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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:IFT88-TNFRSF1A (FusionGDB2 ID:HG8100TG7132)

Fusion Gene Summary for IFT88-TNFRSF1A

check button Fusion gene summary
Fusion gene informationFusion gene name: IFT88-TNFRSF1A
Fusion gene ID: hg8100tg7132
HgeneTgene
Gene symbol

IFT88

TNFRSF1A

Gene ID

8100

7132

Gene nameintraflagellar transport 88TNF receptor superfamily member 1A
SynonymsD13S1056E|DAF19|TG737|TTC10|hTg737CD120a|FPF|TBP1|TNF-R|TNF-R-I|TNF-R55|TNFAR|TNFR1|TNFR55|TNFR60|p55|p55-R|p60
Cytomap('IFT88')('TNFRSF1A')

13q12.11

12p13.31

Type of geneprotein-codingprotein-coding
Descriptionintraflagellar transport protein 88 homologTPR repeat protein 10intraflagellar transport 88 homologpolaris homologprobe hTg737 (polycystic kidney disease, autosomal recessive)recessive polycystic kidney disease protein Tg737 homologtesticular tissuetumor necrosis factor receptor superfamily member 1ATNF-R1TNF-RITNFR-Itumor necrosis factor binding protein 1tumor necrosis factor receptor 1A isoform betatumor necrosis factor receptor type 1tumor necrosis factor-alpha receptor
Modification date2020031320200322
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000319980, ENST00000351808, 
ENST00000382778, ENST00000461115, 
ENST00000537103, 
Fusion gene scores* DoF score5 X 5 X 3=7513 X 13 X 3=507
# samples 615
** MAII scorelog2(6/75*10)=-0.321928094887362
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/507*10)=-1.75702324650746
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: IFT88 [Title/Abstract] AND TNFRSF1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointIFT88(21195197)-TNFRSF1A(6437937), # 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


check button Fusion gene information
* 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


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Fusion Gene ORF analysis for IFT88-TNFRSF1A

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

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 IFT88-TNFRSF1A


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)


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Fusion Protein Features for IFT88-TNFRSF1A


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/:21195197/:6437937)
- 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
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (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.
- 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 IFT88-TNFRSF1A


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 IFT88-TNFRSF1A


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 IFT88-TNFRSF1A


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 IFT88-TNFRSF1A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneIFT88C0085548Autosomal Recessive Polycystic Kidney Disease2CTD_human
HgeneIFT88C0023903Liver neoplasms1CTD_human
HgeneIFT88C0032927Precancerous Conditions1CTD_human
HgeneIFT88C0035334Retinitis Pigmentosa1ORPHANET
HgeneIFT88C0152427Polydactyly1CTD_human
HgeneIFT88C0238198Gastrointestinal Stromal Tumors1CTD_human
HgeneIFT88C0282313Condition, Preneoplastic1CTD_human
HgeneIFT88C0345904Malignant neoplasm of liver1CTD_human
HgeneIFT88C3179349Gastrointestinal Stromal Sarcoma1CTD_human
TgeneC1275126TNF receptor-associated periodic fever syndrome (TRAPS)7CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0011570Mental Depression5PSYGENET
TgeneC0011581Depressive disorder5PSYGENET
TgeneC0026769Multiple Sclerosis2CTD_human
TgeneC0751324Multiple Sclerosis, Acute Fulminating2CTD_human
TgeneC0002152Alloxan Diabetes1CTD_human
TgeneC0003123Anorexia1CTD_human
TgeneC0004364Autoimmune Diseases1CTD_human
TgeneC0006625Cachexia1CTD_human
TgeneC0007786Brain Ischemia1CTD_human
TgeneC0008312Primary biliary cirrhosis1CTD_human
TgeneC0010674Cystic Fibrosis1CTD_human
TgeneC0011853Diabetes Mellitus, Experimental1CTD_human
TgeneC0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
TgeneC0015967Fever1CTD_human
TgeneC0018801Heart failure1CTD_human
TgeneC0018802Congestive heart failure1CTD_human
TgeneC0020517Hypersensitivity1CTD_human
TgeneC0023212Left-Sided Heart Failure1CTD_human
TgeneC0023892Biliary cirrhosis1CTD_human
TgeneC0032285Pneumonia1CTD_human
TgeneC0032300Lobar Pneumonia1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0038433Streptozotocin Diabetes1CTD_human
TgeneC0149910Intermittent joint effusion1ORPHANET
TgeneC0235527Heart Failure, Right-Sided1CTD_human
TgeneC0238065Secondary Biliary Cholangitis1CTD_human
TgeneC0242706Hyperoxia1CTD_human
TgeneC0273115Lung Injury1CTD_human
TgeneC0392164Pulmonary Cystic Fibrosis1CTD_human
TgeneC0751422Hereditary Autoinflammatory Diseases1GENOMICS_ENGLAND
TgeneC0887898Experimental Lung Inflammation1CTD_human
TgeneC0917798Cerebral Ischemia1CTD_human
TgeneC1527304Allergic Reaction1CTD_human
TgeneC1527396Fibrocystic Disease of Pancreas1CTD_human
TgeneC1959583Myocardial Failure1CTD_human
TgeneC1961112Heart Decompensation1CTD_human
TgeneC2350344Chronic Lung Injury1CTD_human
TgeneC3714636Pneumonitis1CTD_human
TgeneC3860213Autoinflammatory disorder1GENOMICS_ENGLAND
TgeneC4551595Biliary Cirrhosis, Primary, 11CTD_human