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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:NFIX-RBM5 (FusionGDB2 ID:58602)

Fusion Gene Summary for NFIX-RBM5

check button Fusion gene summary
Fusion gene informationFusion gene name: NFIX-RBM5
Fusion gene ID: 58602
HgeneTgene
Gene symbol

NFIX

RBM5

Gene ID

4784

10181

Gene namenuclear factor I XRNA binding motif protein 5
SynonymsCTF|MRSHSS|NF-I/X|NF1-X|NF1A|SOTOS2G15|H37|LUCA-15|LUCA15|RMB5
Cytomap

19p13.13

3p21.31

Type of geneprotein-codingprotein-coding
Descriptionnuclear factor 1 X-typeCCAAT-box-binding transcription factorTGGCA-binding proteinnuclear factor 1/XRNA-binding protein 5putative tumor suppressor LUCA15renal carcinoma antigen NY-REN-9
Modification date2020032920200320
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000397661, ENST00000592199, 
ENST00000587760, ENST00000585575, 
ENST00000360105, ENST00000588228, 
ENST00000587260, ENST00000358552, 
ENST00000588680, 		ENST00000347869, 
ENST00000469838, ENST00000441812, 
Fusion gene scores* DoF score27 X 14 X 16=60488 X 7 X 5=280
# samples 428
** MAII scorelog2(42/6048*10)=-3.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/280*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NFIX [Title/Abstract] AND RBM5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNFIX(13206543)-RBM5(50141679), # samples:1
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
HgeneNFIX

GO:0000122

negative regulation of transcription by RNA polymerase II

19706729

HgeneNFIX

GO:0045944

positive regulation of transcription by RNA polymerase II

19706729

TgeneRBM5

GO:0000245

spliceosomal complex assembly

18951082

TgeneRBM5

GO:0000381

regulation of alternative mRNA splicing, via spliceosome

18840686|18951082

TgeneRBM5

GO:0043065

positive regulation of apoptotic process

18840686


check buttonFusion gene breakpoints across NFIX (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across RBM5 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChiTaRS5.0N/ADB028954NFIXchr19

13206543

+RBM5chr3

50141679

+


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Fusion Gene ORF analysis for NFIX-RBM5

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
3UTR-3CDSENST00000397661ENST00000347869NFIXchr19

13206543

+RBM5chr3

50141679

+
3UTR-intronENST00000397661ENST00000469838NFIXchr19

13206543

+RBM5chr3

50141679

+
3UTR-intronENST00000397661ENST00000441812NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-3CDSENST00000592199ENST00000347869NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000592199ENST00000469838NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000592199ENST00000441812NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-3CDSENST00000587760ENST00000347869NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000587760ENST00000469838NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000587760ENST00000441812NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-3CDSENST00000585575ENST00000347869NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000585575ENST00000469838NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000585575ENST00000441812NFIXchr19

13206543

+RBM5chr3

50141679

+
3UTR-3CDSENST00000360105ENST00000347869NFIXchr19

13206543

+RBM5chr3

50141679

+
3UTR-intronENST00000360105ENST00000469838NFIXchr19

13206543

+RBM5chr3

50141679

+
3UTR-intronENST00000360105ENST00000441812NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-3CDSENST00000588228ENST00000347869NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000588228ENST00000469838NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000588228ENST00000441812NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-3CDSENST00000587260ENST00000347869NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000587260ENST00000469838NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000587260ENST00000441812NFIXchr19

13206543

+RBM5chr3

50141679

+
3UTR-3CDSENST00000358552ENST00000347869NFIXchr19

13206543

+RBM5chr3

50141679

+
3UTR-intronENST00000358552ENST00000469838NFIXchr19

13206543

+RBM5chr3

50141679

+
3UTR-intronENST00000358552ENST00000441812NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-3CDSENST00000588680ENST00000347869NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000588680ENST00000469838NFIXchr19

13206543

+RBM5chr3

50141679

+
intron-intronENST00000588680ENST00000441812NFIXchr19

13206543

+RBM5chr3

50141679

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for NFIX-RBM5


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for NFIX-RBM5


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
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: 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.

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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for NFIX-RBM5


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for NFIX-RBM5


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 (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for NFIX-RBM5


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for NFIX-RBM5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNFIXC3553660Malan overgrowth syndrome5GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneNFIXC0265211Marshall-Smith syndrome2CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneNFIXC0005586Bipolar Disorder1PSYGENET