
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-3301041_1274102.01279.0DomainABC transporter 2
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330410_633102.01279.0DomainABC transporter 1
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330714_1005102.01279.0DomainABC transmembrane type-1 2
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-33092_377102.01279.0DomainABC transmembrane type-1 1
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-3211041_1274102.0860.0DomainABC transporter 2
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321410_633102.0860.0DomainABC transporter 1
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321714_1005102.0860.0DomainABC transmembrane type-1 2
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-32192_377102.0860.0DomainABC transmembrane type-1 1
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-3311322_1325102.01326.0MotifNote=PDZ-binding
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-3301322_1325102.01279.0MotifNote=PDZ-binding
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-3211322_1325102.0860.0MotifNote=PDZ-binding
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-3311075_1082102.01326.0Nucleotide bindingATP 2
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331445_452102.01326.0Nucleotide bindingATP 1
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-3301075_1082102.01279.0Nucleotide bindingATP 2
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330445_452102.01279.0Nucleotide bindingATP 1
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-3211075_1082102.0860.0Nucleotide bindingATP 2
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321445_452102.0860.0Nucleotide bindingATP 1
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-3311038_1058102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331136_156102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331207_227102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331228_248102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331328_348102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331351_371102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331440_460102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331710_730102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331771_791102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331836_856102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331858_878102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-33193_113102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331954_974102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000376887-331977_997102.01326.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-3301038_1058102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330136_156102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330207_227102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330228_248102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330328_348102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330351_371102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330440_460102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330710_730102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330771_791102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330836_856102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330858_878102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-33093_113102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330954_974102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000412704-330977_997102.01279.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-3211038_1058102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321136_156102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321207_227102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321228_248102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321328_348102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321351_371102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321440_460102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321710_730102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321771_791102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321836_856102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321858_878102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-32193_113102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321954_974102.0860.0TransmembraneHelical
HgeneABCC4chr13:95899228chr13:115070263ENST00000431522-321977_997102.0860.0TransmembraneHelical
TgeneUPF3Achr13:95899228chr13:115070263ENST00000375299810421_434434.0477.0RegionNote=Required for association with EIF4A3 and ECJ core components CASC3%2C MAGOH and RBM8A


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
ABCC4
UPF3A


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


Top

Related Drugs to ABCC4-UPF3A


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

Top

Related Diseases to ABCC4-UPF3A


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