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Center for Computational Systems Medicine level2
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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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:UVRAG-ACER3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: UVRAG-ACER3
FusionPDB ID: 97779
FusionGDB2.0 ID: 97779
HgeneTgene
Gene symbol

UVRAG

ACER3

Gene ID

7405

55331

Gene nameUV radiation resistance associatedalkaline ceramidase 3
SynonymsDHTX|VPS38|p63APHC|PHCA|PLDECO
Cytomap

11q13.5

11q13.5

Type of geneprotein-codingprotein-coding
DescriptionUV radiation resistance-associated gene proteinbeclin 1 binding proteindisrupted in heterotaxyalkaline ceramidase 3alkCDase 3alkaline CDase 3alkaline dihydroceramidase SB89alkaline phytoceramidasephytoceramidase, alkaline
Modification date2020031320200320
UniProtAcc.

Q9NUN7

Ensembl transtripts involved in fusion geneENST idsENST00000356136, ENST00000528420, 
ENST00000531818, ENST00000532130, 
ENST00000533454, ENST00000539288, 
ENST00000525872, ENST00000538870, 
ENST00000526597, ENST00000530182, 
ENST00000533873, ENST00000538157, 
ENST00000544113, ENST00000532485, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score41 X 18 X 15=1107013 X 10 X 5=650
# samples 4915
** MAII scorelog2(49/11070*10)=-4.49772966266634
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(15/650*10)=-2.11547721741994
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: UVRAG [Title/Abstract] AND ACER3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)UVRAG(75728024)-ACER3(76726060), # samples:3
ACER3(76730820)-UVRAG(75826968), # samples:2
Anticipated loss of major functional domain due to fusion event.ACER3-UVRAG 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.
ACER3-UVRAG 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.
UVRAG-ACER3 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.
UVRAG-ACER3 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.
UVRAG-ACER3 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.
UVRAG-ACER3 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
HgeneUVRAG

GO:0071900

regulation of protein serine/threonine kinase activity

22542840

HgeneUVRAG

GO:0097352

autophagosome maturation

28306502

HgeneUVRAG

GO:0097680

double-strand break repair via classical nonhomologous end joining

22542840

TgeneACER3

GO:0043067

regulation of programmed cell death

20068046

TgeneACER3

GO:0046512

sphingosine biosynthetic process

20068046

TgeneACER3

GO:0046514

ceramide catabolic process

30575723

TgeneACER3

GO:0071602

phytosphingosine biosynthetic process

11356846|20068046


check buttonFusion gene breakpoints across UVRAG (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 ACER3 (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
ChimerDB4SARCTCGA-DX-AB2P-01AUVRAGchr11

75728024

+ACER3chr11

76726060

+
ChimerDB4SARCTCGA-LI-A9QH-01AUVRAGchr11

75728024

-ACER3chr11

76726060

+
ChimerDB4SARCTCGA-LI-A9QH-01AUVRAGchr11

75728024

+ACER3chr11

76726060

+


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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)
ENST00000356136UVRAGchr1175728024+ENST00000532485ACER3chr1176726060+824414671631773536
ENST00000528420UVRAGchr1175728024+ENST00000532485ACER3chr1176726060+79851208961514472
ENST00000533454UVRAGchr1175728024+ENST00000532485ACER3chr1176726060+763986242194752177
ENST00000531818UVRAGchr1175728024+ENST00000532485ACER3chr1176726060+781710404471346299
ENST00000532130UVRAGchr1175728024+ENST00000532485ACER3chr1176726060+736458748893281
ENST00000539288UVRAGchr1175728024+ENST00000532485ACER3chr1176726060+743165440114544177

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
ENST00000356136ENST00000532485UVRAGchr1175728024+ACER3chr1176726060+0.000491230.99950874
ENST00000528420ENST00000532485UVRAGchr1175728024+ACER3chr1176726060+0.0006794460.9993206
ENST00000533454ENST00000532485UVRAGchr1175728024+ACER3chr1176726060+0.0137032510.9862968
ENST00000531818ENST00000532485UVRAGchr1175728024+ACER3chr1176726060+0.0152091830.98479086
ENST00000532130ENST00000532485UVRAGchr1175728024+ACER3chr1176726060+0.0135369550.986463
ENST00000539288ENST00000532485UVRAGchr1175728024+ACER3chr1176726060+0.0133026540.9866974

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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

>97779_97779_1_UVRAG-ACER3_UVRAG_chr11_75728024_ENST00000356136_ACER3_chr11_76726060_ENST00000532485_length(amino acids)=536AA_BP=435
MVGGGKGAAADAGRVPAPPLGGPWIEMSASASVGGPVPQPPPGPAAALPPGSAARALHVELPSQQRRLRHLRNIAARNIVNRNGHQLLDT
YFTLHLCSTEKIYKEFYRSEVIKNSLNPTWRSLDFGIMPDRLDTSVSCFVVKIWGGKENIYQLLIEWKVCLDGLKYLGQQIHARNQNEII
FGLNDGYYGAPFEHKGYSNAQKTILLQVDQNCVRNSYDVFSLLRLHRAQCAIKQTQVTVQKIGKEIEEKLRLTSTSNELKKKSECLQLKI
LVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKECTAKRELFLKTNAQLTIRCRQLLSELSYIYPIDLN
EHKDYFVCGVKLPNSEDFQAKDDGSIAVALGYTAHLVSMISFFLQVPLRYPIIHKGSRSTIKDNINDKLTEKEREVYPWLRGLGYTSLGI

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

>97779_97779_2_UVRAG-ACER3_UVRAG_chr11_75728024_ENST00000528420_ACER3_chr11_76726060_ENST00000532485_length(amino acids)=472AA_BP=371
MRRLRHLRNIAARNIVNRNGHQLLDTYFTLHLCSTEKIYKEFYRSEVIKNSLNPTWRSLDFGIMPDRLDTSVSCFVVKIWGGKENIYQLL
IEWKVCLDGLKYLGQQIHARNQNEIIFGLNDGYYGAPFEHKGYSNAQKTILLQVDQNCVRNSYDVFSLLRLHRAQCAIKQTQVTVQKIGK
EIEEKLRLTSTSNELKKKSECLQLKILVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKECTAKRELFL
KTNAQLTIRCRQLLSELSYIYPIDLNEHKDYFVCGVKLPNSEDFQAKDDGSIAVALGYTAHLVSMISFFLQVPLRYPIIHKGSRSTIKDN
INDKLTEKEREVYPWLRGLGYTSLGIFLLGFLFWNIDNIFCESLRNFRKKVPPIIGITTQFHAWWHILTGLGSYLHILFSLYTRTLYLRY

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

>97779_97779_3_UVRAG-ACER3_UVRAG_chr11_75728024_ENST00000531818_ACER3_chr11_76726060_ENST00000532485_length(amino acids)=299AA_BP=1
MEAVDWSYSYSAILEPPCLFFLKKKSECLQLKILVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKECT
AKRELFLKTNAQLTIRCRQLLSELSYIYPIDLNEHKDYFVCGVKLPNSEDFQAKDDGSIAVALGYTAHLVSMISFFLQVPLRYPIIHKGS
RSTIKDNINDKLTEKEREVYPWLRGLGYTSLGIFLLGFLFWNIDNIFCESLRNFRKKVPPIIGITTQFHAWWHILTGLGSYLHILFSLYT

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

>97779_97779_4_UVRAG-ACER3_UVRAG_chr11_75728024_ENST00000532130_ACER3_chr11_76726060_ENST00000532485_length(amino acids)=281AA_BP=180
MFLKKKKSECLQLKILVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKECTAKRELFLKTNAQLTIRCR
QLLSELSYIYPIDLNEHKDYFVCGVKLPNSEDFQAKDDGSIAVALGYTAHLVSMISFFLQVPLRYPIIHKGSRSTIKDNINDKLTEKERE
VYPWLRGLGYTSLGIFLLGFLFWNIDNIFCESLRNFRKKVPPIIGITTQFHAWWHILTGLGSYLHILFSLYTRTLYLRYRPKVKFLFGIW

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

>97779_97779_5_UVRAG-ACER3_UVRAG_chr11_75728024_ENST00000533454_ACER3_chr11_76726060_ENST00000532485_length(amino acids)=177AA_BP=
MKIFKCLQKLSSVIIPANSELANALKASNNLRLSYESYENNYLLLNLSFSYQRHVYVTRNCFGPVVYDVLLDKHLCKTEYFKENHLQLEF

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

>97779_97779_6_UVRAG-ACER3_UVRAG_chr11_75728024_ENST00000539288_ACER3_chr11_76726060_ENST00000532485_length(amino acids)=177AA_BP=
MKIFKCLQKLSSVIIPANSELANALKASNNLRLSYESYENNYLLLNLSFSYQRHVYVTRNCFGPVVYDVLLDKHLCKTEYFKENHLQLEF

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

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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/chr11:75728024/chr11:76726060)
- 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
.ACER3

Q9NUN7

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 and Golgi ceramidase that catalyzes the hydrolysis of unsaturated long-chain C18:1-, C20:1- and C20:4-ceramides, dihydroceramides and phytoceramides into sphingoid bases like sphingosine and free fatty acids at alkaline pH (PubMed:20068046, PubMed:26792856, PubMed:20207939, PubMed:11356846, PubMed:30575723). Ceramides, sphingosine, and its phosphorylated form sphingosine-1-phosphate are bioactive lipids that mediate cellular signaling pathways regulating several biological processes including cell proliferation, apoptosis and differentiation (PubMed:20068046). Controls the generation of sphingosine in erythrocytes, and thereby sphingosine-1-phosphate in plasma (PubMed:20207939). Through the regulation of ceramides and sphingosine-1-phosphate homeostasis in the brain may play a role in neurons survival and function (By similarity). By regulating the levels of proinflammatory ceramides in immune cells and tissues, may modulate the inflammatory response (By similarity). {ECO:0000250|UniProtKB:Q9D099, ECO:0000269|PubMed:11356846, ECO:0000269|PubMed:20068046, ECO:0000269|PubMed:20207939, ECO:0000269|PubMed:26792856, ECO:0000269|PubMed:30575723, ECO:0000303|PubMed:20068046}.

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
HgeneUVRAGchr11:75728024chr11:76726060ENST00000356136+1215224_305408.6666666666667700.0Coiled coilOntology_term=ECO:0000255
HgeneUVRAGchr11:75728024chr11:76726060ENST00000356136+121523_149408.6666666666667700.0DomainC2
TgeneACER3chr11:75728024chr11:76726060ENST00000532485611163_173165.66666666666666268.0Topological domainLumenal
TgeneACER3chr11:75728024chr11:76726060ENST00000532485611195_215165.66666666666666268.0Topological domainCytoplasmic
TgeneACER3chr11:75728024chr11:76726060ENST00000532485611237_267165.66666666666666268.0Topological domainLumenal
TgeneACER3chr11:75728024chr11:76726060ENST0000054411316109_11832.666666666666664135.0Topological domainLumenal
TgeneACER3chr11:75728024chr11:76726060ENST0000054411316140_14132.666666666666664135.0Topological domainCytoplasmic
TgeneACER3chr11:75728024chr11:76726060ENST0000054411316163_17332.666666666666664135.0Topological domainLumenal
TgeneACER3chr11:75728024chr11:76726060ENST0000054411316195_21532.666666666666664135.0Topological domainCytoplasmic
TgeneACER3chr11:75728024chr11:76726060ENST0000054411316237_26732.666666666666664135.0Topological domainLumenal
TgeneACER3chr11:75728024chr11:76726060ENST000005441131656_6132.666666666666664135.0Topological domainLumenal
TgeneACER3chr11:75728024chr11:76726060ENST000005441131683_8732.666666666666664135.0Topological domainCytoplasmic
TgeneACER3chr11:75728024chr11:76726060ENST00000532485611174_194165.66666666666666268.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST00000532485611216_236165.66666666666666268.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST0000054411316119_13932.666666666666664135.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST0000054411316142_16232.666666666666664135.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST0000054411316174_19432.666666666666664135.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST0000054411316216_23632.666666666666664135.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST000005441131634_5532.666666666666664135.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST000005441131662_8232.666666666666664135.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST000005441131688_10832.666666666666664135.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneACER3chr11:75728024chr11:76726060ENST00000532485611109_118165.66666666666666268.0Topological domainLumenal
TgeneACER3chr11:75728024chr11:76726060ENST00000532485611140_141165.66666666666666268.0Topological domainCytoplasmic
TgeneACER3chr11:75728024chr11:76726060ENST000005324856111_33165.66666666666666268.0Topological domainCytoplasmic
TgeneACER3chr11:75728024chr11:76726060ENST0000053248561156_61165.66666666666666268.0Topological domainLumenal
TgeneACER3chr11:75728024chr11:76726060ENST0000053248561183_87165.66666666666666268.0Topological domainCytoplasmic
TgeneACER3chr11:75728024chr11:76726060ENST00000544113161_3332.666666666666664135.0Topological domainCytoplasmic
TgeneACER3chr11:75728024chr11:76726060ENST00000532485611119_139165.66666666666666268.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST00000532485611142_162165.66666666666666268.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST0000053248561134_55165.66666666666666268.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST0000053248561162_82165.66666666666666268.0TransmembraneHelical
TgeneACER3chr11:75728024chr11:76726060ENST0000053248561188_108165.66666666666666268.0TransmembraneHelical


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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 >>>1145_UVRAG_75728024_ACER3_76726060_1145_UVRAG_75728024_ACER3_76726060_ranked_0.pdbUVRAG7572802475728024ENST00000532485ACER3chr1176726060+
MVGGGKGAAADAGRVPAPPLGGPWIEMSASASVGGPVPQPPPGPAAALPPGSAARALHVELPSQQRRLRHLRNIAARNIVNRNGHQLLDT
YFTLHLCSTEKIYKEFYRSEVIKNSLNPTWRSLDFGIMPDRLDTSVSCFVVKIWGGKENIYQLLIEWKVCLDGLKYLGQQIHARNQNEII
FGLNDGYYGAPFEHKGYSNAQKTILLQVDQNCVRNSYDVFSLLRLHRAQCAIKQTQVTVQKIGKEIEEKLRLTSTSNELKKKSECLQLKI
LVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKECTAKRELFLKTNAQLTIRCRQLLSELSYIYPIDLN
EHKDYFVCGVKLPNSEDFQAKDDGSIAVALGYTAHLVSMISFFLQVPLRYPIIHKGSRSTIKDNINDKLTEKEREVYPWLRGLGYTSLGI
536


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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.
UVRAG_pLDDT.png
all structure
all structure
ACER3_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


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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

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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
UVRAG
ACER3


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 UVRAG-ACER3


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 UVRAG-ACER3


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