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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:RFT1-DCP1A

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RFT1-DCP1A
FusionPDB ID: 73657
FusionGDB2.0 ID: 73657
HgeneTgene
Gene symbol

RFT1

DCP1A

Gene ID

91869

55802

Gene nameRFT1 homologdecapping mRNA 1A
SynonymsCDG1NHSA275986|Nbla00360|SMAD4IP1|SMIF
Cytomap

3p21.1

3p21.1

Type of geneprotein-codingprotein-coding
Descriptionprotein RFT1 homologRFT1, requiring fifty three 1 homologcongenital disorder of glycosylation 1Nputative endoplasmic reticulum multispan transmembrane proteinmRNA-decapping enzyme 1ADCP1 decapping enzyme homolog ADCP1 decapping enzyme-like protein ASmad4-interacting transcriptional co-activatordecapping enzyme hDcp1aputative protein product of Nbla00360transcription factor SMIF
Modification date2020031320200313
UniProtAcc.

Q9NPI6

Ensembl transtripts involved in fusion geneENST idsENST00000296292, ENST00000394738, 
ENST00000294241, ENST00000480258, 
ENST00000606822, ENST00000607628, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 6 X 4=962 X 2 X 2=8
# samples 63
** MAII scorelog2(6/96*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/8*10)=1.90689059560852
Context (manual curation of fusion genes in FusionPDB)

PubMed: RFT1 [Title/Abstract] AND DCP1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RFT1(53137969)-DCP1A(53353500), # samples:3
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

check buttonFusion gene breakpoints across RFT1 (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 DCP1A (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
ChimerDB4BRCATCGA-A7-A13D-01ARFT1chr3

53137969

-DCP1Achr3

53353500

-
ChimerDB4BRCATCGA-A7-A13D-01BRFT1chr3

53137969

-DCP1Achr3

53353500

-
ChimerDB4BRCATCGA-A7-A13DRFT1chr3

53137968

-DCP1Achr3

53353500

-


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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)
ENST00000296292RFT1chr353137968-ENST00000607628DCP1Achr353353500-67661164352614859
ENST00000394738RFT1chr353137968-ENST00000607628DCP1Achr353353500-66401038262488820
ENST00000296292RFT1chr353137969-ENST00000607628DCP1Achr353353500-67661164352614859
ENST00000394738RFT1chr353137969-ENST00000607628DCP1Achr353353500-66401038262488820

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
ENST00000296292ENST00000607628RFT1chr353137968-DCP1Achr353353500-0.0012303330.9987697
ENST00000394738ENST00000607628RFT1chr353137968-DCP1Achr353353500-0.0008734110.9991266
ENST00000296292ENST00000607628RFT1chr353137969-DCP1Achr353353500-0.0012303330.9987697
ENST00000394738ENST00000607628RFT1chr353137969-DCP1Achr353353500-0.0008734110.9991266

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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

>73657_73657_1_RFT1-DCP1A_RFT1_chr3_53137968_ENST00000296292_DCP1A_chr3_53353500_ENST00000607628_length(amino acids)=859AA_BP=376
MVSEPGAEAMGSQEVLGHAARLASSGLLLQVLFRLITFVLNAFILRFLSKEIVGVVNVRLTLLYSTTLFLAREAFRRACLSGGTQRDWSQ
TLNLLWLTVPLGVFWSLFLGWIWLQLLEVPDPNVVPHYATGVVLFGLSAVVELLGEPFWVLAQAHMFVKLKVIAESLSVILKSVLTAFLV
LWLPHWGLYIFSLAQLFYTTVLVLCYVIYFTKLLGSPESTKLQTLPVSRITDLLPNITRNGAFINWKEAKLTWSFFKQSFLKQILTEGER
YVMTFLNVLNFGDQGVYDIVNNLGSLVARLIFQPIEESFYIFFAKVLERGKDATLQKQEDVAVAAAVLESLLKLALLAGLTITVFGFAYS
QLALDIYGGTMLSSGSVSIYSIWFYDKNDCHRIAKLMADVVEEETRRSQQAARDKQSPSQANGCSDHRPIDILEMLSRAKDEYERNQMGD
SNISSPGLQPSTQLSNLGSTETLEEMPSGSQDKSAPSGHKHLTVEELFGTSLPKEQPAVVGLDSEEMERLPGDASQKEPNSFLPFPFEQL
GGAPQSETLGVPSAAHHSVQPEITTPVLITPASITQSNEKHAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPRNSTMMQAVKTTPRQRSPL
LNQPVPELSHASLIANQSPFRAPLNVTNTAGTSLPSVDLLQKLRLTPQHDQIQTQPLGKGAMVASFSPAAGQLATPESFIEPPSKTAAAR
VAASASLSNMVLAPLQSMQQNQDPEVFVQPKVLSSASAIPVAGAPLVTATTTAVSSVLLAPSVFQQTVTRSSDLERKASSPSPLTIGTPE

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

>73657_73657_2_RFT1-DCP1A_RFT1_chr3_53137968_ENST00000394738_DCP1A_chr3_53353500_ENST00000607628_length(amino acids)=820AA_BP=337
MVSEPGAEAMGSQEVLGHAARLASSGLLLQVLFRLITFVLNAFILRFLSKEIVGVVNVRVPLGVFWSLFLGWIWLQLLEVPDPNVVPHYA
TGVVLFGLSAVVELLGEPFWVLAQAHMFVKLKVIAESLSVILKSVLTAFLVLWLPHWGLYIFSLAQLFYTTVLVLCYVIYFTKLLGSPES
TKLQTLPVSRITDLLPNITRNGAFINWKEAKLTWSFFKQSFLKQILTEGERYVMTFLNVLNFGDQGVYDIVNNLGSLVARLIFQPIEESF
YIFFAKVLERGKDATLQKQEDVAVAAAVLESLLKLALLAGLTITVFGFAYSQLALDIYGGTMLSSGSVSIYSIWFYDKNDCHRIAKLMAD
VVEEETRRSQQAARDKQSPSQANGCSDHRPIDILEMLSRAKDEYERNQMGDSNISSPGLQPSTQLSNLGSTETLEEMPSGSQDKSAPSGH
KHLTVEELFGTSLPKEQPAVVGLDSEEMERLPGDASQKEPNSFLPFPFEQLGGAPQSETLGVPSAAHHSVQPEITTPVLITPASITQSNE
KHAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPRNSTMMQAVKTTPRQRSPLLNQPVPELSHASLIANQSPFRAPLNVTNTAGTSLPSVDL
LQKLRLTPQHDQIQTQPLGKGAMVASFSPAAGQLATPESFIEPPSKTAAARVAASASLSNMVLAPLQSMQQNQDPEVFVQPKVLSSASAI
PVAGAPLVTATTTAVSSVLLAPSVFQQTVTRSSDLERKASSPSPLTIGTPESQRKPSIILSKSQLQDTLIHLIKNDSSFLSTLHEVYLQV

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

>73657_73657_3_RFT1-DCP1A_RFT1_chr3_53137969_ENST00000296292_DCP1A_chr3_53353500_ENST00000607628_length(amino acids)=859AA_BP=376
MVSEPGAEAMGSQEVLGHAARLASSGLLLQVLFRLITFVLNAFILRFLSKEIVGVVNVRLTLLYSTTLFLAREAFRRACLSGGTQRDWSQ
TLNLLWLTVPLGVFWSLFLGWIWLQLLEVPDPNVVPHYATGVVLFGLSAVVELLGEPFWVLAQAHMFVKLKVIAESLSVILKSVLTAFLV
LWLPHWGLYIFSLAQLFYTTVLVLCYVIYFTKLLGSPESTKLQTLPVSRITDLLPNITRNGAFINWKEAKLTWSFFKQSFLKQILTEGER
YVMTFLNVLNFGDQGVYDIVNNLGSLVARLIFQPIEESFYIFFAKVLERGKDATLQKQEDVAVAAAVLESLLKLALLAGLTITVFGFAYS
QLALDIYGGTMLSSGSVSIYSIWFYDKNDCHRIAKLMADVVEEETRRSQQAARDKQSPSQANGCSDHRPIDILEMLSRAKDEYERNQMGD
SNISSPGLQPSTQLSNLGSTETLEEMPSGSQDKSAPSGHKHLTVEELFGTSLPKEQPAVVGLDSEEMERLPGDASQKEPNSFLPFPFEQL
GGAPQSETLGVPSAAHHSVQPEITTPVLITPASITQSNEKHAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPRNSTMMQAVKTTPRQRSPL
LNQPVPELSHASLIANQSPFRAPLNVTNTAGTSLPSVDLLQKLRLTPQHDQIQTQPLGKGAMVASFSPAAGQLATPESFIEPPSKTAAAR
VAASASLSNMVLAPLQSMQQNQDPEVFVQPKVLSSASAIPVAGAPLVTATTTAVSSVLLAPSVFQQTVTRSSDLERKASSPSPLTIGTPE

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

>73657_73657_4_RFT1-DCP1A_RFT1_chr3_53137969_ENST00000394738_DCP1A_chr3_53353500_ENST00000607628_length(amino acids)=820AA_BP=337
MVSEPGAEAMGSQEVLGHAARLASSGLLLQVLFRLITFVLNAFILRFLSKEIVGVVNVRVPLGVFWSLFLGWIWLQLLEVPDPNVVPHYA
TGVVLFGLSAVVELLGEPFWVLAQAHMFVKLKVIAESLSVILKSVLTAFLVLWLPHWGLYIFSLAQLFYTTVLVLCYVIYFTKLLGSPES
TKLQTLPVSRITDLLPNITRNGAFINWKEAKLTWSFFKQSFLKQILTEGERYVMTFLNVLNFGDQGVYDIVNNLGSLVARLIFQPIEESF
YIFFAKVLERGKDATLQKQEDVAVAAAVLESLLKLALLAGLTITVFGFAYSQLALDIYGGTMLSSGSVSIYSIWFYDKNDCHRIAKLMAD
VVEEETRRSQQAARDKQSPSQANGCSDHRPIDILEMLSRAKDEYERNQMGDSNISSPGLQPSTQLSNLGSTETLEEMPSGSQDKSAPSGH
KHLTVEELFGTSLPKEQPAVVGLDSEEMERLPGDASQKEPNSFLPFPFEQLGGAPQSETLGVPSAAHHSVQPEITTPVLITPASITQSNE
KHAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPRNSTMMQAVKTTPRQRSPLLNQPVPELSHASLIANQSPFRAPLNVTNTAGTSLPSVDL
LQKLRLTPQHDQIQTQPLGKGAMVASFSPAAGQLATPESFIEPPSKTAAARVAASASLSNMVLAPLQSMQQNQDPEVFVQPKVLSSASAI
PVAGAPLVTATTTAVSSVLLAPSVFQQTVTRSSDLERKASSPSPLTIGTPESQRKPSIILSKSQLQDTLIHLIKNDSSFLSTLHEVYLQV

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

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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/chr3:53137969/chr3:53353500)
- 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
.DCP1A

Q9NPI6

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: Necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Contributes to the transactivation of target genes after stimulation by TGFB1. {ECO:0000269|PubMed:11836524, ECO:0000269|PubMed:12417715}.

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
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-1013123_143367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-1013155_174367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-101316_36367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-1013187_207367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-1013335_355367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-101342_62367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-101385_105367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-1013123_143367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-1013155_174367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-101316_36367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-1013187_207367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-1013335_355367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-101342_62367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-101385_105367.3333333333333542.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-1013376_396367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-1013404_423367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-1013428_450367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-1013470_490367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137968chr3:53353500ENST00000296292-1013499_519367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-1013376_396367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-1013404_423367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-1013428_450367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-1013470_490367.3333333333333542.0TransmembraneHelical
HgeneRFT1chr3:53137969chr3:53353500ENST00000296292-1013499_519367.3333333333333542.0TransmembraneHelical


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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 >>>1647_RFT1_53137969_DCP1A_53353500_ranked_0.pdbRFT15313796953137969ENST00000607628DCP1Achr353353500-
MVSEPGAEAMGSQEVLGHAARLASSGLLLQVLFRLITFVLNAFILRFLSKEIVGVVNVRLTLLYSTTLFLAREAFRRACLSGGTQRDWSQ
TLNLLWLTVPLGVFWSLFLGWIWLQLLEVPDPNVVPHYATGVVLFGLSAVVELLGEPFWVLAQAHMFVKLKVIAESLSVILKSVLTAFLV
LWLPHWGLYIFSLAQLFYTTVLVLCYVIYFTKLLGSPESTKLQTLPVSRITDLLPNITRNGAFINWKEAKLTWSFFKQSFLKQILTEGER
YVMTFLNVLNFGDQGVYDIVNNLGSLVARLIFQPIEESFYIFFAKVLERGKDATLQKQEDVAVAAAVLESLLKLALLAGLTITVFGFAYS
QLALDIYGGTMLSSGSVSIYSIWFYDKNDCHRIAKLMADVVEEETRRSQQAARDKQSPSQANGCSDHRPIDILEMLSRAKDEYERNQMGD
SNISSPGLQPSTQLSNLGSTETLEEMPSGSQDKSAPSGHKHLTVEELFGTSLPKEQPAVVGLDSEEMERLPGDASQKEPNSFLPFPFEQL
GGAPQSETLGVPSAAHHSVQPEITTPVLITPASITQSNEKHAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPRNSTMMQAVKTTPRQRSPL
LNQPVPELSHASLIANQSPFRAPLNVTNTAGTSLPSVDLLQKLRLTPQHDQIQTQPLGKGAMVASFSPAAGQLATPESFIEPPSKTAAAR
VAASASLSNMVLAPLQSMQQNQDPEVFVQPKVLSSASAIPVAGAPLVTATTTAVSSVLLAPSVFQQTVTRSSDLERKASSPSPLTIGTPE
859


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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.
RFT1_pLDDT.png
all structure
all structure
DCP1A_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


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
RFT1
DCP1A


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 RFT1-DCP1A


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 RFT1-DCP1A


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