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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:KPNA1-GMPS

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KPNA1-GMPS
FusionPDB ID: 43360
FusionGDB2.0 ID: 43360
HgeneTgene
Gene symbol

KPNA1

GMPS

Gene ID

3836

8833

Gene namekaryopherin subunit alpha 1guanine monophosphate synthase
SynonymsIPOA5|NPI-1|RCH2|SRP1GATD7
Cytomap

3q21.1

3q25.31

Type of geneprotein-codingprotein-coding
Descriptionimportin subunit alpha-5RAG cohort protein 2SRP1-betaimportin alpha 5importin subunit alpha-1importin-alpha-S1karyopherin alpha 1 (importin alpha 5)nucleoprotein interactor 1recombination activating gene cohort 2GMP synthase [glutamine-hydrolyzing]GMP synthaseGMP synthetaseMLL/GMPS fusion proteinglutamine amidotransferaseguanine monophosphate synthetaseguanosine 5'-monophosphate synthasetesticular tissue protein Li 82
Modification date2020031320200313
UniProtAcc

P52294

P49915

Ensembl transtripts involved in fusion geneENST idsENST00000344337, ENST00000466923, 
ENST00000476145, ENST00000295920, 
ENST00000496455, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score19 X 10 X 13=24708 X 7 X 6=336
# samples 2611
** MAII scorelog2(26/2470*10)=-3.24792751344359
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(11/336*10)=-1.6109577092541
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: KPNA1 [Title/Abstract] AND GMPS [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KPNA1(122215284)-GMPS(155637022), # samples:3
Anticipated loss of major functional domain due to fusion event.KPNA1-GMPS 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.
KPNA1-GMPS 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.
KPNA1-GMPS 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.
KPNA1-GMPS 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
TgeneGMPS

GO:0006177

GMP biosynthetic process

8089153


check buttonFusion gene breakpoints across KPNA1 (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 GMPS (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
ChimerDB4LUADTCGA-78-7147-01AKPNA1chr3

122215283

-GMPSchr3

155637021

+
ChimerDB4LUADTCGA-78-7147-01AKPNA1chr3

122215284

-GMPSchr3

155637022

+
ChimerDB4LUADTCGA-78-7147KPNA1chr3

122215283

-GMPSchr3

155637021

+


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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)
ENST00000344337KPNA1chr3122215284-ENST00000496455GMPSchr3155637022+7510306511175374
ENST00000344337KPNA1chr3122215284-ENST00000295920GMPSchr3155637022+1194306511175374
ENST00000344337KPNA1chr3122215283-ENST00000496455GMPSchr3155637021+7510306511175374
ENST00000344337KPNA1chr3122215283-ENST00000295920GMPSchr3155637021+1194306511175374

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
ENST00000344337ENST00000496455KPNA1chr3122215284-GMPSchr3155637022+0.0012906140.99870944
ENST00000344337ENST00000295920KPNA1chr3122215284-GMPSchr3155637022+0.0039523540.9960477
ENST00000344337ENST00000496455KPNA1chr3122215283-GMPSchr3155637021+0.0012906140.99870944
ENST00000344337ENST00000295920KPNA1chr3122215283-GMPSchr3155637021+0.0039523540.9960477

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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

>43360_43360_1_KPNA1-GMPS_KPNA1_chr3_122215283_ENST00000344337_GMPS_chr3_155637021_ENST00000295920_length(amino acids)=374AA_BP=85
MVSTAEARASSSRLCAGVARRAGERGANFSGGTGIGCLEPEIMTTPGKENFRLKSYKNKSLNPDEMRRRREEEGLQLRKQKREEQGKVIE
PLKDFHKDEVRILGRELGLPEELVSRHPFPGPGLAIRVICAEEPYICKDFPETNNILKIVADFSASVKKPHTLLQRVKACTTEEDQEKLM
QITSLHSLNAFLLPIKTVGVQGDCRSYSYVCGISSKDEPDWESLIFLARLIPRMCHNVNRVVYIFGPPVKEPPTDVTPTFLTTGVLSTLR
QADFEAHNILRESGYAGKISQMPVILTPLHFDRDPLQKQPSCQRSVVIRTFITSDFMTGIPATPGNEIPVEVVLKMVTEIKKIPGISRIM

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

>43360_43360_2_KPNA1-GMPS_KPNA1_chr3_122215283_ENST00000344337_GMPS_chr3_155637021_ENST00000496455_length(amino acids)=374AA_BP=85
MVSTAEARASSSRLCAGVARRAGERGANFSGGTGIGCLEPEIMTTPGKENFRLKSYKNKSLNPDEMRRRREEEGLQLRKQKREEQGKVIE
PLKDFHKDEVRILGRELGLPEELVSRHPFPGPGLAIRVICAEEPYICKDFPETNNILKIVADFSASVKKPHTLLQRVKACTTEEDQEKLM
QITSLHSLNAFLLPIKTVGVQGDCRSYSYVCGISSKDEPDWESLIFLARLIPRMCHNVNRVVYIFGPPVKEPPTDVTPTFLTTGVLSTLR
QADFEAHNILRESGYAGKISQMPVILTPLHFDRDPLQKQPSCQRSVVIRTFITSDFMTGIPATPGNEIPVEVVLKMVTEIKKIPGISRIM

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>43360_43360_3_KPNA1-GMPS_KPNA1_chr3_122215284_ENST00000344337_GMPS_chr3_155637022_ENST00000295920_length(amino acids)=374AA_BP=85
MVSTAEARASSSRLCAGVARRAGERGANFSGGTGIGCLEPEIMTTPGKENFRLKSYKNKSLNPDEMRRRREEEGLQLRKQKREEQGKVIE
PLKDFHKDEVRILGRELGLPEELVSRHPFPGPGLAIRVICAEEPYICKDFPETNNILKIVADFSASVKKPHTLLQRVKACTTEEDQEKLM
QITSLHSLNAFLLPIKTVGVQGDCRSYSYVCGISSKDEPDWESLIFLARLIPRMCHNVNRVVYIFGPPVKEPPTDVTPTFLTTGVLSTLR
QADFEAHNILRESGYAGKISQMPVILTPLHFDRDPLQKQPSCQRSVVIRTFITSDFMTGIPATPGNEIPVEVVLKMVTEIKKIPGISRIM

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

>43360_43360_4_KPNA1-GMPS_KPNA1_chr3_122215284_ENST00000344337_GMPS_chr3_155637022_ENST00000496455_length(amino acids)=374AA_BP=85
MVSTAEARASSSRLCAGVARRAGERGANFSGGTGIGCLEPEIMTTPGKENFRLKSYKNKSLNPDEMRRRREEEGLQLRKQKREEQGKVIE
PLKDFHKDEVRILGRELGLPEELVSRHPFPGPGLAIRVICAEEPYICKDFPETNNILKIVADFSASVKKPHTLLQRVKACTTEEDQEKLM
QITSLHSLNAFLLPIKTVGVQGDCRSYSYVCGISSKDEPDWESLIFLARLIPRMCHNVNRVVYIFGPPVKEPPTDVTPTFLTTGVLSTLR
QADFEAHNILRESGYAGKISQMPVILTPLHFDRDPLQKQPSCQRSVVIRTFITSDFMTGIPATPGNEIPVEVVLKMVTEIKKIPGISRIM

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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/chr3:122215284/chr3:155637022)
- 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
KPNA1

P52294

GMPS

P49915

FUNCTION: Functions in nuclear protein import as an adapter protein for nuclear receptor KPNB1. Binds specifically and directly to substrates containing either a simple or bipartite NLS motif. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus. In vitro, mediates the nuclear import of human cytomegalovirus UL84 by recognizing a non-classical NLS.FUNCTION: Involved in the de novo synthesis of guanine nucleotides which are not only essential for DNA and RNA synthesis, but also provide GTP, which is involved in a number of cellular processes important for cell division.

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
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-21425_2843.0539.0Compositional biasNote=Poly-Arg
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-21425_2843.0539.0Compositional biasNote=Poly-Arg

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-2141_5743.0539.0DomainIBB
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-2141_5743.0539.0DomainIBB
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-21442_5143.0539.0MotifNuclear localization signal
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-21442_5143.0539.0MotifNuclear localization signal
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214149_24143.0539.0RegionNLS binding site (major)
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214245_43743.0539.0RegionNote=Binding to RAG1
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214318_40643.0539.0RegionNLS binding site (minor)
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214149_24143.0539.0RegionNLS binding site (major)
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214245_43743.0539.0RegionNote=Binding to RAG1
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214318_40643.0539.0RegionNLS binding site (minor)
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214118_16143.0539.0RepeatNote=ARM 2
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214162_20643.0539.0RepeatNote=ARM 3
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214207_24543.0539.0RepeatNote=ARM 4
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214246_29043.0539.0RepeatNote=ARM 5
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214291_33043.0539.0RepeatNote=ARM 6
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214331_37243.0539.0RepeatNote=ARM 7
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214373_41243.0539.0RepeatNote=ARM 8
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214413_45743.0539.0RepeatNote=ARM 9
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-214460_50443.0539.0RepeatNote=ARM 10%3B atypical
HgeneKPNA1chr3:122215283chr3:155637021ENST00000344337-21477_11743.0539.0RepeatNote=ARM 1%3B truncated
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214118_16143.0539.0RepeatNote=ARM 2
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214162_20643.0539.0RepeatNote=ARM 3
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214207_24543.0539.0RepeatNote=ARM 4
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214246_29043.0539.0RepeatNote=ARM 5
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214291_33043.0539.0RepeatNote=ARM 6
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214331_37243.0539.0RepeatNote=ARM 7
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214373_41243.0539.0RepeatNote=ARM 8
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214413_45743.0539.0RepeatNote=ARM 9
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-214460_50443.0539.0RepeatNote=ARM 10%3B atypical
HgeneKPNA1chr3:122215284chr3:155637022ENST00000344337-21477_11743.0539.0RepeatNote=ARM 1%3B truncated
TgeneGMPSchr3:122215283chr3:155637021ENST00000496455816217_435404.0694.0DomainGMPS ATP-PPase
TgeneGMPSchr3:122215283chr3:155637021ENST0000049645581627_216404.0694.0DomainGlutamine amidotransferase type-1
TgeneGMPSchr3:122215284chr3:155637022ENST00000496455816217_435404.0694.0DomainGMPS ATP-PPase
TgeneGMPSchr3:122215284chr3:155637022ENST0000049645581627_216404.0694.0DomainGlutamine amidotransferase type-1
TgeneGMPSchr3:122215283chr3:155637021ENST00000496455816244_250404.0694.0Nucleotide bindingATP
TgeneGMPSchr3:122215284chr3:155637022ENST00000496455816244_250404.0694.0Nucleotide bindingATP


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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 >>>739_KPNA1_122215283_GMPS_155637021_ranked_0.pdbKPNA1122215283122215283ENST00000295920GMPSchr3155637021+
MVSTAEARASSSRLCAGVARRAGERGANFSGGTGIGCLEPEIMTTPGKENFRLKSYKNKSLNPDEMRRRREEEGLQLRKQKREEQGKVIE
PLKDFHKDEVRILGRELGLPEELVSRHPFPGPGLAIRVICAEEPYICKDFPETNNILKIVADFSASVKKPHTLLQRVKACTTEEDQEKLM
QITSLHSLNAFLLPIKTVGVQGDCRSYSYVCGISSKDEPDWESLIFLARLIPRMCHNVNRVVYIFGPPVKEPPTDVTPTFLTTGVLSTLR
QADFEAHNILRESGYAGKISQMPVILTPLHFDRDPLQKQPSCQRSVVIRTFITSDFMTGIPATPGNEIPVEVVLKMVTEIKKIPGISRIM
374


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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.
KPNA1_pLDDT.png
all structure
all structure
GMPS_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
KPNA1
GMPSall 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 KPNA1-GMPS


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 KPNA1-GMPS


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