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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:H2AFY-ZNF788 (FusionGDB2 ID:35497)

Fusion Gene Summary for H2AFY-ZNF788

check button Fusion gene summary
Fusion gene informationFusion gene name: H2AFY-ZNF788
Fusion gene ID: 35497
HgeneTgene
Gene symbol

H2AFY

ZNF788

Gene ID

9555

388507

Gene namemacroH2A.1 histonezinc finger family member 788, pseudogene
SynonymsH2A.y|H2A/y|H2AF12M|H2AFY|MACROH2A1.1|mH2A1|macroH2A1.2ZNF788
Cytomap

5q31.1

19p13.2

Type of geneprotein-codingprotein-coding
Descriptioncore histone macro-H2A.1H2A histone family member Yhistone H2A.yhistone macroH2A1histone macroH2A1.1histone macroH2A1.2medulloblastoma antigen MU-MB-50.205putative KRAB domain-containing protein ZNF788KRAB domain-containing protein ZNF788zinc finger family member 788zinc finger protein 788
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000304332, ENST00000312469, 
ENST00000510038, ENST00000511689, 
ENST00000423969, ENST00000512507, 
ENST00000430298, ENST00000397755, 
ENST00000397759, ENST00000596883, 
ENST00000339302, 
Fusion gene scores* DoF score8 X 9 X 4=2884 X 4 X 4=64
# samples 94
** MAII scorelog2(9/288*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/64*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: H2AFY [Title/Abstract] AND ZNF788 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointH2AFY(134696184)-ZNF788(12224136), # samples:1
Anticipated loss of major functional domain due to fusion event.H2AFY-ZNF788 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
H2AFY-ZNF788 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted 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
HgeneH2AFY

GO:0007549

dosage compensation

15053874

HgeneH2AFY

GO:0034184

positive regulation of maintenance of mitotic sister chromatid cohesion

26373281

HgeneH2AFY

GO:1904815

negative regulation of protein localization to chromosome, telomeric region

26373281


check buttonFusion gene breakpoints across H2AFY (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 ZNF788 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChiTaRS5.0N/ABP429307H2AFYchr5

134696184

-ZNF788chr19

12224136

+


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Fusion Gene ORF analysis for H2AFY-ZNF788

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-3UTRENST00000304332ENST00000430298H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-3UTRENST00000312469ENST00000430298H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-3UTRENST00000510038ENST00000430298H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-3UTRENST00000511689ENST00000430298H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000304332ENST00000397755H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000304332ENST00000397759H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000304332ENST00000596883H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000312469ENST00000397755H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000312469ENST00000397759H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000312469ENST00000596883H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000510038ENST00000397755H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000510038ENST00000397759H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000510038ENST00000596883H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000511689ENST00000397755H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000511689ENST00000397759H2AFYchr5

134696184

-ZNF788chr19

12224136

+
5CDS-intronENST00000511689ENST00000596883H2AFYchr5

134696184

-ZNF788chr19

12224136

+
Frame-shiftENST00000304332ENST00000339302H2AFYchr5

134696184

-ZNF788chr19

12224136

+
Frame-shiftENST00000312469ENST00000339302H2AFYchr5

134696184

-ZNF788chr19

12224136

+
Frame-shiftENST00000511689ENST00000339302H2AFYchr5

134696184

-ZNF788chr19

12224136

+
In-frameENST00000510038ENST00000339302H2AFYchr5

134696184

-ZNF788chr19

12224136

+
intron-3CDSENST00000423969ENST00000339302H2AFYchr5

134696184

-ZNF788chr19

12224136

+
intron-3CDSENST00000512507ENST00000339302H2AFYchr5

134696184

-ZNF788chr19

12224136

+
intron-3UTRENST00000423969ENST00000430298H2AFYchr5

134696184

-ZNF788chr19

12224136

+
intron-3UTRENST00000512507ENST00000430298H2AFYchr5

134696184

-ZNF788chr19

12224136

+
intron-intronENST00000423969ENST00000397755H2AFYchr5

134696184

-ZNF788chr19

12224136

+
intron-intronENST00000423969ENST00000397759H2AFYchr5

134696184

-ZNF788chr19

12224136

+
intron-intronENST00000423969ENST00000596883H2AFYchr5

134696184

-ZNF788chr19

12224136

+
intron-intronENST00000512507ENST00000397755H2AFYchr5

134696184

-ZNF788chr19

12224136

+
intron-intronENST00000512507ENST00000397759H2AFYchr5

134696184

-ZNF788chr19

12224136

+
intron-intronENST00000512507ENST00000596883H2AFYchr5

134696184

-ZNF788chr19

12224136

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000510038H2AFYchr5134696184-ENST00000339302ZNF788chr1912224136+2075720132836234

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
ENST00000510038ENST00000339302H2AFYchr5134696184-ZNF788chr1912224136+0.0018946550.9981053

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Fusion Genomic Features for H2AFY-ZNF788


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.
genomic feature

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for H2AFY-ZNF788


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/chr5:134696184/chr19:12224136)
- 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: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneH2AFYchr5:134696184chr19:12224136ENST00000304332-59118_162195372.0Compositional biasNote=Lys-rich
HgeneH2AFYchr5:134696184chr19:12224136ENST00000312469-59118_162196370.0Compositional biasNote=Lys-rich
HgeneH2AFYchr5:134696184chr19:12224136ENST00000510038-59118_162196373.0Compositional biasNote=Lys-rich
HgeneH2AFYchr5:134696184chr19:12224136ENST00000511689-59118_162196373.0Compositional biasNote=Lys-rich
HgeneH2AFYchr5:134696184chr19:12224136ENST00000304332-592_117195372.0DomainNote=Histone H2A
HgeneH2AFYchr5:134696184chr19:12224136ENST00000312469-592_117196370.0DomainNote=Histone H2A
HgeneH2AFYchr5:134696184chr19:12224136ENST00000510038-592_117196373.0DomainNote=Histone H2A
HgeneH2AFYchr5:134696184chr19:12224136ENST00000511689-592_117196373.0DomainNote=Histone H2A
TgeneZNF788chr5:134696184chr19:12224136ENST000003393020324_820616.0DomainKRAB

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneH2AFYchr5:134696184chr19:12224136ENST00000304332-59184_370195372.0DomainMacro
HgeneH2AFYchr5:134696184chr19:12224136ENST00000312469-59184_370196370.0DomainMacro
HgeneH2AFYchr5:134696184chr19:12224136ENST00000510038-59184_370196373.0DomainMacro
HgeneH2AFYchr5:134696184chr19:12224136ENST00000511689-59184_370196373.0DomainMacro


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Fusion Gene Sequence for H2AFY-ZNF788


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>35497_35497_1_H2AFY-ZNF788_H2AFY_chr5_134696184_ENST00000510038_ZNF788_chr19_12224136_ENST00000339302_length(transcript)=2075nt_BP=720nt
GTCTACATTAGTAATTCCCAACTTGGGTCCGAAAGTGAACTTTTGCTGAAGCGAAGTAGCTAACCGCTTCCATGTGCAAGGCAGGTTCCA
GACTTCGGGTGTGCTCACTGATCCGCCTCCAGGGCCACCGCCATGTCGAGCCGCGGTGGGAAGAAGAAGTCCACCAAGACGTCCAGGTCT
GCCAAAGCAGGAGTCATCTTTCCCGTGGGGCGGATGCTGCGGTACATCAAGAAAGGCCACCCCAAGTACAGGATTGGAGTGGGGGCACCC
GTGTACATGGCCGCCGTCCTGGAATACCTGACAGCGGAGATTCTGGAGCTGGCTGGCAATGCAGCGAGAGACAACAAGAAGGGACGGGTC
ACACCCCGGCACATCCTGCTGGCTGTGGCCAATGATGAAGAGCTGAATCAGCTGCTAAAAGGAGTCACCATAGCCAGTGGGGGTGTGTTA
CCCAACATCCACCCCGAGTTGCTAGCGAAGAAGCGGGGATCCAAAGGAAAGTTGGAAGCCATCATCACACCACCCCCAGCCAAAAAGGCC
AAGTCTCCATCCCAGAAGAAGCCTGTATCTAAAAAAGCAGGAGGCAAGAAAGGGGCCCGGAAATCCAAGAAGAAGCAGGGTGAAGTCAGT
AAGGCAGCCAGCGCCGACAGCACAACCGAGGGCACACCTGCCGACGGCTTCACAGTCCTCTCCACCAAGAGCCTCTTCCTTGGCCAGAAG
GGAAGGTATTCAGTTTTTCCCGTTCCTTTCGTAGATATGAAAGGGCACACACTGGCGAAAAGCCCTGTGAATAAACAATGTGGGAAAGGA
TTTTTCATATCTTCTGTGGAGCTTTGAATGCATGAAAAGACAGACTACAGAGAAATGCTAAATGTAAGGCGTGTATAAAAGCATTTAGTA
ATTTCTCTTCCTTGCTTATACATGGAAGGATGCACACTGGAGAGAAGCCATATGAATGTAAGAATTGTGGGAAAGCCTTCACATCTGCCA
AGAGCCTTCAAAATCATGGAAGGACACACACCGGAGAGAAACCATGTGAATGCAAGCAATGTGGCAAAGCTTTCATTTGTTCCAGTTCCT
GTCAGAGACATGAAGAGACACATTCTGTTAATATGCATTCAGTTATCCTAATTCCTTTGAAACACAGAAAAAGAGTAGGGAAAGGACCTC
TGAGATAACTGTTTTCTGAGTTGAGAAGAGCTACTTGTGAATGGACAATTAAATCTAGATGTATTTAGATCTGATACAATTCATCTGTAG
CCAACCTTTTTTTAAATTTTTTTATTTTTTAGATGGAGTCTTGCTCTGTCGCCCAGACTGGAGTGCAGTGGCACGATCTTGGCTCACTGC
AACCTCCGCCTCCTGGGTTTAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGTAACCGCCATCACGCCTGGCTAATT
TTAGAGATGGAGTTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAAGTGATCCACCCACCTCGGCCTCCCAAAGTGCTGGG
ATTACAGGCGTGAGCCACTGCGCCCTGCCACCTATAGCCAATCTTAATGAGATTTCATAGGCACAGACAAGGAAGGTTATCAGTCACATA
TTAGAGGCACCACACAGGGAGAGCAGTGTGTGGCCACATGCTTCAGCCCATTTTTTCTGATTCTCTTGCTTGCAAATTAAGAGTATTCTC
CAAATCACTTGACTTTCCTTTTCTCAGAGTTATAGTTCTCCAGAGATGTCACCAGATGATTCACATTAAAGGTACATTTCCAGTTGACTT
TTTTATTTCAGATATTAGTAAATGATTACCAGAGAACTAATTCAAACTGTCATGGTTGGAAATACTCTGATGCTCAACTCCCTAATCTAT
AGAGTGAGTTAAGGTCTATACTCTTTTGCAAGCATTGTTCTAGTGGCAGTGACCCTGTTCATGATTCAGCCTGACATTTACTATGCTGCC
CTGAAAACCAACTAGATGGGAGCTTGTTTCTCTCTGCATTGTGTAGTGAGTGGTGTCACCCAGGACTTTCATGTGAGAAAAAGCACCTTG

>35497_35497_1_H2AFY-ZNF788_H2AFY_chr5_134696184_ENST00000510038_ZNF788_chr19_12224136_ENST00000339302_length(amino acids)=234AA_BP=196
MSSRGGKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAGNAARDNKKGRVTPRHILLAVANDEE
LNQLLKGVTIASGGVLPNIHPELLAKKRGSKGKLEAIITPPPAKKAKSPSQKKPVSKKAGGKKGARKSKKKQGEVSKAASADSTTEGTPA

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Fusion Gene PPI Analysis for H2AFY-ZNF788


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 (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for H2AFY-ZNF788


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for H2AFY-ZNF788


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource