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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:RYBP-FHIT

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RYBP-FHIT
FusionPDB ID: 78780
FusionGDB2.0 ID: 78780
HgeneTgene
Gene symbol

RYBP

FHIT

Gene ID

23429

2272

Gene nameRING1 and YY1 binding proteinfragile histidine triad diadenosine triphosphatase
SynonymsAAP1|APAP-1|DEDAF|YEAF1AP3Aase|FRA3B
Cytomap

3p13

3p14.2

Type of geneprotein-codingprotein-coding
DescriptionRING1 and YY1-binding proteinDED-associated factorYY1 and E4TF1 associated factor 1apoptin-associating protein 1death effector domain-associated factorring1 interactor RYBPbis(5'-adenosyl)-triphosphataseAP3A hydrolasediadenosine 5',5'''-P1,P3-triphosphate hydrolasedinucleosidetriphosphatase
Modification date2020031320200313
UniProtAcc.

P49789

Ensembl transtripts involved in fusion geneENST idsENST00000477973, ENST00000341848, 
ENST00000466788, ENST00000468189, 
ENST00000476844, ENST00000492590, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score9 X 4 X 6=21627 X 20 X 11=5940
# samples 1132
** MAII scorelog2(11/216*10)=-0.973527788638809
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(32/5940*10)=-4.21431912080077
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: RYBP [Title/Abstract] AND FHIT [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RYBP(72495647)-FHIT(59738047), # samples:3
Anticipated loss of major functional domain due to fusion event.RYBP-FHIT 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.
RYBP-FHIT 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.
RYBP-FHIT 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.
RYBP-FHIT 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
HgeneRYBP

GO:0035518

histone H2A monoubiquitination

16943429

TgeneFHIT

GO:0006163

purine nucleotide metabolic process

9323207


check buttonFusion gene breakpoints across RYBP (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 FHIT (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
ChimerDB4PRADTCGA-KK-A8IJ-01ARYBPchr3

72495647

-FHITchr3

59738047

-
ChimerDB4THYMTCGA-4V-A9QJ-01ARYBPchr3

72495647

-FHITchr3

59738047

-
ChimerDB4THYMTCGA-4V-A9QJRYBPchr3

72495646

-FHITchr3

59738047

-
ChimerDB4THYMTCGA-4V-A9QJRYBPchr3

72495647

-FHITchr3

59738047

-


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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)
ENST00000477973RYBPchr372495646-ENST00000476844FHITchr359738047-78342382564160
ENST00000477973RYBPchr372495646-ENST00000492590FHITchr359738047-7944236361212
ENST00000477973RYBPchr372495647-ENST00000476844FHITchr359738047-78342382564160
ENST00000477973RYBPchr372495647-ENST00000492590FHITchr359738047-7944236361212

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
ENST00000477973ENST00000476844RYBPchr372495646-FHITchr359738047-0.25316330.74683666
ENST00000477973ENST00000492590RYBPchr372495646-FHITchr359738047-0.259035560.7409644
ENST00000477973ENST00000476844RYBPchr372495647-FHITchr359738047-0.25316330.74683666
ENST00000477973ENST00000492590RYBPchr372495647-FHITchr359738047-0.259035560.7409644

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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

>78780_78780_1_RYBP-FHIT_RYBP_chr3_72495646_ENST00000477973_FHIT_chr3_59738047_ENST00000476844_length(amino acids)=160AA_BP=113
MQGASGGARFPSSLSLPVPGKGGWVVSRAKFPALDSCEITTAHPRLCFAVSPPFSCSLPLPSLFPHSPLLGRPKRQAKPAADEGFWDCSV

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

>78780_78780_2_RYBP-FHIT_RYBP_chr3_72495646_ENST00000477973_FHIT_chr3_59738047_ENST00000492590_length(amino acids)=212AA_BP=0
MKKLHFHADSVPLGERRGAVFKLVGNSSFAGIQDLKNICVTESRPAELRLLLPFPPLISKRQESPPCHVSGAGGGAFPHIADAAFKGFST
VSEGADATIPKPFVCGRFRLSFWPSEEWRVGEKGGKRQGAGKRGRDSKTQTRVSRRNFAGIQCWKLRSGDHPPTLSGDWKRERGREPGAP

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

>78780_78780_3_RYBP-FHIT_RYBP_chr3_72495647_ENST00000477973_FHIT_chr3_59738047_ENST00000476844_length(amino acids)=160AA_BP=113
MQGASGGARFPSSLSLPVPGKGGWVVSRAKFPALDSCEITTAHPRLCFAVSPPFSCSLPLPSLFPHSPLLGRPKRQAKPAADEGFWDCSV

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

>78780_78780_4_RYBP-FHIT_RYBP_chr3_72495647_ENST00000477973_FHIT_chr3_59738047_ENST00000492590_length(amino acids)=212AA_BP=0
MKKLHFHADSVPLGERRGAVFKLVGNSSFAGIQDLKNICVTESRPAELRLLLPFPPLISKRQESPPCHVSGAGGGAFPHIADAAFKGFST
VSEGADATIPKPFVCGRFRLSFWPSEEWRVGEKGGKRQGAGKRGRDSKTQTRVSRRNFAGIQCWKLRSGDHPPTLSGDWKRERGREPGAP

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

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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/chr3:72495647/chr3:59738047)
- 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
.FHIT

P49789

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: Possesses dinucleoside triphosphate hydrolase activity (PubMed:12574506, PubMed:15182206, PubMed:8794732, PubMed:9323207, PubMed:9576908, PubMed:9543008). Cleaves P(1)-P(3)-bis(5'-adenosyl) triphosphate (Ap3A) to yield AMP and ADP (PubMed:12574506, PubMed:15182206, PubMed:8794732, PubMed:9323207, PubMed:9576908, PubMed:9543008). Can also hydrolyze P(1)-P(4)-bis(5'-adenosyl) tetraphosphate (Ap4A), but has extremely low activity with ATP (PubMed:8794732). Exhibits adenylylsulfatase activity, hydrolyzing adenosine 5'-phosphosulfate to yield AMP and sulfate (PubMed:18694747). Exhibits adenosine 5'-monophosphoramidase activity, hydrolyzing purine nucleotide phosphoramidates with a single phosphate group such as adenosine 5'monophosphoramidate (AMP-NH2) to yield AMP and NH2 (PubMed:18694747). Exhibits adenylylsulfate-ammonia adenylyltransferase, catalyzing the ammonolysis of adenosine 5'-phosphosulfate resulting in the formation of adenosine 5'-phosphoramidate (PubMed:26181368). Also catalyzes the ammonolysis of adenosine 5-phosphorofluoridate and diadenosine triphosphate (PubMed:26181368). Modulates transcriptional activation by CTNNB1 and thereby contributes to regulate the expression of genes essential for cell proliferation and survival, such as CCND1 and BIRC5 (PubMed:18077326). Plays a role in the induction of apoptosis via SRC and AKT1 signaling pathways (PubMed:16407838). Inhibits MDM2-mediated proteasomal degradation of p53/TP53 and thereby plays a role in p53/TP53-mediated apoptosis (PubMed:15313915). Induction of apoptosis depends on the ability of FHIT to bind P(1)-P(3)-bis(5'-adenosyl) triphosphate or related compounds, but does not require its catalytic activity, it may in part come from the mitochondrial form, which sensitizes the low-affinity Ca(2+) transporters, enhancing mitochondrial calcium uptake (PubMed:12574506, PubMed:19622739). Functions as tumor suppressor (By similarity). {ECO:0000250|UniProtKB:O89106, ECO:0000269|PubMed:12574506, ECO:0000269|PubMed:15313915, ECO:0000269|PubMed:16407838, ECO:0000269|PubMed:18077326, ECO:0000269|PubMed:18694747, ECO:0000269|PubMed:19622739, ECO:0000269|PubMed:26181368, ECO:0000269|PubMed:8794732, ECO:0000269|PubMed:9323207, ECO:0000269|PubMed:9543008}.

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
HgeneRYBPchr3:72495646chr3:59738047ENST00000477973-1473_76141.0317.3333333333333Compositional biasNote=Poly-Pro
HgeneRYBPchr3:72495646chr3:59738047ENST00000477973-1477_119141.0317.3333333333333Compositional biasNote=Lys-rich
HgeneRYBPchr3:72495647chr3:59738047ENST00000477973-1473_76141.0317.3333333333333Compositional biasNote=Poly-Pro
HgeneRYBPchr3:72495647chr3:59738047ENST00000477973-1477_119141.0317.3333333333333Compositional biasNote=Lys-rich
HgeneRYBPchr3:72495646chr3:59738047ENST00000477973-1421_50141.0317.3333333333333Zinc fingerRanBP2-type
HgeneRYBPchr3:72495647chr3:59738047ENST00000477973-1421_50141.0317.3333333333333Zinc fingerRanBP2-type

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRYBPchr3:72495646chr3:59738047ENST00000477973-14179_214141.0317.3333333333333Compositional biasNote=Ser-rich
HgeneRYBPchr3:72495647chr3:59738047ENST00000477973-14179_214141.0317.3333333333333Compositional biasNote=Ser-rich
TgeneFHITchr3:72495646chr3:59738047ENST00000341848352_109116.0148.0DomainHIT
TgeneFHITchr3:72495646chr3:59738047ENST00000468189792_109116.0148.0DomainHIT
TgeneFHITchr3:72495646chr3:59738047ENST000004768447102_109116.0214.0DomainHIT
TgeneFHITchr3:72495646chr3:59738047ENST000004925907102_109116.0205.33333333333334DomainHIT
TgeneFHITchr3:72495647chr3:59738047ENST00000341848352_109116.0148.0DomainHIT
TgeneFHITchr3:72495647chr3:59738047ENST00000468189792_109116.0148.0DomainHIT
TgeneFHITchr3:72495647chr3:59738047ENST000004768447102_109116.0214.0DomainHIT
TgeneFHITchr3:72495647chr3:59738047ENST000004925907102_109116.0205.33333333333334DomainHIT
TgeneFHITchr3:72495646chr3:59738047ENST000003418483594_98116.0148.0MotifHistidine triad motif
TgeneFHITchr3:72495646chr3:59738047ENST000004681897994_98116.0148.0MotifHistidine triad motif
TgeneFHITchr3:72495646chr3:59738047ENST0000047684471094_98116.0214.0MotifHistidine triad motif
TgeneFHITchr3:72495646chr3:59738047ENST0000049259071094_98116.0205.33333333333334MotifHistidine triad motif
TgeneFHITchr3:72495647chr3:59738047ENST000003418483594_98116.0148.0MotifHistidine triad motif
TgeneFHITchr3:72495647chr3:59738047ENST000004681897994_98116.0148.0MotifHistidine triad motif
TgeneFHITchr3:72495647chr3:59738047ENST0000047684471094_98116.0214.0MotifHistidine triad motif
TgeneFHITchr3:72495647chr3:59738047ENST0000049259071094_98116.0205.33333333333334MotifHistidine triad motif
TgeneFHITchr3:72495646chr3:59738047ENST000003418483589_92116.0148.0Nucleotide bindingSubstrate
TgeneFHITchr3:72495646chr3:59738047ENST000004681897989_92116.0148.0Nucleotide bindingSubstrate
TgeneFHITchr3:72495646chr3:59738047ENST0000047684471089_92116.0214.0Nucleotide bindingSubstrate
TgeneFHITchr3:72495646chr3:59738047ENST0000049259071089_92116.0205.33333333333334Nucleotide bindingSubstrate
TgeneFHITchr3:72495647chr3:59738047ENST000003418483589_92116.0148.0Nucleotide bindingSubstrate
TgeneFHITchr3:72495647chr3:59738047ENST000004681897989_92116.0148.0Nucleotide bindingSubstrate
TgeneFHITchr3:72495647chr3:59738047ENST0000047684471089_92116.0214.0Nucleotide bindingSubstrate
TgeneFHITchr3:72495647chr3:59738047ENST0000049259071089_92116.0205.33333333333334Nucleotide bindingSubstrate


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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 >>>307_RYBP_72495647_FHIT_59738047_ranked_0.pdbRYBP7249564772495647ENST00000492590FHITchr359738047-
MKKLHFHADSVPLGERRGAVFKLVGNSSFAGIQDLKNICVTESRPAELRLLLPFPPLISKRQESPPCHVSGAGGGAFPHIADAAFKGFST
VSEGADATIPKPFVCGRFRLSFWPSEEWRVGEKGGKRQGAGKRGRDSKTQTRVSRRNFAGIQCWKLRSGDHPPTLSGDWKRERGREPGAP
212


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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.
RYBP_pLDDT.png
all structure
all structure
FHIT_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
FHITFHIT, UBE2I, CTNNB1, LEF1, TRIM23, RAB40B, MDM2, REL, TP53, ARHGAP19, MTMR6, RABL2A, CHEK1, DDIT4L, SPERT, FDCSP, GAST, GGH, BCAS2, PRPF6, YTHDF1, Rbm14,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
RYBP
FHITall 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
HgeneRYBPchr3:72495646chr3:59738047ENST00000477973-14143_226141.0317.3333333333333GABPB1 and FANK1
HgeneRYBPchr3:72495647chr3:59738047ENST00000477973-14143_226141.0317.3333333333333GABPB1 and FANK1


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Related Drugs to RYBP-FHIT


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 RYBP-FHIT


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
TgeneFHITC0024121Lung Neoplasms2CTD_human
TgeneFHITC0025500Mesothelioma2CTD_human
TgeneFHITC0242379Malignant neoplasm of lung2CTD_human
TgeneFHITC0007097Carcinoma1CTD_human
TgeneFHITC0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneFHITC0013146Drug abuse1CTD_human
TgeneFHITC0013170Drug habituation1CTD_human
TgeneFHITC0013222Drug Use Disorders1CTD_human
TgeneFHITC0023903Liver neoplasms1CTD_human
TgeneFHITC0024623Malignant neoplasm of stomach1CTD_human
TgeneFHITC0029231Organic Mental Disorders, Substance-Induced1CTD_human
TgeneFHITC0033578Prostatic Neoplasms1CTD_human
TgeneFHITC0038356Stomach Neoplasms1CTD_human
TgeneFHITC0038580Substance Dependence1CTD_human
TgeneFHITC0038586Substance Use Disorders1CTD_human
TgeneFHITC0042076Urologic Neoplasms1CTD_human
TgeneFHITC0205696Anaplastic carcinoma1CTD_human
TgeneFHITC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneFHITC0205698Undifferentiated carcinoma1CTD_human
TgeneFHITC0205699Carcinomatosis1CTD_human
TgeneFHITC0236733Amphetamine-Related Disorders1CTD_human
TgeneFHITC0236804Amphetamine Addiction1CTD_human
TgeneFHITC0236807Amphetamine Abuse1CTD_human
TgeneFHITC0236969Substance-Related Disorders1CTD_human
TgeneFHITC0345904Malignant neoplasm of liver1CTD_human
TgeneFHITC0376358Malignant neoplasm of prostate1CTD_human
TgeneFHITC0740858Substance abuse problem1CTD_human
TgeneFHITC0751571Cancer of Urinary Tract1CTD_human
TgeneFHITC1510472Drug Dependence1CTD_human
TgeneFHITC1708349Hereditary Diffuse Gastric Cancer1CTD_human
TgeneFHITC4316881Prescription Drug Abuse1CTD_human