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Center for Computational Systems Medicine level3
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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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Potential Active Site Information

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Potentially Interacting Small Molecules through Virtual Screening

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Biochemical Features of Small Molecules with ADME

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Drug Toxicity Information

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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:NUP98-HOXC13

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NUP98-HOXC13
FusionPDB ID: 61118
FusionGDB2.0 ID: 61118
HgeneTgene
Gene symbol

NUP98

HOXC13

Gene ID

4928

3229

Gene namenucleoporin 98 and 96 precursorhomeobox C13
SynonymsADIR2|NUP196|NUP96|Nup98-96ECTD9|HOX3|HOX3G
Cytomap

11p15.4

12q13.13

Type of geneprotein-codingprotein-coding
Descriptionnuclear pore complex protein Nup98-Nup96nuclear pore complex protein Nup98GLFG-repeat containing nucleoporinNUP98/PHF23 fusion 2 proteinNup98-Nup96nucleoporin 96nucleoporin 98kDnucleoporin 98kDahomeobox protein Hox-C13NUP98/HOXC13homeo box 3Ghomeobox protein Hox-3G
Modification date2020031320200313
UniProtAcc

P52948

P31276

Ensembl transtripts involved in fusion geneENST idsENST00000359171, ENST00000324932, 
ENST00000355260, ENST00000397004, 
ENST00000397007, ENST00000488828, 
ENST00000243056, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score35 X 37 X 11=142452 X 4 X 4=32
# samples 313
** MAII scorelog2(31/14245*10)=-5.52204359593698
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/32*10)=-0.0931094043914815
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: NUP98 [Title/Abstract] AND HOXC13 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NUP98(3756553)-HOXC13(54338780), # samples:1
NUP98(3744387)-HOXC13(54338780), # samples:1
Anticipated loss of major functional domain due to fusion event.NUP98-HOXC13 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.
NUP98-HOXC13 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.
NUP98-HOXC13 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.
NUP98-HOXC13 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.
NUP98-HOXC13 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
NUP98-HOXC13 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
NUP98-HOXC13 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
NUP98-HOXC13 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
NUP98-HOXC13 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted 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 NUP98 (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 HOXC13 (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
ChimerDB4acute myeloid leukemiaAJ438986NUP98chr11

3756553

HOXC13chr12

54338780
ChimerKB3..NUP98chr11

3744386

-HOXC13chr12

54338783

+
ChimerKB4..NUP98chr11

3744685

-HOXC13chr12

3744685

+
ChiTaRS5.0N/AAJ438986NUP98chr11

3744387

-HOXC13chr12

54338780

+


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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)
ENST00000324932NUP98chr113744386-ENST00000243056HOXC13chr1254338783+411225673972823808
ENST00000355260NUP98chr113744386-ENST00000243056HOXC13chr1254338783+37782233632489808
ENST00000397004NUP98chr113744386-ENST00000243056HOXC13chr1254338783+386123161462572808
ENST00000397007NUP98chr113744386-ENST00000243056HOXC13chr1254338783+391823731522629825
ENST00000324932NUP98chr113744387-ENST00000243056HOXC13chr1254338780+411225673972823808
ENST00000355260NUP98chr113744387-ENST00000243056HOXC13chr1254338780+37782233632489808
ENST00000397004NUP98chr113744387-ENST00000243056HOXC13chr1254338780+386123161462572808
ENST00000397007NUP98chr113744387-ENST00000243056HOXC13chr1254338780+391823731522629825

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
ENST00000324932ENST00000243056NUP98chr113744387-HOXC13chr1254338780+0.0019373220.9980627
ENST00000355260ENST00000243056NUP98chr113744387-HOXC13chr1254338780+0.002086570.9979134
ENST00000397004ENST00000243056NUP98chr113744387-HOXC13chr1254338780+0.0019991790.9980008
ENST00000397007ENST00000243056NUP98chr113744387-HOXC13chr1254338780+0.0020914070.9979086

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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

>61118_61118_1_NUP98-HOXC13_NUP98_chr11_3744386_ENST00000324932_HOXC13_chr12_54338783_ENST00000243056_length(amino acids)=808AA_BP=721
MKQRLILKMFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAFGSSNNTGGLFGNSQTKPGGLFGTSSFSQPATSTSTGFGFG
TSTGTANTLFGTASTGTSLFSSQNNAFAQNKPTGFGNFGTSTSSGGLFGTTNTTSNPFGSTSGSLFGPSSFTAAPTGTTIKFNPPTGTDT
MVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGLFSSSTTNSGFAYGQNKTAFGTS
TTGFGTNPGGLFGQQNQQTTSLFSKPFGQATTTQNTGFSFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTAFGTGTGLFGQ
TNTGFGAVGSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFGFGTNTSGNSIFGSKPAPGTLGTGLGAGFGTALGAGQASLFGNNQPKIGGP
LGTGAFGAPGFNTTTATLGFGAPQAPVALTDPNASAAQQAVLQQHINSLTYSPFGDSPLFRNPMSDPKKKEERLKPTNPAAQKALTTPTH
YKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKLVLKNLNNSNLFSPVNRDSENLASPSEYPENGERFSFLSK
PVDENHQQDGDEDSLVSHFYTNPIAKPIPQTPESAGNKHSNSNSVDDTIVALNMRAALRNGLEGSSEETSFHDESLQDDREEIENNSYHM

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

>61118_61118_2_NUP98-HOXC13_NUP98_chr11_3744386_ENST00000355260_HOXC13_chr12_54338783_ENST00000243056_length(amino acids)=808AA_BP=721
MKQRLILKMFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAFGSSNNTGGLFGNSQTKPGGLFGTSSFSQPATSTSTGFGFG
TSTGTANTLFGTASTGTSLFSSQNNAFAQNKPTGFGNFGTSTSSGGLFGTTNTTSNPFGSTSGSLFGPSSFTAAPTGTTIKFNPPTGTDT
MVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGLFSSSTTNSGFAYGQNKTAFGTS
TTGFGTNPGGLFGQQNQQTTSLFSKPFGQATTTQNTGFSFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTAFGTGTGLFGQ
TNTGFGAVGSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFGFGTNTSGNSIFGSKPAPGTLGTGLGAGFGTALGAGQASLFGNNQPKIGGP
LGTGAFGAPGFNTTTATLGFGAPQAPVALTDPNASAAQQAVLQQHINSLTYSPFGDSPLFRNPMSDPKKKEERLKPTNPAAQKALTTPTH
YKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKLVLKNLNNSNLFSPVNRDSENLASPSEYPENGERFSFLSK
PVDENHQQDGDEDSLVSHFYTNPIAKPIPQTPESAGNKHSNSNSVDDTIVALNMRAALRNGLEGSSEETSFHDESLQDDREEIENNSYHM

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

>61118_61118_3_NUP98-HOXC13_NUP98_chr11_3744386_ENST00000397004_HOXC13_chr12_54338783_ENST00000243056_length(amino acids)=808AA_BP=721
MKQRLILKMFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAFGSSNNTGGLFGNSQTKPGGLFGTSSFSQPATSTSTGFGFG
TSTGTANTLFGTASTGTSLFSSQNNAFAQNKPTGFGNFGTSTSSGGLFGTTNTTSNPFGSTSGSLFGPSSFTAAPTGTTIKFNPPTGTDT
MVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGLFSSSTTNSGFAYGQNKTAFGTS
TTGFGTNPGGLFGQQNQQTTSLFSKPFGQATTTQNTGFSFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTAFGTGTGLFGQ
TNTGFGAVGSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFGFGTNTSGNSIFGSKPAPGTLGTGLGAGFGTALGAGQASLFGNNQPKIGGP
LGTGAFGAPGFNTTTATLGFGAPQAPVALTDPNASAAQQAVLQQHINSLTYSPFGDSPLFRNPMSDPKKKEERLKPTNPAAQKALTTPTH
YKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKLVLKNLNNSNLFSPVNRDSENLASPSEYPENGERFSFLSK
PVDENHQQDGDEDSLVSHFYTNPIAKPIPQTPESAGNKHSNSNSVDDTIVALNMRAALRNGLEGSSEETSFHDESLQDDREEIENNSYHM

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

>61118_61118_4_NUP98-HOXC13_NUP98_chr11_3744386_ENST00000397007_HOXC13_chr12_54338783_ENST00000243056_length(amino acids)=825AA_BP=738
MKQRLILKMFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAFGSSNNTGGLFGNSQTKPGGLFGTSSFSQPATSTSTGFGFG
TSTGTANTLFGTASTGTSLFSSQNNAFAQNKPTGFGNFGTSTSSGGLFGTTNTTSNPFGSTSGSLFGPSSFTAAPTGTTIKFNPPTGTDT
MVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGLFSSSTTNSGFAYGQNKTAFGTS
TTGFGTNPGGLFGQQNQQTTSLFSKPFGQATTTQNTGFSFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTAFGTGTGLFGQ
TNTGFGAVGSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFGNKPTLTLGTNTNTSNFGFGTNTSGNSIFGSKPAPGTLGTGLGAGFGTALG
AGQASLFGNNQPKIGGPLGTGAFGAPGFNTTTATLGFGAPQAPVALTDPNASAAQQAVLQQHINSLTYSPFGDSPLFRNPMSDPKKKEER
LKPTNPAAQKALTTPTHYKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKLVLKNLNNSNLFSPVNRDSENLA
SPSEYPENGERFSFLSKPVDENHQQDGDEDSLVSHFYTNPIAKPIPQTPESAGNKHSNSNSVDDTIVALNMRAALRNGLEGSSEETSFHD
ESLQDDREEIENNSYHMHPADVVPLQPEVSSYRRGRKKRVPYTKVQLKELEKEYAASKFITKEKRRRISATTNLSERQVTIWFQNRRVKE

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

>61118_61118_5_NUP98-HOXC13_NUP98_chr11_3744387_ENST00000324932_HOXC13_chr12_54338780_ENST00000243056_length(amino acids)=808AA_BP=721
MKQRLILKMFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAFGSSNNTGGLFGNSQTKPGGLFGTSSFSQPATSTSTGFGFG
TSTGTANTLFGTASTGTSLFSSQNNAFAQNKPTGFGNFGTSTSSGGLFGTTNTTSNPFGSTSGSLFGPSSFTAAPTGTTIKFNPPTGTDT
MVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGLFSSSTTNSGFAYGQNKTAFGTS
TTGFGTNPGGLFGQQNQQTTSLFSKPFGQATTTQNTGFSFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTAFGTGTGLFGQ
TNTGFGAVGSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFGFGTNTSGNSIFGSKPAPGTLGTGLGAGFGTALGAGQASLFGNNQPKIGGP
LGTGAFGAPGFNTTTATLGFGAPQAPVALTDPNASAAQQAVLQQHINSLTYSPFGDSPLFRNPMSDPKKKEERLKPTNPAAQKALTTPTH
YKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKLVLKNLNNSNLFSPVNRDSENLASPSEYPENGERFSFLSK
PVDENHQQDGDEDSLVSHFYTNPIAKPIPQTPESAGNKHSNSNSVDDTIVALNMRAALRNGLEGSSEETSFHDESLQDDREEIENNSYHM

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

>61118_61118_6_NUP98-HOXC13_NUP98_chr11_3744387_ENST00000355260_HOXC13_chr12_54338780_ENST00000243056_length(amino acids)=808AA_BP=721
MKQRLILKMFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAFGSSNNTGGLFGNSQTKPGGLFGTSSFSQPATSTSTGFGFG
TSTGTANTLFGTASTGTSLFSSQNNAFAQNKPTGFGNFGTSTSSGGLFGTTNTTSNPFGSTSGSLFGPSSFTAAPTGTTIKFNPPTGTDT
MVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGLFSSSTTNSGFAYGQNKTAFGTS
TTGFGTNPGGLFGQQNQQTTSLFSKPFGQATTTQNTGFSFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTAFGTGTGLFGQ
TNTGFGAVGSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFGFGTNTSGNSIFGSKPAPGTLGTGLGAGFGTALGAGQASLFGNNQPKIGGP
LGTGAFGAPGFNTTTATLGFGAPQAPVALTDPNASAAQQAVLQQHINSLTYSPFGDSPLFRNPMSDPKKKEERLKPTNPAAQKALTTPTH
YKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKLVLKNLNNSNLFSPVNRDSENLASPSEYPENGERFSFLSK
PVDENHQQDGDEDSLVSHFYTNPIAKPIPQTPESAGNKHSNSNSVDDTIVALNMRAALRNGLEGSSEETSFHDESLQDDREEIENNSYHM

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

>61118_61118_7_NUP98-HOXC13_NUP98_chr11_3744387_ENST00000397004_HOXC13_chr12_54338780_ENST00000243056_length(amino acids)=808AA_BP=721
MKQRLILKMFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAFGSSNNTGGLFGNSQTKPGGLFGTSSFSQPATSTSTGFGFG
TSTGTANTLFGTASTGTSLFSSQNNAFAQNKPTGFGNFGTSTSSGGLFGTTNTTSNPFGSTSGSLFGPSSFTAAPTGTTIKFNPPTGTDT
MVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGLFSSSTTNSGFAYGQNKTAFGTS
TTGFGTNPGGLFGQQNQQTTSLFSKPFGQATTTQNTGFSFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTAFGTGTGLFGQ
TNTGFGAVGSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFGFGTNTSGNSIFGSKPAPGTLGTGLGAGFGTALGAGQASLFGNNQPKIGGP
LGTGAFGAPGFNTTTATLGFGAPQAPVALTDPNASAAQQAVLQQHINSLTYSPFGDSPLFRNPMSDPKKKEERLKPTNPAAQKALTTPTH
YKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKLVLKNLNNSNLFSPVNRDSENLASPSEYPENGERFSFLSK
PVDENHQQDGDEDSLVSHFYTNPIAKPIPQTPESAGNKHSNSNSVDDTIVALNMRAALRNGLEGSSEETSFHDESLQDDREEIENNSYHM

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

>61118_61118_8_NUP98-HOXC13_NUP98_chr11_3744387_ENST00000397007_HOXC13_chr12_54338780_ENST00000243056_length(amino acids)=825AA_BP=738
MKQRLILKMFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAFGSSNNTGGLFGNSQTKPGGLFGTSSFSQPATSTSTGFGFG
TSTGTANTLFGTASTGTSLFSSQNNAFAQNKPTGFGNFGTSTSSGGLFGTTNTTSNPFGSTSGSLFGPSSFTAAPTGTTIKFNPPTGTDT
MVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGLFSSSTTNSGFAYGQNKTAFGTS
TTGFGTNPGGLFGQQNQQTTSLFSKPFGQATTTQNTGFSFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTAFGTGTGLFGQ
TNTGFGAVGSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFGNKPTLTLGTNTNTSNFGFGTNTSGNSIFGSKPAPGTLGTGLGAGFGTALG
AGQASLFGNNQPKIGGPLGTGAFGAPGFNTTTATLGFGAPQAPVALTDPNASAAQQAVLQQHINSLTYSPFGDSPLFRNPMSDPKKKEER
LKPTNPAAQKALTTPTHYKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKLVLKNLNNSNLFSPVNRDSENLA
SPSEYPENGERFSFLSKPVDENHQQDGDEDSLVSHFYTNPIAKPIPQTPESAGNKHSNSNSVDDTIVALNMRAALRNGLEGSSEETSFHD
ESLQDDREEIENNSYHMHPADVVPLQPEVSSYRRGRKKRVPYTKVQLKELEKEYAASKFITKEKRRRISATTNLSERQVTIWFQNRRVKE

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

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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/chr11:3756553/chr12:54338780)
- 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
NUP98

P52948

HOXC13

P31276

FUNCTION: Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance. NUP98 and NUP96 are involved in the bidirectional transport across the NPC (PubMed:33097660). May anchor NUP153 and TPR to the NPC. In cooperation with DHX9, plays a role in transcription and alternative splicing activation of a subset of genes (PubMed:28221134). Involved in the localization of DHX9 in discrete intranuclear foci (GLFG-body) (PubMed:28221134). {ECO:0000269|PubMed:15229283, ECO:0000269|PubMed:33097660}.; FUNCTION: (Microbial infection) Interacts with HIV-1 capsid protein P24 and nucleocapsid protein P7 and may thereby promote the integration of the virus in the host nucleus (in vitro) (PubMed:23523133). Binding affinity to HIV-1 CA-NC complexes bearing the capsid change ASN-74-ASP is reduced (in vitro) (PubMed:23523133). {ECO:0000269|PubMed:23523133}.FUNCTION: Transcription factor which plays a role in hair follicle differentiation. Regulates FOXQ1 expression and that of other hair-specific genes (By similarity). {ECO:0000250}.

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
HgeneNUP98chr11:3744387chr12:54338780ENST00000324932-16337_480715.33333333333341801.0Compositional biasNote=Gly/Thr-rich
HgeneNUP98chr11:3744387chr12:54338780ENST00000355260-16327_480715.33333333333341727.0Compositional biasNote=Gly/Thr-rich
HgeneNUP98chr11:3744387chr12:54338780ENST00000397004-16207_480715.3333333333334921.0Compositional biasNote=Gly/Thr-rich
HgeneNUP98chr11:3744387chr12:54338780ENST00000397007-16207_480732.3333333333334938.0Compositional biasNote=Gly/Thr-rich
HgeneNUP98chr11:3744387chr12:54338780ENST00000324932-16331_156715.33333333333341801.0RegionNote=FG repeats 1
HgeneNUP98chr11:3744387chr12:54338780ENST00000324932-1633214_480715.33333333333341801.0RegionNote=FG repeats 2
HgeneNUP98chr11:3744387chr12:54338780ENST00000355260-16321_156715.33333333333341727.0RegionNote=FG repeats 1
HgeneNUP98chr11:3744387chr12:54338780ENST00000355260-1632214_480715.33333333333341727.0RegionNote=FG repeats 2
HgeneNUP98chr11:3744387chr12:54338780ENST00000397004-16201_156715.3333333333334921.0RegionNote=FG repeats 1
HgeneNUP98chr11:3744387chr12:54338780ENST00000397004-1620214_480715.3333333333334921.0RegionNote=FG repeats 2
HgeneNUP98chr11:3744387chr12:54338780ENST00000397007-16201_156732.3333333333334938.0RegionNote=FG repeats 1
HgeneNUP98chr11:3744387chr12:54338780ENST00000397007-1620214_480732.3333333333334938.0RegionNote=FG repeats 2
TgeneHOXC13chr11:3744387chr12:54338780ENST0000024305602260_319245.33333333333334331.0DNA bindingHomeobox

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNUP98chr11:3744387chr12:54338780ENST00000324932-1633890_894715.33333333333341801.0Compositional biasNote=Poly-Glu
HgeneNUP98chr11:3744387chr12:54338780ENST00000355260-1632890_894715.33333333333341727.0Compositional biasNote=Poly-Glu
HgeneNUP98chr11:3744387chr12:54338780ENST00000397004-1620890_894715.3333333333334921.0Compositional biasNote=Poly-Glu
HgeneNUP98chr11:3744387chr12:54338780ENST00000397007-1620890_894732.3333333333334938.0Compositional biasNote=Poly-Glu
HgeneNUP98chr11:3744387chr12:54338780ENST00000324932-1633738_880715.33333333333341801.0DomainPeptidase S59
HgeneNUP98chr11:3744387chr12:54338780ENST00000355260-1632738_880715.33333333333341727.0DomainPeptidase S59
HgeneNUP98chr11:3744387chr12:54338780ENST00000397004-1620738_880715.3333333333334921.0DomainPeptidase S59
HgeneNUP98chr11:3744387chr12:54338780ENST00000397007-1620738_880732.3333333333334938.0DomainPeptidase S59
TgeneHOXC13chr11:3744387chr12:54338780ENST000002430560227_61245.33333333333334331.0Compositional biasNote=Gly-rich


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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 (654) >>>654.pdbFusion protein BP residue: 721
CIF file (654) >>>654.cif		NUP98chr113744386-HOXC13chr1254338783+
MKQRLILKMFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAF
GSSNNTGGLFGNSQTKPGGLFGTSSFSQPATSTSTGFGFGTSTGTANTLF
GTASTGTSLFSSQNNAFAQNKPTGFGNFGTSTSSGGLFGTTNTTSNPFGS
TSGSLFGPSSFTAAPTGTTIKFNPPTGTDTMVKAGVSTNISTKHQCITAM
KEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGLFS
SSTTNSGFAYGQNKTAFGTSTTGFGTNPGGLFGQQNQQTTSLFSKPFGQA
TTTQNTGFSFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTA
FGTGTGLFGQTNTGFGAVGSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFG
FGTNTSGNSIFGSKPAPGTLGTGLGAGFGTALGAGQASLFGNNQPKIGGP
LGTGAFGAPGFNTTTATLGFGAPQAPVALTDPNASAAQQAVLQQHINSLT
YSPFGDSPLFRNPMSDPKKKEERLKPTNPAAQKALTTPTHYKLTPRPATR
VRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKLVLKNLNNSN
LFSPVNRDSENLASPSEYPENGERFSFLSKPVDENHQQDGDEDSLVSHFY
TNPIAKPIPQTPESAGNKHSNSNSVDDTIVALNMRAALRNGLEGSSEETS
FHDESLQDDREEIENNSYHMHPADVVPLQPEVSSYRRGRKKRVPYTKVQL
KELEKEYAASKFITKEKRRRISATTNLSERQVTIWFQNRRVKEKKVVSKS
808
3D view using mol* of 654 (AA BP:721)
PDB file (667) >>>667.pdbFusion protein BP residue: 738
CIF file (667) >>>667.cif		NUP98chr113744386-HOXC13chr1254338783+
MKQRLILKMFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAF
GSSNNTGGLFGNSQTKPGGLFGTSSFSQPATSTSTGFGFGTSTGTANTLF
GTASTGTSLFSSQNNAFAQNKPTGFGNFGTSTSSGGLFGTTNTTSNPFGS
TSGSLFGPSSFTAAPTGTTIKFNPPTGTDTMVKAGVSTNISTKHQCITAM
KEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGLFS
SSTTNSGFAYGQNKTAFGTSTTGFGTNPGGLFGQQNQQTTSLFSKPFGQA
TTTQNTGFSFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTA
FGTGTGLFGQTNTGFGAVGSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFG
NKPTLTLGTNTNTSNFGFGTNTSGNSIFGSKPAPGTLGTGLGAGFGTALG
AGQASLFGNNQPKIGGPLGTGAFGAPGFNTTTATLGFGAPQAPVALTDPN
ASAAQQAVLQQHINSLTYSPFGDSPLFRNPMSDPKKKEERLKPTNPAAQK
ALTTPTHYKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFM
PKKSIKKLVLKNLNNSNLFSPVNRDSENLASPSEYPENGERFSFLSKPVD
ENHQQDGDEDSLVSHFYTNPIAKPIPQTPESAGNKHSNSNSVDDTIVALN
MRAALRNGLEGSSEETSFHDESLQDDREEIENNSYHMHPADVVPLQPEVS
SYRRGRKKRVPYTKVQLKELEKEYAASKFITKEKRRRISATTNLSERQVT
825
3D view using mol* of 667 (AA BP:738)


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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.
NUP98_pLDDT.png
all structure
all structure
HOXC13_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.
NUP98_HOXC13_654_pLDDT.png (AA BP:721)
all structure
NUP98_HOXC13_654_pLDDT_and_active_sites.png (AA BP:721)
all structure
NUP98_HOXC13_654_violinplot.png (AA BP:721)
all structure
NUP98_HOXC13_667_pLDDT.png (AA BP:738)
all structure
NUP98_HOXC13_667_pLDDT_and_active_sites.png (AA BP:738)
all structure
NUP98_HOXC13_667_violinplot.png (AA BP:738)
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
NUP98_HOXC13_654.png
all structure
NUP98_HOXC13_667.png
all structure

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Potential Active Site Information


check button The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite.
Fusion AA seq ID in FusionPDBSite scoreSizeD scoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues
6540.709430.67209.230.760.6210.7430.1320.9780.1351.411Chain A: 168,169,170,171,172,197,208,211,212,215,2
20,222,223,224,226
6670.733480.724117.6490.6760.5770.8290.3470.840.4120.996Chain A: 519,520,521,522,523,527,528,529,530,531,5
32,533,536,537,540

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Potentially Interacting Small Molecules through Virtual Screening


check button The FDA-approved small molecule library molecules were subjected to virtual screening using the Glide.
Fusion AA seq ID in FusionPDBZINC IDDrugBank IDDrug nameDocking scoreGlide gscore

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check button Drug information from DrugBank of the top 20 interacting small molecules.
ZINC IDDrugBank IDDrug nameDrug typeSMILESDrug group

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Biochemical Features of Small Molecules


check button ADME (Absorption, Distribution, Metabolism, and Excretion) of drugs using QikProp(v3.9)
ZINC IDmol_MWdipoleSASAFOSAFISAPISAWPSAvolumedonorHBaccptHBIPHuman Oral AbsorptionPercent Human Oral AbsorptionRule Of FiveRule Of Three


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Drug Toxicity Information


check button Toxicity information of individual drugs using eToxPred
ZINC IDSmileSurface AccessibilityToxicity


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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
NUP98MOB1A, PARP11, QRICH2, TPR, NUP88, CREBBP, EP300, NUP133, Rae1, KPNB1, RAE1, TNPO2, CRM1, KAP104, NXF1, TNPO1, USP7, NPM1, PTTG1, APC, HDAC1, tat, NUP82, NUP159, Nup188, Nup98, Nup107, Nup214, SIRT7, NUP107, RAPGEF3, rev, NUMA1, ECT2, CSNK2A1, HNRNPUL1, LMNA, HDAC8, HDAC11, FBXO6, ARFGEF2, CDC73, PAF1, CDC37, CUL7, OBSL1, EED, MAPK8, COMTD1, SEC13, PNKD, NUP43, CLEC11A, RNF166, UNK, NUP54, NUP85, SEH1L, XPO5, KRAS, IFI16, NUP160, NUP35, B9D2, UBE2I, NUPL1, NUP153, PIM2, NUDT21, NCBP2, CHMP4B, GTF2H5, Ranbp2, Ube2i, Ssna1, Rcc1, Xpo1, Kifc1, Nup155, FOXI2, FOXL1, FOXQ1, FAF1, C11orf30, DUSP13, SPAST, FAM136A, UXS1, CD70, VASN, TRIM25, G3BP1, ORF10, CDC27, ANAPC4, ANAPC10, MAD2L1, CDC20, FZR1, PIN1, CTNNB1, TGFB1, NKX2-1, ESR2, NUP155, EZH2, DCPS, CDK9, DYNLT1, TOMM20, KIAA1429, DISC1, NR2C2, AGRN, HIST1H4A, PTPMT1, ORF6, BIRC3, LMBR1L, FAM105A, PLEKHA4, TTC9, HIST1H2BH, HIST3H3, M, nsp16, nsp4, nsp6, ORF7b, GLE1, NEK4, CIT, KIF14, KIF20A, PRC1, ARHGEF19, MYO9A, PTPN1, SEC61B, NFX1, HULC, NUPR1, BRD4, LGALS9, DYRK1A, NUP37, DDX58, CKAP4, DERL1, EMD, HSD17B11, HSD3B7, LMNB1, LRRC59, METTL7A, NUP50, REEP5, SEC62, SSR1, STIM1, SYNE3, TMPO, WDR5, NAA40, OCIAD1, CADPS, TACSTD2, RGPD1, TPST2, CD40, SLFN11, FBXO32, RCHY1, SIRT6, ETV6,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
NUP98all structure
HOXC13all 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 NUP98-HOXC13


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 NUP98-HOXC13


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
HgeneNUP98C0002871Anemia1CTD_human
HgeneNUP98C0023467Leukemia, Myelocytic, Acute1CTD_human
HgeneNUP98C0024312Lymphopenia1CTD_human
HgeneNUP98C0026998Acute Myeloid Leukemia, M11CTD_human
HgeneNUP98C0027947Neutropenia1CTD_human
HgeneNUP98C1879321Acute Myeloid Leukemia (AML-M2)1CTD_human
HgeneNUP98C2930974Acute erythroleukemia1CTD_human
HgeneNUP98C2930975Acute erythroleukemia - M6a subtype1CTD_human
HgeneNUP98C2930976Acute myeloid leukemia FAB-M61CTD_human
HgeneNUP98C2930977Acute erythroleukemia - M6b subtype1CTD_human
TgeneHOXC13C1865951Ectodermal Dysplasia, Pure Hair-Nail Type2CTD_human;ORPHANET
TgeneHOXC13C3554127ECTODERMAL DYSPLASIA 9, HAIR/NAIL TYPE2CTD_human;GENOMICS_ENGLAND;UNIPROT