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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:RBM4B-FADD (FusionGDB2 ID:72494)

Fusion Gene Summary for RBM4B-FADD

check button Fusion gene summary
Fusion gene informationFusion gene name: RBM4B-FADD
Fusion gene ID: 72494
HgeneTgene
Gene symbol

RBM4B

FADD

Gene ID

83759

8772

Gene nameRNA binding motif protein 4BFas associated via death domain
SynonymsRBM30|RBM4L|ZCCHC15|ZCCHC21B|ZCRB3BGIG3|MORT1
Cytomap

11q13.2

11q13.3

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein 4BRNA-binding motif protein 30zinc finger CCHC-type and RNA binding motif 3BFAS-associated death domain proteinFas (TNFRSF6)-associated via death domainFas-associating death domain-containing proteinFas-associating protein with death domaingrowth-inhibiting gene 3 proteinmediator of receptor-induced toxicity
Modification date2020032720200313
UniProtAcc.

Q13158

Ensembl transtripts involved in fusion geneENST00000525754, ENST00000310046, 
ENST00000531969, ENST00000529195, 
ENST00000524637, ENST00000531036, 
ENST00000301838, 
Fusion gene scores* DoF score6 X 5 X 3=905 X 2 X 4=40
# samples 66
** MAII scorelog2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/40*10)=0.584962500721156
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: RBM4B [Title/Abstract] AND FADD [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRBM4B(66444139)-FADD(70052239), # samples:2
Anticipated loss of major functional domain due to fusion event.RBM4B-FADD seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneFADD

GO:0032757

positive regulation of interleukin-8 production

16127453

TgeneFADD

GO:0032760

positive regulation of tumor necrosis factor production

16127453

TgeneFADD

GO:0036462

TRAIL-activated apoptotic signaling pathway

21785459

TgeneFADD

GO:0043065

positive regulation of apoptotic process

11821383

TgeneFADD

GO:0045862

positive regulation of proteolysis

18387192

TgeneFADD

GO:0045944

positive regulation of transcription by RNA polymerase II

16127453

TgeneFADD

GO:0097190

apoptotic signaling pathway

11101870

TgeneFADD

GO:0097191

extrinsic apoptotic signaling pathway

21785459

TgeneFADD

GO:0097202

activation of cysteine-type endopeptidase activity

18387192


check buttonFusion gene breakpoints across RBM4B (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 FADD (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
ChimerDB4SARCTCGA-3B-A9HR-01ARBM4Bchr11

66444139

-FADDchr11

70052239

+
ChimerDB4SARCTCGA-3B-A9HR-01ARBM4Bchr11

66444139

-FADDchr11

70052239

+


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Fusion Gene ORF analysis for RBM4B-FADD

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
Frame-shiftENST00000525754ENST00000301838RBM4Bchr11

66444139

-FADDchr11

70052239

+
Frame-shiftENST00000310046ENST00000301838RBM4Bchr11

66444139

-FADDchr11

70052239

+
In-frameENST00000531969ENST00000301838RBM4Bchr11

66444139

-FADDchr11

70052239

+
intron-3CDSENST00000529195ENST00000301838RBM4Bchr11

66444139

-FADDchr11

70052239

+
Frame-shiftENST00000524637ENST00000301838RBM4Bchr11

66444139

-FADDchr11

70052239

+
intron-3CDSENST00000531036ENST00000301838RBM4Bchr11

66444139

-FADDchr11

70052239

+

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)
ENST00000531969RBM4Bchr1166444139-ENST00000301838FADDchr1170052239+174348573825250

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
ENST00000531969ENST00000301838RBM4Bchr1166444139-FADDchr1170052239+0.0064737710.9935262

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Fusion Genomic Features for RBM4B-FADD


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)
RBM4Bchr1166444138-FADDchr1170052238+5.37E-050.99994624
RBM4Bchr1166444138-FADDchr1170052238+5.37E-050.99994624

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 RBM4B-FADD


check button Go to

FGviewer for the breakpoints of chr11:66444139-chr11:70052239

.
- 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
.FADD

Q13158

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: Apoptotic adaptor molecule that recruits caspase-8 or caspase-10 to the activated Fas (CD95) or TNFR-1 receptors. The resulting aggregate called the death-inducing signaling complex (DISC) performs caspase-8 proteolytic activation. Active caspase-8 initiates the subsequent cascade of caspases mediating apoptosis. Involved in interferon-mediated antiviral immune response, playing a role in the positive regulation of interferon signaling. {ECO:0000269|PubMed:16762833, ECO:0000269|PubMed:19118384, ECO:0000269|PubMed:20935634, ECO:0000269|PubMed:21109225}.

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
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000310046-242_72137.33333333333334585.3333333333334DomainRRM 1
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000525754-132_72137.33333333333334193.33333333333334DomainRRM 1
TgeneFADDchr11:66444139chr11:70052239ENST000003018380297_18195.33333333333333209.0DomainDeath

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000310046-24231_240137.33333333333334585.3333333333334Compositional biasNote=Poly-Ala
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000310046-24286_293137.33333333333334585.3333333333334Compositional biasNote=Poly-Ala
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000525754-13231_240137.33333333333334193.33333333333334Compositional biasNote=Poly-Ala
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000525754-13286_293137.33333333333334193.33333333333334Compositional biasNote=Poly-Ala
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000310046-2478_148137.33333333333334585.3333333333334DomainRRM 2
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000525754-1378_148137.33333333333334193.33333333333334DomainRRM 2
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000310046-24160_177137.33333333333334585.3333333333334Zinc fingerCCHC-type
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000525754-13160_177137.33333333333334193.33333333333334Zinc fingerCCHC-type
TgeneFADDchr11:66444139chr11:70052239ENST00000301838023_8195.33333333333333209.0DomainDED


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Fusion Gene Sequence for RBM4B-FADD


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.
>In-frame_ENST00000531969_ENST00000301838_TCGA-3B-A9HR-01A_RBM4B_chr11_66444139_-_FADD_chr11_70052239_length(transcript)=1743nt_BP=485nt
CGTCGCCATTTTGTAAGGTTCTCTCTGACGTGGGAGCCGCCGTCGCTGCCGCCACCCGGAGGCTCTTGTCAGGATGGTGAAGCTGTTCAT
CGGAAACCTTCCCCGGGAGGCTACAGAGCAGGAGATTCGCTCACTCTTCGAGCAGTATGGGAAGGTGCTGGAATGTGACATCATTAAGAA
TTACGGCTTTGTGCACATAGAAGACAAGACGGCAGCTGAGGATGCCATACGCAACCTGCACCATTACAAGCTTCATGGGGTGAACATCAA
CGTGGAAGCCAGCAAGAATAAGAGCAAAGCTTCAACCAAGTTACACGTGGGTAACATCAGCCCCACTTGTACCAACCAAGAGCTTCGAGC
CAAGTTTGAGGAGTATGGTCCGGTCATCGAATGTGACATCGTGAAAGATTATGCCTTCGTACACATGGAGCGGGCAGAGGATGCAGTGGA
GGCCATCAGGGGCCTTGACAACACAGAGTTTCAAGACCTGTGTGCAGCATTTAACGTCATATGTGATAATGTGGGGAAAGATTGGAGAAG
GCTGGCTCGTCAGCTCAAAGTCTCAGACACCAAGATCGACAGCATCGAGGACAGATACCCCCGCAACCTGACAGAGCGTGTGCGGGAGTC
ACTGAGAATCTGGAAGAACACAGAGAAGGAGAACGCAACAGTGGCCCACCTGGTGGGGGCTCTCAGGTCCTGCCAGATGAACCTGGTGGC
TGACCTGGTACAAGAGGTTCAGCAGGCCCGTGACCTCCAGAACAGGAGTGGGGCCATGTCCCCGATGTCATGGAACTCAGACGCATCTAC
CTCCGAAGCGTCCTGATGGGCCGCTGCTTTGCGCTGGTGGACCACAGGCATCTACACAGCCTGGACTTTGGTTCTCTCCAGGAAGGTAGC
CCAGCACTGTGAAGACCCAGCAGGAAGCCAGGCTGAGTGAGCCACAGACCACCTGCTTCTGAACTCAAGCTGCGTTTATTAATGCCTCTC
CCGCACCAGGCCGGGCTTGGGCCCTGCACAGATATTTCCATTTCTTCCTCACTATGACACTGAGCAAGATCTTGTCTCCACTAAATGAGC
TCCTGCGGGAGTAGTTGGAAAGTTGGAACCGTGTCCAGCACAGAAGGAATCTGTGCAGATGAGCAGTCACACTGTTACTCCACAGCGGAG
GAGACCAGCTCAGAGGCCCAGGAATCGGAGCGAAGCAGAGAGGTGGAGAACTGGGATTTGAACCCCCGCCATCCTTCACCAGAGCCCATG
CTCAACCACTGTGGCGTTCTGCTGCCCCTGCAGTTGGCAGAAAGGATGTTTTGTCCCATTTCCTTGGAGGCCACCGGGACAGACCTGGAC
ACTAGGGTCAGGCGGGGTGCTGTGGTGGGGAGAGGCATGGCTGGGGTGGGGGTGGGGAGACCTGGTTGGCCGTGGTCCAGCTCTTGGCCC
CTGTGTGAGTTGAGTCTCCTCTCTGAGACTGCTAAGTAGGGGCAGTGATGGTTGCCAGGACGAATTGAGATAATATCTGTGAGGTGCTGA
TGAGTGATTGACACACAGCACTCTCTAAATCTTCCTTGTGAGGATTATGGGTCCTGCAATTCTACAGTTTCTTACTGTTTTGTATCAAAA
TCACTATCTTTCTGATAACAGAATTGCCAAGGCAGCGGGATCTCGTATCTTTAAAAAGCAGTCCTCTTATTCCTAAGGTAATCCTATTAA

>In-frame_ENST00000531969_ENST00000301838_TCGA-3B-A9HR-01A_RBM4B_chr11_66444139_-_FADD_chr11_70052239_length(amino acids)=250AA_start in transcript=73_stop in transcript=825
MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASTKLHVGNISPTCT
NQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQDLCAAFNVICDNVGKDWRRLARQLKVSDTKIDSIEDRYPRNLT

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

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Fusion Gene PPI Analysis for RBM4B-FADD


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
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000310046-24196_359137.33333333333334585.3333333333334TNPO3
HgeneRBM4Bchr11:66444139chr11:70052239ENST00000525754-13196_359137.33333333333334193.33333333333334TNPO3


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 RBM4B-FADD


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 RBM4B-FADD


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneFADDC3151062INFECTIONS, RECURRENT, WITH ENCEPHALOPATHY, HEPATIC DYSFUNCTION, AND CARDIOVASCULAR MALFORMATIONS2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneFADDC0018784Sensorineural Hearing Loss (disorder)1CTD_human
TgeneFADDC0027627Neoplasm Metastasis1CTD_human
TgeneFADDC0038368Stomatognathic Diseases1CTD_human
TgeneFADDC0376634Craniofacial Abnormalities1CTD_human
TgeneFADDC1691779Sensory hearing loss1CTD_human
TgeneFADDC1704330Dental Diseases1CTD_human
TgeneFADDC2750325Oculootodental syndrome1ORPHANET
TgeneFADDC3279150Functional hyposplenism1GENOMICS_ENGLAND
TgeneFADDC4049796Abnormality of cardiovascular system morphology1GENOMICS_ENGLAND
TgeneFADDC4317009Diverticular Diseases1CTD_human
TgeneFADDC4505353Diverticular Bleeding1CTD_human