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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:HERC3-AFF1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: HERC3-AFF1
FusionPDB ID: 36171
FusionGDB2.0 ID: 36171
HgeneTgene
Gene symbol

HERC3

AFF1

Gene ID

8916

4299

Gene nameHECT and RLD domain containing E3 ubiquitin protein ligase 3AF4/FMR2 family member 1
Synonyms-AF4|MLLT2|PBM1
Cytomap

4q22.1

4q21.3-q22.1

Type of geneprotein-codingprotein-coding
Descriptionprobable E3 ubiquitin-protein ligase HERC3HECT domain and RCC1-like domain-containing protein 3HECT-type E3 ubiquitin transferase HERC3hect domain and RLD 3AF4/FMR2 family member 1ALL1-fused gene from chromosome 4 proteinmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 2pre-B-cell monocytic leukemia partner 1proto-oncogene AF4
Modification date2020031320200313
UniProtAcc

Q15034

P51825

Ensembl transtripts involved in fusion geneENST idsENST00000264345, ENST00000402738, 
ENST00000407637, ENST00000543130, 
ENST00000601319, 
ENST00000511996, 
ENST00000307808, ENST00000395146, 
ENST00000544085, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 3 X 4=4819 X 137 X 9=23427
# samples 4141
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(141/23427*10)=-4.05440515056027
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: HERC3 [Title/Abstract] AND AFF1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)HERC3(89571150)-AFF1(88052944), # samples:1
Anticipated loss of major functional domain due to fusion event.HERC3-AFF1 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.
HERC3-AFF1 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

check buttonFusion gene breakpoints across HERC3 (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 AFF1 (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
ChimerDB4THCATCGA-DJ-A3VMHERC3chr4

89571150

+AFF1chr4

88052944

+


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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)
ENST00000402738HERC3chr489571150+ENST00000395146AFF1chr488052944+65346252391180313
ENST00000402738HERC3chr489571150+ENST00000307808AFF1chr488052944+65156252391177312
ENST00000402738HERC3chr489571150+ENST00000544085AFF1chr488052944+15916252391180313
ENST00000407637HERC3chr489571150+ENST00000395146AFF1chr488052944+64615521661107313
ENST00000407637HERC3chr489571150+ENST00000307808AFF1chr488052944+64425521661104312
ENST00000407637HERC3chr489571150+ENST00000544085AFF1chr488052944+15185521661107313
ENST00000264345HERC3chr489571150+ENST00000395146AFF1chr488052944+632541630971313
ENST00000264345HERC3chr489571150+ENST00000307808AFF1chr488052944+630641630968312
ENST00000264345HERC3chr489571150+ENST00000544085AFF1chr488052944+138241630971313

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
ENST00000402738ENST00000395146HERC3chr489571150+AFF1chr488052944+0.0017780840.99822193
ENST00000402738ENST00000307808HERC3chr489571150+AFF1chr488052944+0.0016288070.9983712
ENST00000402738ENST00000544085HERC3chr489571150+AFF1chr488052944+0.0198047270.9801952
ENST00000407637ENST00000395146HERC3chr489571150+AFF1chr488052944+0.0017397450.9982603
ENST00000407637ENST00000307808HERC3chr489571150+AFF1chr488052944+0.0015917640.99840826
ENST00000407637ENST00000544085HERC3chr489571150+AFF1chr488052944+0.0210134460.97898656
ENST00000264345ENST00000395146HERC3chr489571150+AFF1chr488052944+0.0016806940.9983193
ENST00000264345ENST00000307808HERC3chr489571150+AFF1chr488052944+0.0015383830.9984616
ENST00000264345ENST00000544085HERC3chr489571150+AFF1chr488052944+0.0190603450.9809396

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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

>36171_36171_1_HERC3-AFF1_HERC3_chr4_89571150_ENST00000264345_AFF1_chr4_88052944_ENST00000307808_length(amino acids)=312AA_BP=128
MLCWGYWSLGQPGISTNLQGIVAEPQVCGFISDRSVKEVACGGNHSVFLLEDGEVYTCGLNTKGQLGHEREGNKPEQIGALADQHIIHVA
CGESHSLALSDRGQLFSWGAGSDGQLGLMTTEDSVAVPRFIMSLKSFSDATAPTQEKIFAVLCMRCQSILNMAMFRCKKDIAIKYSRTLN
KHFESSSKVAQAPSPCIASTGTPSPLSPMPSPASSVGSQSSAGSVGSSGVAATISTPVTIQNMTSSYVTITSHVLTAFDLWEQAEALTRK

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

>36171_36171_2_HERC3-AFF1_HERC3_chr4_89571150_ENST00000264345_AFF1_chr4_88052944_ENST00000395146_length(amino acids)=313AA_BP=128
MLCWGYWSLGQPGISTNLQGIVAEPQVCGFISDRSVKEVACGGNHSVFLLEDGEVYTCGLNTKGQLGHEREGNKPEQIGALADQHIIHVA
CGESHSLALSDRGQLFSWGAGSDGQLGLMTTEDSVAVPRFIMSLKSFSDATAPTQEKIFAVLCMRCQSILNMAMFRCKKDIAIKYSRTLN
KHFESSSKVAQAPSPCIARSTGTPSPLSPMPSPASSVGSQSSAGSVGSSGVAATISTPVTIQNMTSSYVTITSHVLTAFDLWEQAEALTR

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

>36171_36171_3_HERC3-AFF1_HERC3_chr4_89571150_ENST00000264345_AFF1_chr4_88052944_ENST00000544085_length(amino acids)=313AA_BP=128
MLCWGYWSLGQPGISTNLQGIVAEPQVCGFISDRSVKEVACGGNHSVFLLEDGEVYTCGLNTKGQLGHEREGNKPEQIGALADQHIIHVA
CGESHSLALSDRGQLFSWGAGSDGQLGLMTTEDSVAVPRFIMSLKSFSDATAPTQEKIFAVLCMRCQSILNMAMFRCKKDIAIKYSRTLN
KHFESSSKVAQAPSPCIARSTGTPSPLSPMPSPASSVGSQSSAGSVGSSGVAATISTPVTIQNMTSSYVTITSHVLTAFDLWEQAEALTR

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

>36171_36171_4_HERC3-AFF1_HERC3_chr4_89571150_ENST00000402738_AFF1_chr4_88052944_ENST00000307808_length(amino acids)=312AA_BP=128
MLCWGYWSLGQPGISTNLQGIVAEPQVCGFISDRSVKEVACGGNHSVFLLEDGEVYTCGLNTKGQLGHEREGNKPEQIGALADQHIIHVA
CGESHSLALSDRGQLFSWGAGSDGQLGLMTTEDSVAVPRFIMSLKSFSDATAPTQEKIFAVLCMRCQSILNMAMFRCKKDIAIKYSRTLN
KHFESSSKVAQAPSPCIASTGTPSPLSPMPSPASSVGSQSSAGSVGSSGVAATISTPVTIQNMTSSYVTITSHVLTAFDLWEQAEALTRK

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

>36171_36171_5_HERC3-AFF1_HERC3_chr4_89571150_ENST00000402738_AFF1_chr4_88052944_ENST00000395146_length(amino acids)=313AA_BP=128
MLCWGYWSLGQPGISTNLQGIVAEPQVCGFISDRSVKEVACGGNHSVFLLEDGEVYTCGLNTKGQLGHEREGNKPEQIGALADQHIIHVA
CGESHSLALSDRGQLFSWGAGSDGQLGLMTTEDSVAVPRFIMSLKSFSDATAPTQEKIFAVLCMRCQSILNMAMFRCKKDIAIKYSRTLN
KHFESSSKVAQAPSPCIARSTGTPSPLSPMPSPASSVGSQSSAGSVGSSGVAATISTPVTIQNMTSSYVTITSHVLTAFDLWEQAEALTR

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

>36171_36171_6_HERC3-AFF1_HERC3_chr4_89571150_ENST00000402738_AFF1_chr4_88052944_ENST00000544085_length(amino acids)=313AA_BP=128
MLCWGYWSLGQPGISTNLQGIVAEPQVCGFISDRSVKEVACGGNHSVFLLEDGEVYTCGLNTKGQLGHEREGNKPEQIGALADQHIIHVA
CGESHSLALSDRGQLFSWGAGSDGQLGLMTTEDSVAVPRFIMSLKSFSDATAPTQEKIFAVLCMRCQSILNMAMFRCKKDIAIKYSRTLN
KHFESSSKVAQAPSPCIARSTGTPSPLSPMPSPASSVGSQSSAGSVGSSGVAATISTPVTIQNMTSSYVTITSHVLTAFDLWEQAEALTR

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

>36171_36171_7_HERC3-AFF1_HERC3_chr4_89571150_ENST00000407637_AFF1_chr4_88052944_ENST00000307808_length(amino acids)=312AA_BP=128
MLCWGYWSLGQPGISTNLQGIVAEPQVCGFISDRSVKEVACGGNHSVFLLEDGEVYTCGLNTKGQLGHEREGNKPEQIGALADQHIIHVA
CGESHSLALSDRGQLFSWGAGSDGQLGLMTTEDSVAVPRFIMSLKSFSDATAPTQEKIFAVLCMRCQSILNMAMFRCKKDIAIKYSRTLN
KHFESSSKVAQAPSPCIASTGTPSPLSPMPSPASSVGSQSSAGSVGSSGVAATISTPVTIQNMTSSYVTITSHVLTAFDLWEQAEALTRK

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

>36171_36171_8_HERC3-AFF1_HERC3_chr4_89571150_ENST00000407637_AFF1_chr4_88052944_ENST00000395146_length(amino acids)=313AA_BP=128
MLCWGYWSLGQPGISTNLQGIVAEPQVCGFISDRSVKEVACGGNHSVFLLEDGEVYTCGLNTKGQLGHEREGNKPEQIGALADQHIIHVA
CGESHSLALSDRGQLFSWGAGSDGQLGLMTTEDSVAVPRFIMSLKSFSDATAPTQEKIFAVLCMRCQSILNMAMFRCKKDIAIKYSRTLN
KHFESSSKVAQAPSPCIARSTGTPSPLSPMPSPASSVGSQSSAGSVGSSGVAATISTPVTIQNMTSSYVTITSHVLTAFDLWEQAEALTR

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

>36171_36171_9_HERC3-AFF1_HERC3_chr4_89571150_ENST00000407637_AFF1_chr4_88052944_ENST00000544085_length(amino acids)=313AA_BP=128
MLCWGYWSLGQPGISTNLQGIVAEPQVCGFISDRSVKEVACGGNHSVFLLEDGEVYTCGLNTKGQLGHEREGNKPEQIGALADQHIIHVA
CGESHSLALSDRGQLFSWGAGSDGQLGLMTTEDSVAVPRFIMSLKSFSDATAPTQEKIFAVLCMRCQSILNMAMFRCKKDIAIKYSRTLN
KHFESSSKVAQAPSPCIARSTGTPSPLSPMPSPASSVGSQSSAGSVGSSGVAATISTPVTIQNMTSSYVTITSHVLTAFDLWEQAEALTR

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

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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/chr4:89571150/chr4:88052944)
- 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
HERC3

Q15034

AFF1

P51825

FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. {ECO:0000250}.

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
HgeneHERC3chr4:89571150chr4:88052944ENST00000264345+2241_51128.666666666666661051.0RepeatNote=RCC1 1
HgeneHERC3chr4:89571150chr4:88052944ENST00000264345+22452_101128.666666666666661051.0RepeatNote=RCC1 2
HgeneHERC3chr4:89571150chr4:88052944ENST00000402738+4261_51128.666666666666661051.0RepeatNote=RCC1 1
HgeneHERC3chr4:89571150chr4:88052944ENST00000402738+42652_101128.666666666666661051.0RepeatNote=RCC1 2

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneHERC3chr4:89571150chr4:88052944ENST00000264345+224951_1050128.666666666666661051.0DomainHECT
HgeneHERC3chr4:89571150chr4:88052944ENST00000402738+426951_1050128.666666666666661051.0DomainHECT
HgeneHERC3chr4:89571150chr4:88052944ENST00000264345+224102_154128.666666666666661051.0RepeatNote=RCC1 3
HgeneHERC3chr4:89571150chr4:88052944ENST00000264345+224156_207128.666666666666661051.0RepeatNote=RCC1 4
HgeneHERC3chr4:89571150chr4:88052944ENST00000264345+224208_259128.666666666666661051.0RepeatNote=RCC1 5
HgeneHERC3chr4:89571150chr4:88052944ENST00000264345+224261_311128.666666666666661051.0RepeatNote=RCC1 6
HgeneHERC3chr4:89571150chr4:88052944ENST00000264345+224313_366128.666666666666661051.0RepeatNote=RCC1 7
HgeneHERC3chr4:89571150chr4:88052944ENST00000402738+426102_154128.666666666666661051.0RepeatNote=RCC1 3
HgeneHERC3chr4:89571150chr4:88052944ENST00000402738+426156_207128.666666666666661051.0RepeatNote=RCC1 4
HgeneHERC3chr4:89571150chr4:88052944ENST00000402738+426208_259128.666666666666661051.0RepeatNote=RCC1 5
HgeneHERC3chr4:89571150chr4:88052944ENST00000402738+426261_311128.666666666666661051.0RepeatNote=RCC1 6
HgeneHERC3chr4:89571150chr4:88052944ENST00000402738+426313_366128.666666666666661051.0RepeatNote=RCC1 7
TgeneAFF1chr4:89571150chr4:88052944ENST000003078081520483_4921026.66666666666671211.0Compositional biasNote=Poly-Ser
TgeneAFF1chr4:89571150chr4:88052944ENST000003078081520835_8431026.66666666666671211.0Compositional biasNote=Poly-Ser
TgeneAFF1chr4:89571150chr4:88052944ENST000003078081520866_8691026.66666666666671211.0Compositional biasNote=Poly-Pro
TgeneAFF1chr4:89571150chr4:88052944ENST000003078081520871_8741026.66666666666671211.0Compositional biasNote=Poly-Ser
TgeneAFF1chr4:89571150chr4:88052944ENST000003951461621483_4921033.66666666666671219.0Compositional biasNote=Poly-Ser
TgeneAFF1chr4:89571150chr4:88052944ENST000003951461621835_8431033.66666666666671219.0Compositional biasNote=Poly-Ser
TgeneAFF1chr4:89571150chr4:88052944ENST000003951461621866_8691033.66666666666671219.0Compositional biasNote=Poly-Pro
TgeneAFF1chr4:89571150chr4:88052944ENST000003951461621871_8741033.66666666666671219.0Compositional biasNote=Poly-Ser


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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
AFF1MLLT1, CCNT1, NT5E, MLLT3, CDK9, AFF4, KMT2A, AFF1, BRD4, RELA, NPM1, PCSK1, MLLT10, DOT1L, POLR2A, DDX6, HEXIM1, HIST3H3, NSD1, CARM1, SIAH1, SIAH2, SMAD9, tat, MED26, EAF1, ELL2, LARP7, ELL3, HDAC1, MYH7, SLC16A6, ZNF526, Mllt1, Mad2l1bp, Rrbp1, Rcc1, VDR, PIP4K2A, CAMKV, TRIM25, HNRNPL, ESR2, KIAA1429, SASH1, DYRK1A, ARFIP1, MRPL12, KIF20A, CCAR2, FGF12, PLCD3, EPB41L1, EPB41L3,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
HERC3
AFF1all structure


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 HERC3-AFF1


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 HERC3-AFF1


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