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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:HMCES-HMCES (FusionGDB2 ID:36774)

Fusion Gene Summary for HMCES-HMCES

check button Fusion gene summary
Fusion gene informationFusion gene name: HMCES-HMCES
Fusion gene ID: 36774
HgeneTgene
Gene symbol

HMCES

HMCES

Gene ID

56941

56941

Gene name5-hydroxymethylcytosine binding, ES cell specific5-hydroxymethylcytosine binding, ES cell specific
SynonymsC3orf37|DC12|SRAPD1C3orf37|DC12|SRAPD1
Cytomap

3q21.3

3q21.3

Type of geneprotein-codingprotein-coding
Descriptionabasic site processing protein HMCES5-hydroxymethylcytosine (hmC) binding, ES cell-specificES cell-specific 5hmC-binding proteinSOS response associated peptidase domain containing 1SRAP domain-containing protein 1UPF0361 protein C3orf37embryonic steabasic site processing protein HMCES5-hydroxymethylcytosine (hmC) binding, ES cell-specificES cell-specific 5hmC-binding proteinSOS response associated peptidase domain containing 1SRAP domain-containing protein 1UPF0361 protein C3orf37embryonic ste
Modification date2020031320200313
UniProtAcc

Q96FZ2

Q96FZ2

Ensembl transtripts involved in fusion geneENST00000383463, ENST00000502878, 
ENST00000389735, ENST00000417226, 
ENST00000383463, ENST00000389735, 
ENST00000417226, ENST00000502878, 
Fusion gene scores* DoF score4 X 5 X 2=406 X 5 X 4=120
# samples 57
** MAII scorelog2(5/40*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(7/120*10)=-0.777607578663552
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HMCES [Title/Abstract] AND HMCES [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHMCES(129024976)-HMCES(129024318), # samples:1
HMCES(129024258)-HMCES(129024307), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneHMCES

GO:0006974

cellular response to DNA damage stimulus

30554877

TgeneHMCES

GO:0006974

cellular response to DNA damage stimulus

30554877


check buttonFusion gene breakpoints across HMCES (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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

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/ABF513139HMCESchr3

129024976

-HMCESchr3

129024318

+
ChiTaRS5.0N/ABG259212HMCESchr3

129024258

-HMCESchr3

129024307

+


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Fusion Gene ORF analysis for HMCES-HMCES

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
3UTR-3UTRENST00000383463ENST00000383463HMCESchr3

129024976

-HMCESchr3

129024318

+
3UTR-3UTRENST00000383463ENST00000383463HMCESchr3

129024258

-HMCESchr3

129024307

+
3UTR-3UTRENST00000502878ENST00000383463HMCESchr3

129024258

-HMCESchr3

129024307

+
3UTR-intronENST00000383463ENST00000389735HMCESchr3

129024976

-HMCESchr3

129024318

+
3UTR-intronENST00000383463ENST00000389735HMCESchr3

129024258

-HMCESchr3

129024307

+
3UTR-intronENST00000383463ENST00000417226HMCESchr3

129024976

-HMCESchr3

129024318

+
3UTR-intronENST00000383463ENST00000417226HMCESchr3

129024258

-HMCESchr3

129024307

+
3UTR-intronENST00000383463ENST00000502878HMCESchr3

129024976

-HMCESchr3

129024318

+
3UTR-intronENST00000383463ENST00000502878HMCESchr3

129024258

-HMCESchr3

129024307

+
3UTR-intronENST00000502878ENST00000389735HMCESchr3

129024258

-HMCESchr3

129024307

+
3UTR-intronENST00000502878ENST00000417226HMCESchr3

129024258

-HMCESchr3

129024307

+
3UTR-intronENST00000502878ENST00000502878HMCESchr3

129024258

-HMCESchr3

129024307

+
intron-3UTRENST00000389735ENST00000383463HMCESchr3

129024976

-HMCESchr3

129024318

+
intron-3UTRENST00000389735ENST00000383463HMCESchr3

129024258

-HMCESchr3

129024307

+
intron-3UTRENST00000417226ENST00000383463HMCESchr3

129024976

-HMCESchr3

129024318

+
intron-3UTRENST00000417226ENST00000383463HMCESchr3

129024258

-HMCESchr3

129024307

+
intron-3UTRENST00000502878ENST00000383463HMCESchr3

129024976

-HMCESchr3

129024318

+
intron-intronENST00000389735ENST00000389735HMCESchr3

129024976

-HMCESchr3

129024318

+
intron-intronENST00000389735ENST00000389735HMCESchr3

129024258

-HMCESchr3

129024307

+
intron-intronENST00000389735ENST00000417226HMCESchr3

129024976

-HMCESchr3

129024318

+
intron-intronENST00000389735ENST00000417226HMCESchr3

129024258

-HMCESchr3

129024307

+
intron-intronENST00000389735ENST00000502878HMCESchr3

129024976

-HMCESchr3

129024318

+
intron-intronENST00000389735ENST00000502878HMCESchr3

129024258

-HMCESchr3

129024307

+
intron-intronENST00000417226ENST00000389735HMCESchr3

129024976

-HMCESchr3

129024318

+
intron-intronENST00000417226ENST00000389735HMCESchr3

129024258

-HMCESchr3

129024307

+
intron-intronENST00000417226ENST00000417226HMCESchr3

129024976

-HMCESchr3

129024318

+
intron-intronENST00000417226ENST00000417226HMCESchr3

129024258

-HMCESchr3

129024307

+
intron-intronENST00000417226ENST00000502878HMCESchr3

129024976

-HMCESchr3

129024318

+
intron-intronENST00000417226ENST00000502878HMCESchr3

129024258

-HMCESchr3

129024307

+
intron-intronENST00000502878ENST00000389735HMCESchr3

129024976

-HMCESchr3

129024318

+
intron-intronENST00000502878ENST00000417226HMCESchr3

129024976

-HMCESchr3

129024318

+
intron-intronENST00000502878ENST00000502878HMCESchr3

129024976

-HMCESchr3

129024318

+

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)

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

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Fusion Genomic Features for HMCES-HMCES


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.

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 HMCES-HMCES


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/:129024976/:129024318)
- 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
HMCES

Q96FZ2

HMCES

Q96FZ2

FUNCTION: Sensor of abasic sites in single-stranded DNA (ssDNA) required to preserve genome integrity by promoting error-free repair of abasic sites (PubMed:30554877, PubMed:31235915, PubMed:31235913). Acts as an enzyme that recognizes and binds abasic sites in ssDNA at replication forks and chemically modifies the lesion by forming a covalent cross-link with DNA: forms a stable thiazolidine linkage between a ring-opened abasic site and the alpha-amino and sulfhydryl substituents of its N-terminal catalytic cysteine residue (PubMed:30554877, PubMed:31235913). The HMCES DNA-protein cross-link is then degraded by the proteasome (PubMed:30554877). Promotes error-free repair of abasic sites by acting as a 'suicide' enzyme that is degraded, thereby protecting abasic sites from translesion synthesis (TLS) polymerases and endonucleases that are error-prone and would generate mutations and double-strand breaks (PubMed:30554877). Has preference for ssDNA, but can also accommodate double-stranded DNA with 3' or 5' overhang (dsDNA), and dsDNA-ssDNA 3' junction (PubMed:31235915, PubMed:31806351). Also involved in class switch recombination (CSR) in B-cells independently of the formation of a DNA-protein cross-link: acts by binding and protecting ssDNA overhangs to promote DNA double-strand break repair through the microhomology-mediated alternative-end-joining (Alt-EJ) pathway (By similarity). Acts as a protease: mediates autocatalytic processing of its N-terminal methionine in order to expose the catalytic cysteine (By similarity). {ECO:0000250|UniProtKB:Q8R1M0, ECO:0000269|PubMed:30554877, ECO:0000269|PubMed:31235913, ECO:0000269|PubMed:31235915, ECO:0000269|PubMed:31806351}.FUNCTION: Sensor of abasic sites in single-stranded DNA (ssDNA) required to preserve genome integrity by promoting error-free repair of abasic sites (PubMed:30554877, PubMed:31235915, PubMed:31235913). Acts as an enzyme that recognizes and binds abasic sites in ssDNA at replication forks and chemically modifies the lesion by forming a covalent cross-link with DNA: forms a stable thiazolidine linkage between a ring-opened abasic site and the alpha-amino and sulfhydryl substituents of its N-terminal catalytic cysteine residue (PubMed:30554877, PubMed:31235913). The HMCES DNA-protein cross-link is then degraded by the proteasome (PubMed:30554877). Promotes error-free repair of abasic sites by acting as a 'suicide' enzyme that is degraded, thereby protecting abasic sites from translesion synthesis (TLS) polymerases and endonucleases that are error-prone and would generate mutations and double-strand breaks (PubMed:30554877). Has preference for ssDNA, but can also accommodate double-stranded DNA with 3' or 5' overhang (dsDNA), and dsDNA-ssDNA 3' junction (PubMed:31235915, PubMed:31806351). Also involved in class switch recombination (CSR) in B-cells independently of the formation of a DNA-protein cross-link: acts by binding and protecting ssDNA overhangs to promote DNA double-strand break repair through the microhomology-mediated alternative-end-joining (Alt-EJ) pathway (By similarity). Acts as a protease: mediates autocatalytic processing of its N-terminal methionine in order to expose the catalytic cysteine (By similarity). {ECO:0000250|UniProtKB:Q8R1M0, ECO:0000269|PubMed:30554877, ECO:0000269|PubMed:31235913, ECO:0000269|PubMed:31235915, ECO:0000269|PubMed:31806351}.

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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for HMCES-HMCES


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.

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Fusion Gene PPI Analysis for HMCES-HMCES


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 HMCES-HMCES


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 HMCES-HMCES


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