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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:UBE4B-APITD1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: UBE4B-APITD1
FusionPDB ID: 96319
FusionGDB2.0 ID: 96321
HgeneTgene
Gene symbol

UBE4B

APITD1

Gene ID

10277

100526739

Gene nameubiquitination factor E4BCENPS-CORT readthrough
SynonymsE4|HDNB1|UBOX3|UFD2|UFD2AAPITD1|APITD1-CORT|CENP-S|CENPS|FAAP16|MHF1
Cytomap

1p36.22

1p36.22

Type of geneprotein-codingprotein-coding
Descriptionubiquitin conjugation factor E4 BRING-type E3 ubiquitin transferase E4 BUFD2A-III/UBE4B-III splice isoformhomologous to yeast UFD2homozygously deleted in neuroblastoma-1ubiquitin-fusion degradation protein 2ubiquitination factor E4B (UFD2 homolog, yAPITD1-CORT proteinAPITD1-CORT readthroughApoptosis-inducing TAF9-like domain-containing protein 1Centromere protein SFANCM-associated histone fold protein 1FANCM-interacting histone fold protein 1Fanconi anemia-associated polypeptide of 16 kDa
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000253251, ENST00000343090, 
ENST00000377153, ENST00000377157, 
ENST00000475795, 		ENST00000462462, 
ENST00000309048, ENST00000602296, 
ENST00000602787, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score18 X 13 X 10=23403 X 4 X 3=36
# samples 235
** MAII scorelog2(23/2340*10)=-3.34680276352639
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/36*10)=0.473931188332412
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: UBE4B [Title/Abstract] AND APITD1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)UBE4B(10093752)-APITD1(10493898), # samples:1
UBE4B(10093752)-APITD1(10500404), # samples:1
UBE4B(10093754)-APITD1(10490519), # samples:1
UBE4B(10093752)-APITD1(10493899), # samples:1
Anticipated loss of major functional domain due to fusion event.UBE4B-APITD1 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.
UBE4B-APITD1 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
HgeneUBE4B

GO:0008626

granzyme-mediated apoptotic signaling pathway

11802788

HgeneUBE4B

GO:0009411

response to UV

11802788

HgeneUBE4B

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

23509263


check buttonFusion gene breakpoints across UBE4B (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 APITD1 (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
ChimerDB4BLCATCGA-UY-A78N-01AUBE4Bchr1

10093752

+APITD1chr1

10493899

+
ChimerDB4BLCATCGA-UY-A78N-01AUBE4Bchr1

10093752

+APITD1chr1

10500404

+
ChimerDB4BLCATCGA-UY-A78N-01AUBE4Bchr1

10093754

+APITD1chr1

10490519

+
ChimerDB4BLCATCGA-UY-A78NUBE4Bchr1

10093752

+APITD1chr1

10493898

+


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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)
ENST00000253251UBE4Bchr110093752+ENST00000602296APITD1chr110493898+17988631334936132
ENST00000253251UBE4Bchr110093752+ENST00000602787APITD1chr110493898+18658631401883172
ENST00000253251UBE4Bchr110093752+ENST00000309048APITD1chr110493898+16338638391228129
ENST00000343090UBE4Bchr110093752+ENST00000602296APITD1chr110493898+103499570172132
ENST00000343090UBE4Bchr110093752+ENST00000602787APITD1chr110493898+110199637119172
ENST00000343090UBE4Bchr110093752+ENST00000309048APITD1chr110493898+8699975464129
ENST00000377153UBE4Bchr110093752+ENST00000602296APITD1chr110493898+1356421892494132
ENST00000377153UBE4Bchr110093752+ENST00000602787APITD1chr110493898+1423421959441172
ENST00000377153UBE4Bchr110093752+ENST00000309048APITD1chr110493898+1191421397786129
ENST00000253251UBE4Bchr110093752+ENST00000602296APITD1chr110493899+17988631334936132
ENST00000253251UBE4Bchr110093752+ENST00000602787APITD1chr110493899+18658631401883172
ENST00000253251UBE4Bchr110093752+ENST00000309048APITD1chr110493899+16338638391228129
ENST00000343090UBE4Bchr110093752+ENST00000602296APITD1chr110493899+103499570172132
ENST00000343090UBE4Bchr110093752+ENST00000602787APITD1chr110493899+110199637119172
ENST00000343090UBE4Bchr110093752+ENST00000309048APITD1chr110493899+8699975464129
ENST00000377153UBE4Bchr110093752+ENST00000602296APITD1chr110493899+1356421892494132
ENST00000377153UBE4Bchr110093752+ENST00000602787APITD1chr110493899+1423421959441172
ENST00000377153UBE4Bchr110093752+ENST00000309048APITD1chr110493899+1191421397786129

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
ENST00000253251ENST00000602296UBE4Bchr110093752+APITD1chr110493898+0.750365260.24963476
ENST00000253251ENST00000602787UBE4Bchr110093752+APITD1chr110493898+0.0213095080.9786905
ENST00000253251ENST00000309048UBE4Bchr110093752+APITD1chr110493898+0.0073284720.9926715
ENST00000343090ENST00000602296UBE4Bchr110093752+APITD1chr110493898+0.89275380.10724627
ENST00000343090ENST00000602787UBE4Bchr110093752+APITD1chr110493898+0.0284717050.97152835
ENST00000343090ENST00000309048UBE4Bchr110093752+APITD1chr110493898+0.011876270.9881237
ENST00000377153ENST00000602296UBE4Bchr110093752+APITD1chr110493898+0.83195790.16804217
ENST00000377153ENST00000602787UBE4Bchr110093752+APITD1chr110493898+0.0394402560.9605598
ENST00000377153ENST00000309048UBE4Bchr110093752+APITD1chr110493898+0.0100868150.9899131
ENST00000253251ENST00000602296UBE4Bchr110093752+APITD1chr110493899+0.750365260.24963476
ENST00000253251ENST00000602787UBE4Bchr110093752+APITD1chr110493899+0.0213095080.9786905
ENST00000253251ENST00000309048UBE4Bchr110093752+APITD1chr110493899+0.0073284720.9926715
ENST00000343090ENST00000602296UBE4Bchr110093752+APITD1chr110493899+0.89275380.10724627
ENST00000343090ENST00000602787UBE4Bchr110093752+APITD1chr110493899+0.0284717050.97152835
ENST00000343090ENST00000309048UBE4Bchr110093752+APITD1chr110493899+0.011876270.9881237
ENST00000377153ENST00000602296UBE4Bchr110093752+APITD1chr110493899+0.83195790.16804217
ENST00000377153ENST00000602787UBE4Bchr110093752+APITD1chr110493899+0.0394402560.9605598
ENST00000377153ENST00000309048UBE4Bchr110093752+APITD1chr110493899+0.0100868150.9899131

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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

>96319_96319_1_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000253251_APITD1_chr1_10493898_ENST00000309048_length(amino acids)=129AA_BP=8
MEELSADERLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKYITDK

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

>96319_96319_2_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000253251_APITD1_chr1_10493898_ENST00000602296_length(amino acids)=132AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

>96319_96319_3_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000253251_APITD1_chr1_10493898_ENST00000602787_length(amino acids)=172AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

>96319_96319_4_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000253251_APITD1_chr1_10493899_ENST00000309048_length(amino acids)=129AA_BP=8
MEELSADERLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKYITDK

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

>96319_96319_5_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000253251_APITD1_chr1_10493899_ENST00000602296_length(amino acids)=132AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

>96319_96319_6_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000253251_APITD1_chr1_10493899_ENST00000602787_length(amino acids)=172AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

>96319_96319_7_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000343090_APITD1_chr1_10493898_ENST00000309048_length(amino acids)=129AA_BP=8
MEELSADERLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKYITDK

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

>96319_96319_8_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000343090_APITD1_chr1_10493898_ENST00000602296_length(amino acids)=132AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

>96319_96319_9_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000343090_APITD1_chr1_10493898_ENST00000602787_length(amino acids)=172AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

>96319_96319_10_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000343090_APITD1_chr1_10493899_ENST00000309048_length(amino acids)=129AA_BP=8
MEELSADERLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKYITDK

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

>96319_96319_11_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000343090_APITD1_chr1_10493899_ENST00000602296_length(amino acids)=132AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

>96319_96319_12_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000343090_APITD1_chr1_10493899_ENST00000602787_length(amino acids)=172AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

>96319_96319_13_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000377153_APITD1_chr1_10493898_ENST00000309048_length(amino acids)=129AA_BP=8
MEELSADERLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKYITDK

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

>96319_96319_14_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000377153_APITD1_chr1_10493898_ENST00000602296_length(amino acids)=132AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

>96319_96319_15_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000377153_APITD1_chr1_10493898_ENST00000602787_length(amino acids)=172AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

>96319_96319_16_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000377153_APITD1_chr1_10493899_ENST00000309048_length(amino acids)=129AA_BP=8
MEELSADERLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKYITDK

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

>96319_96319_17_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000377153_APITD1_chr1_10493899_ENST00000602296_length(amino acids)=132AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

>96319_96319_18_UBE4B-APITD1_UBE4B_chr1_10093752_ENST00000377153_APITD1_chr1_10493899_ENST00000602787_length(amino acids)=172AA_BP=
MTWEGGEERSLLLNTFYSGLSLHLREHSWVRFYLQEEKVFQKKFLQGILSRRADCWGGAPSCRLATSRASSPMRGPALAWEVHSNHQARK

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

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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/chr1:10093752/chr1:10493898)
- 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
..
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: 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

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneUBE4Bchr1:10093752chr1:10493898ENST00000253251+1271227_13008.01174.0DomainNote=U-box
HgeneUBE4Bchr1:10093752chr1:10493898ENST00000343090+1281227_13008.01303.0DomainNote=U-box
HgeneUBE4Bchr1:10093752chr1:10493898ENST00000377157+1271227_130001062.0DomainNote=U-box
HgeneUBE4Bchr1:10093752chr1:10493899ENST00000253251+1271227_13008.01174.0DomainNote=U-box
HgeneUBE4Bchr1:10093752chr1:10493899ENST00000343090+1281227_13008.01303.0DomainNote=U-box
HgeneUBE4Bchr1:10093752chr1:10493899ENST00000377157+1271227_130001062.0DomainNote=U-box


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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
UBE4B
APITD1


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 UBE4B-APITD1


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 UBE4B-APITD1


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