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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:NINL-NAA20

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NINL-NAA20
FusionPDB ID: 59154
FusionGDB2.0 ID: 59154
HgeneTgene
Gene symbol

NINL

NAA20

Gene ID

22981

51126

Gene nameninein likeN-alpha-acetyltransferase 20, NatB catalytic subunit
SynonymsNLPNAT3|NAT3P|NAT5|NAT5P|dJ1002M8.1
Cytomap

20p11.21

20p11.23

Type of geneprotein-codingprotein-coding
Descriptionninein-like proteinN-alpha-acetyltransferase 20N-acetyltransferase 3 homologN-acetyltransferase 5 (ARD1 homolog, S. cerevisiae)N-acetyltransferase 5 (GCN5-related, putative)N-acetyltransferase 5, ARD1 subunit (arrest-defective 1, S. cerevisiae, homolog)N-terminal acety
Modification date2020031320200320
UniProtAcc

Q9Y2I6

P61599

Ensembl transtripts involved in fusion geneENST idsENST00000278886, ENST00000422516, 
ENST00000464285, 
ENST00000310450, 
ENST00000398602, ENST00000484480, 
ENST00000334982, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 6 X 6=2163 X 4 X 2=24
# samples 84
** MAII scorelog2(8/216*10)=-1.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: NINL [Title/Abstract] AND NAA20 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NINL(25507044)-NAA20(20007428), # samples:3
Anticipated loss of major functional domain due to fusion event.NINL-NAA20 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.
NINL-NAA20 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.
NINL-NAA20 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.
NINL-NAA20 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

check buttonFusion gene breakpoints across NINL (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 NAA20 (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-G9-6351-01ANINLchr20

25507044

-NAA20chr20

20007428

+
ChimerDB4PRADTCGA-G9-6351NINLchr20

25507043

-NAA20chr20

20007427

+
ChimerDB4PRADTCGA-G9-6351NINLchr20

25507044

-NAA20chr20

20007428

+


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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)
ENST00000278886NINLchr2025507044-ENST00000334982NAA20chr2020007428+1064254256621121
ENST00000422516NINLchr2025507044-ENST00000334982NAA20chr2020007428+1064254256621121
ENST00000278886NINLchr2025507043-ENST00000334982NAA20chr2020007427+1064254256621121
ENST00000422516NINLchr2025507043-ENST00000334982NAA20chr2020007427+1064254256621121

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
ENST00000278886ENST00000334982NINLchr2025507044-NAA20chr2020007428+0.0083232030.9916768
ENST00000422516ENST00000334982NINLchr2025507044-NAA20chr2020007428+0.0083232030.9916768
ENST00000278886ENST00000334982NINLchr2025507043-NAA20chr2020007427+0.0083232030.9916768
ENST00000422516ENST00000334982NINLchr2025507043-NAA20chr2020007427+0.0083232030.9916768

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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

>59154_59154_1_NINL-NAA20_NINL_chr20_25507043_ENST00000278886_NAA20_chr20_20007427_ENST00000334982_length(amino acids)=121AA_BP=0
MGKAEGSVAREEWHGHVTALSVAPEFRRLGLAAKLMELLEEISERKGGFFVDLFVRVSNQVAVNMYKQLGYSVYRTVIEYYSASNGEPDE

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

>59154_59154_2_NINL-NAA20_NINL_chr20_25507043_ENST00000422516_NAA20_chr20_20007427_ENST00000334982_length(amino acids)=121AA_BP=0
MGKAEGSVAREEWHGHVTALSVAPEFRRLGLAAKLMELLEEISERKGGFFVDLFVRVSNQVAVNMYKQLGYSVYRTVIEYYSASNGEPDE

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

>59154_59154_3_NINL-NAA20_NINL_chr20_25507044_ENST00000278886_NAA20_chr20_20007428_ENST00000334982_length(amino acids)=121AA_BP=0
MGKAEGSVAREEWHGHVTALSVAPEFRRLGLAAKLMELLEEISERKGGFFVDLFVRVSNQVAVNMYKQLGYSVYRTVIEYYSASNGEPDE

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>59154_59154_4_NINL-NAA20_NINL_chr20_25507044_ENST00000422516_NAA20_chr20_20007428_ENST00000334982_length(amino acids)=121AA_BP=0
MGKAEGSVAREEWHGHVTALSVAPEFRRLGLAAKLMELLEEISERKGGFFVDLFVRVSNQVAVNMYKQLGYSVYRTVIEYYSASNGEPDE

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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/chr20:25507044/chr20:20007428)
- 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
NINL

Q9Y2I6

NAA20

P61599

FUNCTION: Involved in the microtubule organization in interphase cells. Overexpression induces the fragmentation of the Golgi, and causes lysosomes to disperse toward the cell periphery; it also interferes with mitotic spindle assembly. May play a role in ovarian carcinogenesis. {ECO:0000269|PubMed:12852856, ECO:0000269|PubMed:16254247, ECO:0000269|PubMed:18538832}.FUNCTION: Catalytic subunit of the NatB complex which catalyzes acetylation of the N-terminal methionine residues of peptides beginning with Met-Asp, Met-Glu, Met-Asn and Met-Gln. Proteins with cell cycle functions are overrepresented in the pool of NatB substrates. Required for maintaining the structure and function of actomyosin fibers and for proper cellular migration. {ECO:0000269|PubMed:18570629}.

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
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-2247_4260.01383.0DomainEF-hand 1
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-2237_4260.01034.0DomainEF-hand 1
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-2247_4260.01383.0DomainEF-hand 1
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-2237_4260.01034.0DomainEF-hand 1

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-224246_25760.01383.0Calcium bindingOntology_term=ECO:0000255
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-223246_25760.01034.0Calcium bindingOntology_term=ECO:0000255
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-224246_25760.01383.0Calcium bindingOntology_term=ECO:0000255
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-223246_25760.01034.0Calcium bindingOntology_term=ECO:0000255
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-2241046_137560.01383.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-224384_42460.01383.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-224484_57960.01383.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-224616_69960.01383.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-2231046_137560.01034.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-223384_42460.01034.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-223484_57960.01034.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-223616_69960.01034.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-2241046_137560.01383.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-224384_42460.01383.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-224484_57960.01383.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-224616_69960.01383.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-2231046_137560.01034.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-223384_42460.01034.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-223484_57960.01034.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-223616_69960.01034.0Coiled coilOntology_term=ECO:0000255
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-224296_29960.01383.0Compositional biasNote=Poly-Thr
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-224805_81060.01383.0Compositional biasNote=Poly-Glu
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-223296_29960.01034.0Compositional biasNote=Poly-Thr
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-223805_81060.01034.0Compositional biasNote=Poly-Glu
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-224296_29960.01383.0Compositional biasNote=Poly-Thr
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-224805_81060.01383.0Compositional biasNote=Poly-Glu
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-223296_29960.01034.0Compositional biasNote=Poly-Thr
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-223805_81060.01034.0Compositional biasNote=Poly-Glu
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-224196_23160.01383.0DomainEF-hand 3
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-224233_26860.01383.0DomainEF-hand 4
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-22441_7660.01383.0DomainEF-hand 2
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-223196_23160.01034.0DomainEF-hand 3
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-223233_26860.01034.0DomainEF-hand 4
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-22341_7660.01034.0DomainEF-hand 2
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-224196_23160.01383.0DomainEF-hand 3
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-224233_26860.01383.0DomainEF-hand 4
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-22441_7660.01383.0DomainEF-hand 2
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-223196_23160.01034.0DomainEF-hand 3
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-223233_26860.01034.0DomainEF-hand 4
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-22341_7660.01034.0DomainEF-hand 2
HgeneNINLchr20:25507043chr20:20007427ENST00000278886-224633_64160.01383.0MotifNote=D-box
HgeneNINLchr20:25507043chr20:20007427ENST00000422516-223633_64160.01034.0MotifNote=D-box
HgeneNINLchr20:25507044chr20:20007428ENST00000278886-224633_64160.01383.0MotifNote=D-box
HgeneNINLchr20:25507044chr20:20007428ENST00000422516-223633_64160.01034.0MotifNote=D-box
TgeneNAA20chr20:25507043chr20:20007427ENST00000310450252_15756.333333333333336112.0DomainN-acetyltransferase
TgeneNAA20chr20:25507043chr20:20007427ENST00000334982262_15756.333333333333336179.0DomainN-acetyltransferase
TgeneNAA20chr20:25507044chr20:20007428ENST00000310450252_15756.333333333333336112.0DomainN-acetyltransferase
TgeneNAA20chr20:25507044chr20:20007428ENST00000334982262_15756.333333333333336179.0DomainN-acetyltransferase


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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 >>>51_NINL_25507044_NAA20_20007428_ranked_0.pdbNINL2550704325507044ENST00000334982NAA20chr2020007428+
MGKAEGSVAREEWHGHVTALSVAPEFRRLGLAAKLMELLEEISERKGGFFVDLFVRVSNQVAVNMYKQLGYSVYRTVIEYYSASNGEPDE
121


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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.
NINL_pLDDT.png
all structure
all structure
NAA20_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
NINL
NAA20


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 NINL-NAA20


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 NINL-NAA20


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